def main(source_base, binary_base):
"""Main entry point of the script."""
print "Executing test for breakpoint_calculator"
print "========================="
print
ph = app_tests.TestPathHelper(source_base, binary_base, "extras/apps/breakpoint_calculator/tests") # tests dir
# ============================================================
# Auto-detect the binary path.
# ============================================================
path_to_program = app_tests.autolocateBinary(
binary_base, "extras/apps/breakpoint_calculator", "breakpoint_calculator"
)
# ============================================================
# Built TestConf list.
# ============================================================
# Build list with TestConf objects, analoguely to how the output
# was generated in generate_outputs.sh.
conf_list = []
# ============================================================
# Run breakpoint_calculator
# ============================================================
# pairwise counts, xmfa format
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile("d2_xmfa.stdout"),
args=["-d2", ph.inFile("alignment.xmfa")],
to_diff=[(ph.inFile("d2_xmfa.stdout"), ph.outFile("d2_xmfa.stdout"))],
)
conf_list.append(conf)
# pairwise counts, maf format, detailed list of all pairs
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile("d2_maf.stdout"),
args=["-d2", "-d", ph.inFile("alignment.maf")],
to_diff=[(ph.inFile("d2_maf.stdout"), ph.outFile("d2_maf.stdout"))],
)
conf_list.append(conf)
# threeway counts, xmfa format, format directly specified
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile("d3_xmfa.stdout"),
args=["-d3", "-f", "xmfa", ph.inFile("alignment.xmfa")],
to_diff=[(ph.inFile("d3_xmfa.stdout"), ph.outFile("d3_xmfa.stdout"))],
)
conf_list.append(conf)
# threeway counts, maf format, detailed list of all triplets
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile("d3_maf.stdout"),
args=["-d3", "-d", ph.inFile("alignment.maf")],
to_diff=[(ph.inFile("d3_maf.stdout"), ph.outFile("d3_maf.stdout"))],
)
conf_list.append(conf)
# ============================================================
# Execute the tests.
# ============================================================
failures = 0
for conf in conf_list:
res = app_tests.runTest(conf)
# Output to the user.
print " ".join(["breakpoint_calculator"] + conf.args),
if res:
print "OK"
else:
failures += 1
print "FAILED"
# Cleanup.
ph.deleteTempDir()
print "=============================="
print " total tests: %d" % len(conf_list)
print " failed tests: %d" % failures
print "successful tests: %d" % (len(conf_list) - failures)
print "=============================="
# Compute and return return code.
return failures != 0
def main(source_base, binary_base):
"""Main entry point of the script."""
print 'Executing test for razers2'
print '==========================='
print
ph = app_tests.TestPathHelper(
source_base, binary_base,
'apps/razers2/tests') # tests dir
# ============================================================
# Auto-detect the binary path.
# ============================================================
path_to_program = app_tests.autolocateBinary(
binary_base, 'apps/razers2', 'razers2')
# ============================================================
# Built TestConf list.
# ============================================================
# Build list with TestConf objects, analoguely to how the output
# was generated in generate_outputs.sh.
conf_list = []
# ============================================================
# Run Adeno Single-End Tests
# ============================================================
# We run the following for all read lengths we have reads for.
for rl in [36, 100]:
# Run with default options.
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('se-adeno-reads%d_1.stdout' % rl),
args=['--low-memory',
ph.inFile('adeno-genome.fa'),
ph.inFile('adeno-reads%d_1.fa' % rl),
'-o', ph.outFile('se-adeno-reads%d_1.razers' % rl)],
to_diff=[(ph.inFile('se-adeno-reads%d_1.razers' % rl),
ph.outFile('se-adeno-reads%d_1.razers' % rl)),
(ph.inFile('se-adeno-reads%d_1.stdout' % rl),
ph.outFile('se-adeno-reads%d_1.stdout' % rl))])
conf_list.append(conf)
# Allow indels.
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('se-adeno-reads%d_1-id.stdout' % rl),
args=['--low-memory', '-id',
ph.inFile('adeno-genome.fa'),
ph.inFile('adeno-reads%d_1.fa' % rl),
'-o', ph.outFile('se-adeno-reads%d_1-id.razers' % rl)],
to_diff=[(ph.inFile('se-adeno-reads%d_1-id.razers' % rl),
ph.outFile('se-adeno-reads%d_1-id.razers' % rl)),
(ph.inFile('se-adeno-reads%d_1-id.stdout' % rl),
ph.outFile('se-adeno-reads%d_1-id.stdout' % rl))])
conf_list.append(conf)
# Compute forward/reverse matches only.
for o in ['-r', '-f']:
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('se-adeno-reads%d_1-id%s.stdout' % (rl, o)),
args=['--low-memory', '-id', o,
ph.inFile('adeno-genome.fa'),
ph.inFile('adeno-reads%d_1.fa' % rl),
'-o', ph.outFile('se-adeno-reads%d_1-id%s.razers' % (rl, o))],
to_diff=[(ph.inFile('se-adeno-reads%d_1-id%s.razers' % (rl, o)),
ph.outFile('se-adeno-reads%d_1-id%s.razers' % (rl, o))),
(ph.inFile('se-adeno-reads%d_1-id%s.stdout' % (rl, o)),
ph.outFile('se-adeno-reads%d_1-id%s.stdout' % (rl, o)))])
conf_list.append(conf)
# Compute with different identity rates.
for i in range(90, 101):
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('se-adeno-reads%d_1-id-i%d.stdout' % (rl, i)),
args=['--low-memory', '-id', '-i', str(i),
ph.inFile('adeno-genome.fa'),
ph.inFile('adeno-reads%d_1.fa' % rl),
'-o', ph.outFile('se-adeno-reads%d_1-id-i%d.razers' % (rl, i))],
to_diff=[(ph.inFile('se-adeno-reads%d_1-id-i%d.razers' % (rl, i)),
ph.outFile('se-adeno-reads%d_1-id-i%d.razers' % (rl, i))),
(ph.inFile('se-adeno-reads%d_1-id-i%d.stdout' % (rl, i)),
ph.outFile('se-adeno-reads%d_1-id-i%d.stdout' % (rl, i)))])
conf_list.append(conf)
# Compute with different output formats.
for suffix in ['razers', 'fa', 'eland', 'gff', 'sam', 'afg']:
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('se-adeno-reads%d_1-id.%s.stdout' % (rl, suffix)),
args=['--low-memory', '-id',
ph.inFile('adeno-genome.fa'),
ph.inFile('adeno-reads%d_1.fa' % rl),
'-o', ph.outFile('se-adeno-reads%d_1-id.%s' % (rl, suffix))],
to_diff=[(ph.inFile('se-adeno-reads%d_1-id.%s' % (rl, suffix)),
ph.outFile('se-adeno-reads%d_1-id.%s' % (rl, suffix))),
(ph.inFile('se-adeno-reads%d_1-id.%s.stdout' % (rl, suffix)),
ph.outFile('se-adeno-reads%d_1-id.%s.stdout' % (rl, suffix)))])
conf_list.append(conf)
# Compute with different sort orders.
for so in [0, 1]:
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('se-adeno-reads%d_1-id-so%d.stdout' % (rl, so)),
args=['--low-memory', '-id', '-so', str(so),
ph.inFile('adeno-genome.fa'),
ph.inFile('adeno-reads%d_1.fa' % rl),
'-o', ph.outFile('se-adeno-reads%d_1-id-so%d.razers' % (rl, so))],
to_diff=[(ph.inFile('se-adeno-reads%d_1-id-so%d.razers' % (rl, so)),
ph.outFile('se-adeno-reads%d_1-id-so%d.razers' % (rl, so))),
(ph.inFile('se-adeno-reads%d_1-id-so%d.stdout' % (rl, so)),
ph.outFile('se-adeno-reads%d_1-id-so%d.stdout' % (rl, so)))])
conf_list.append(conf)
# ============================================================
# Run Adeno Paired-End Tests
# ============================================================
# We run the following for all read lengths we have reads for.
for rl in [36, 100]:
# Run with default options.
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('pe-adeno-reads%d_2.stdout' % rl),
args=['--low-memory',
ph.inFile('adeno-genome.fa'),
ph.inFile('adeno-reads%d_1.fa' % rl),
ph.inFile('adeno-reads%d_2.fa' % rl),
'-o', ph.outFile('pe-adeno-reads%d_2.razers' % rl)],
to_diff=[(ph.inFile('pe-adeno-reads%d_2.razers' % rl),
ph.outFile('pe-adeno-reads%d_2.razers' % rl)),
(ph.inFile('pe-adeno-reads%d_2.stdout' % rl),
ph.outFile('pe-adeno-reads%d_2.stdout' % rl))])
conf_list.append(conf)
# Allow indels.
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('pe-adeno-reads%d_2-id.stdout' % rl),
args=['--low-memory', '-id',
ph.inFile('adeno-genome.fa'),
ph.inFile('adeno-reads%d_1.fa' % rl),
ph.inFile('adeno-reads%d_2.fa' % rl),
'-o', ph.outFile('pe-adeno-reads%d_2-id.razers' % rl)],
to_diff=[(ph.inFile('pe-adeno-reads%d_2-id.razers' % rl),
ph.outFile('pe-adeno-reads%d_2-id.razers' % rl)),
(ph.inFile('pe-adeno-reads%d_2-id.stdout' % rl),
ph.outFile('pe-adeno-reads%d_2-id.stdout' % rl))])
conf_list.append(conf)
# Compute forward/reverse matches only.
for o in ['-r', '-f']:
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('pe-adeno-reads%d_2-id%s.stdout' % (rl, o)),
args=['--low-memory', '-id', o,
ph.inFile('adeno-genome.fa'),
ph.inFile('adeno-reads%d_1.fa' % rl),
ph.inFile('adeno-reads%d_2.fa' % rl),
'-o', ph.outFile('pe-adeno-reads%d_2-id%s.razers' % (rl, o))],
to_diff=[(ph.inFile('pe-adeno-reads%d_2-id%s.razers' % (rl, o)),
ph.outFile('pe-adeno-reads%d_2-id%s.razers' % (rl, o))),
(ph.inFile('pe-adeno-reads%d_2-id%s.stdout' % (rl, o)),
ph.outFile('pe-adeno-reads%d_2-id%s.stdout' % (rl, o)))])
conf_list.append(conf)
# Compute with different identity rates.
for i in range(90, 101):
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('pe-adeno-reads%d_2-id-i%d.stdout' % (rl, i)),
args=['--low-memory', '-id', '-i', str(i),
ph.inFile('adeno-genome.fa'),
ph.inFile('adeno-reads%d_1.fa' % rl),
ph.inFile('adeno-reads%d_2.fa' % rl),
'-o', ph.outFile('pe-adeno-reads%d_2-id-i%d.razers' % (rl, i))],
to_diff=[(ph.inFile('pe-adeno-reads%d_2-id-i%d.razers' % (rl, i)),
ph.outFile('pe-adeno-reads%d_2-id-i%d.razers' % (rl, i))),
(ph.inFile('pe-adeno-reads%d_2-id-i%d.stdout' % (rl, i)),
ph.outFile('pe-adeno-reads%d_2-id-i%d.stdout' % (rl, i)))])
conf_list.append(conf)
# Compute with different output formats.
for suffix in ['razers', 'fa', 'eland', 'gff', 'sam', 'afg']:
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('pe-adeno-reads%d_2-id.%s.stdout' % (rl, suffix)),
args=['--low-memory', '-id',
ph.inFile('adeno-genome.fa'),
ph.inFile('adeno-reads%d_1.fa' % rl),
ph.inFile('adeno-reads%d_2.fa' % rl),
'-o', ph.outFile('pe-adeno-reads%d_2-id.%s' % (rl, suffix))],
to_diff=[(ph.inFile('pe-adeno-reads%d_2-id.%s' % (rl, suffix)),
ph.outFile('pe-adeno-reads%d_2-id.%s' % (rl, suffix))),
(ph.inFile('pe-adeno-reads%d_2-id.%s.stdout' % (rl, suffix)),
ph.outFile('pe-adeno-reads%d_2-id.%s.stdout' % (rl, suffix)))])
conf_list.append(conf)
# Compute with different sort orders.
for so in [0, 1]:
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('pe-adeno-reads%d_2-id-so%d.stdout' % (rl, so)),
args=['--low-memory', '-id', '-so', str(so),
ph.inFile('adeno-genome.fa'),
ph.inFile('adeno-reads%d_1.fa' % rl),
ph.inFile('adeno-reads%d_2.fa' % rl),
'-o', ph.outFile('pe-adeno-reads%d_2-id-so%d.razers' % (rl, so))],
to_diff=[(ph.inFile('pe-adeno-reads%d_2-id-so%d.razers' % (rl, so)),
ph.outFile('pe-adeno-reads%d_2-id-so%d.razers' % (rl, so))),
(ph.inFile('pe-adeno-reads%d_2-id-so%d.stdout' % (rl, so)),
ph.outFile('pe-adeno-reads%d_2-id-so%d.stdout' % (rl, so)))])
conf_list.append(conf)
# Execute the tests.
failures = 0
for conf in conf_list:
res = app_tests.runTest(conf)
# Output to the user.
print ' '.join(['razers2'] + conf.args),
if res:
print 'OK'
else:
failures += 1
print 'FAILED'
# Cleanup.
ph.deleteTempDir()
print '=============================='
print ' total tests: %d' % len(conf_list)
print ' failed tests: %d' % failures
print 'successful tests: %d' % (len(conf_list) - failures)
print '=============================='
# Compute and return return code.
return failures != 0
def main(source_base, binary_base):
"""Main entry point of the script."""
print 'Executing test for snp_store'
print '========================='
print
ph = app_tests.TestPathHelper(
source_base, binary_base,
'apps/snp_store/tests') # tests dir
# ============================================================
# Auto-detect the binary path.
# ============================================================
path_to_program = app_tests.autolocateBinary(
binary_base, 'apps/snp_store', 'snp_store')
# ============================================================
# Built TestConf list.
# ============================================================
# Build list with TestConf objects, analoguely to how the output
# was generated in generate_outputs.sh.
conf_list = []
# We prepare a list of transforms to apply to the output files. This is
# used to strip the input/output paths from the programs' output to
# make it more canonical and host independent.
ph.outFile('-') # To ensure that the out path is set.
transforms = [
app_tests.RegexpReplaceTransform("#.*snp_store.exe", "#snp_store"),
app_tests.RegexpReplaceTransform("#[^ ]+snp_store", "#snp_store"),
app_tests.ReplaceTransform(ph.inFile(''), ''),
app_tests.ReplaceTransform(ph.outFile(''), ''),
]
# ============================================================
# First Section.
# ============================================================
# App TestConf objects to conf_list, just like this for each
# test you want to run.
# default
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('snp_store_default.stdout'),
args=[ph.inFile('human-chr22-inf2.fa'),
ph.inFile('human-reads2.gff'),
'-o', ph.outFile('snps_default.vcf'),
'-id', ph.outFile('indels_default.gff'),],
to_diff=[(ph.inFile('snp_store_default.stdout'),
ph.outFile('snp_store_default.stdout')),
(ph.inFile('snps_default.vcf'),
ph.outFile('snps_default.vcf'),
transforms),
(ph.inFile('indels_default.gff'),
ph.outFile('indels_default.gff',))])
conf_list.append(conf)
# test 2
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('snp_store_realign.stdout'),
args=[ph.inFile('human-chr22-inf2.fa'),
ph.inFile('human-reads2.sam'),
'-re',
'-o', ph.outFile('snps_realign.vcf'),
'-id', ph.outFile('indels_realign.gff')],
to_diff=[(ph.inFile('snp_store_realign.stdout'),
ph.outFile('snp_store_realign.stdout')),
(ph.inFile('snps_realign.vcf'),
ph.outFile('snps_realign.vcf'),
transforms),
(ph.inFile('indels_realign.gff'),
ph.outFile('indels_realign.gff'))])
conf_list.append(conf)
# test 3
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('snp_store_realign_m1mp1oa.stdout'),
args=[ph.inFile('human-chr22-inf2.fa'),
ph.inFile('human-reads2.sam'),
'-it', str(1), '-re', '-oa', '-mp', str(1), '-m', 'maq', '-hq',
'-o', ph.outFile('snps_realign_m1mp1oa.vcf'),
'-id', ph.outFile('indels_realign_m1mp1oa.gff')],
to_diff=[(ph.inFile('snp_store_realign_m1mp1oa.stdout'),
ph.outFile('snp_store_realign_m1mp1oa.stdout')),
(ph.inFile('snps_realign_m1mp1oa.vcf'),
ph.outFile('snps_realign_m1mp1oa.vcf'),
transforms),
(ph.inFile('indels_realign_m1mp1oa.gff'),
ph.outFile('indels_realign_m1mp1oa.gff'))])
conf_list.append(conf)
# test 4
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('snp_store_realign_m0mp1oa.stdout'),
args=[ph.inFile('human-chr22-inf2.fa'),
ph.inFile('human-reads2.gff'),
'-it', str(2), '-re', '-oa', '-mp', str(1), '-hq',
'-o', ph.outFile('snps_realign_m0mp1oa.vcf'),
'-id', ph.outFile('indels_realign_m0mp1oa.gff')],
to_diff=[(ph.inFile('snp_store_realign_m0mp1oa.stdout'),
ph.outFile('snp_store_realign_m0mp1oa.stdout')),
(ph.inFile('snps_realign_m0mp1oa.vcf'),
ph.outFile('snps_realign_m0mp1oa.vcf'),
transforms),
(ph.inFile('indels_realign_m0mp1oa.gff'),
ph.outFile('indels_realign_m0mp1oa.gff'))])
conf_list.append(conf)
# test 5
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('snp_store_realign_m0mp1oa_it1ipt01.stdout'),
args=[ph.inFile('human-chr22-inf2.fa'),
ph.inFile('human-reads2.sam'),
'-it', str(1), '-ipt', str(0.1), '-osc', '-re', '-oa', '-hq',
'-o', ph.outFile('snps_realign_m0mp1oa_it1ipt01.vcf'),
'-id', ph.outFile('indels_realign_m0mp1oa_it1ipt01.gff')],
to_diff=[(ph.inFile('snp_store_realign_m0mp1oa_it1ipt01.stdout'),
ph.outFile('snp_store_realign_m0mp1oa_it1ipt01.stdout')),
(ph.inFile('snps_realign_m0mp1oa_it1ipt01.vcf'),
ph.outFile('snps_realign_m0mp1oa_it1ipt01.vcf'),
transforms),
(ph.inFile('indels_realign_m0mp1oa_it1ipt01.gff'),
ph.outFile('indels_realign_m0mp1oa_it1ipt01.gff'))])
conf_list.append(conf)
# ============================================================
# Execute the tests.
# ============================================================
failures = 0
for conf in conf_list:
res = app_tests.runTest(conf)
# Output to the user.
print ' '.join(['snp_store'] + conf.args),
if res:
print 'OK'
else:
failures += 1
print 'FAILED'
# Cleanup.
ph.deleteTempDir()
print '=============================='
print ' total tests: %d' % len(conf_list)
print ' failed tests: %d' % failures
print 'successful tests: %d' % (len(conf_list) - failures)
print '=============================='
# Compute and return return code.
return failures != 0
def main(source_base, binary_base):
"""Main entry point of the script."""
print 'Executing test for sgip'
print '========================='
print
ph = app_tests.TestPathHelper(
source_base, binary_base,
'apps/sgip/tests') # tests dir
# ============================================================
# Auto-detect the binary path.
# ============================================================
path_to_program = app_tests.autolocateBinary(
binary_base, 'apps/sgip', 'sgip')
# ============================================================
# Built TestConf list.
# ============================================================
# Build list with TestConf objects, analoguely to how the output
# was generated in generate_outputs.sh.
conf_list = []
# ============================================================
# First Section.
# ============================================================
# App TestConf objects to conf_list, just like this for each
# test you want to run.
# Example 1
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('iso_r01_m200.A00_B00.stdout'),
args=['-o', ph.inFile('../example/r01/iso_r01_m200.A00'), '-c',
ph.inFile('../example/r01/iso_r01_m200.B00'), '-v', '2', '-i'],
to_diff=[(ph.inFile('iso_r01_m200.A00_B00.stdout'),
ph.outFile('iso_r01_m200.A00_B00.stdout'))])
conf_list.append(conf)
# Example 2
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('iso_r01_m200.A01_B01.stdout'),
args=['-o', ph.inFile('../example/r01/iso_r01_m200.A01'), '-c',
ph.inFile('../example/r01/iso_r01_m200.B01'), '-v', '2', '-i'],
to_diff=[(ph.inFile('iso_r01_m200.A01_B01.stdout'),
ph.outFile('iso_r01_m200.A01_B01.stdout'))])
conf_list.append(conf)
# Example 3
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('iso_r01_m200.A00_B01.stdout'),
args=['-o', ph.inFile('../example/r01/iso_r01_m200.A00'), '-c',
ph.inFile('../example/r01/iso_r01_m200.B01'), '-v', '2','-i'],
to_diff=[(ph.inFile('iso_r01_m200.A00_B01.stdout'),
ph.outFile('iso_r01_m200.A00_B01.stdout'))])
conf_list.append(conf)
# Example 4
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('iso_r01_m200.A00.stdout'),
args=['-o', ph.inFile('../example/r01/iso_r01_m200.A00'), '-v', '2'],
to_diff=[(ph.inFile('iso_r01_m200.A00.stdout'),
ph.outFile('iso_r01_m200.A00.stdout'))])
conf_list.append(conf)
# Example 5
#Example 6
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('srg_latin-4.stdout'),
args=['-o', ph.inFile('../example/srg/latin-4'), '-v', '2'],
to_diff=[(ph.inFile('srg_latin-4.stdout'),
ph.outFile('srg_latin-4.stdout'))])
conf_list.append(conf)
# Example 7
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('srg_lattice-4.stdout'),
args=['-o', ph.inFile('../example/srg/lattice-4'), '-v', '2'],
to_diff=[(ph.inFile('srg_lattice-4.stdout'),
ph.outFile('srg_lattice-4.stdout'))])
conf_list.append(conf)
# Example 8
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('srg_paley-5.stdout'),
args=['-o', ph.inFile('../example/srg/paley-5'), '-v', '2'],
to_diff=[(ph.inFile('srg_paley-5.stdout'),
ph.outFile('srg_paley-5.stdout'))])
conf_list.append(conf)
# Example 9
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('srg_sts7.stdout'),
args=['-o', ph.inFile('../example/srg/sts-7'), '-v', '2'],
to_diff=[(ph.inFile('srg_sts7.stdout'),
ph.outFile('srg_sts7.stdout'))])
conf_list.append(conf)
# Example 10
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('srg_triang-5.stdout'),
args=['-o', ph.inFile('../example/srg/triang-5'), '-v', '2'],
to_diff=[(ph.inFile('srg_triang-5.stdout'),
ph.outFile('srg_triang-5.stdout'))])
conf_list.append(conf)
# ============================================================
# Execute the tests.
# ============================================================
failures = 0
for conf in conf_list:
res = app_tests.runTest(conf)
# Output to the user.
print ' '.join(['sgip'] + conf.args),
if res:
print 'OK'
else:
failures += 1
print 'FAILED'
# Cleanup.
ph.deleteTempDir()
print '=============================='
print ' total tests: %d' % len(conf_list)
print ' failed tests: %d' % failures
print 'successful tests: %d' % (len(conf_list) - failures)
print '=============================='
# Compute and return return code.
return failures != 0
def main(source_base, binary_base, num_threads=1):
"""Main entry point of the script."""
print 'Executing test for razers3'
print '==========================='
print
ph = app_tests.TestPathHelper(
source_base, binary_base,
'apps/razers3/tests') # tests dir
# ============================================================
# Auto-detect the binary path.
# ============================================================
path_to_program = app_tests.autolocateBinary(
binary_base, 'bin', 'razers3')
# ============================================================
# Built TestConf list.
# ============================================================
# Build list with TestConf objects, analoguely to how the output
# was generated in generate_outputs.sh.
conf_list = []
# We prepare a list of transforms to apply to the output files. This is
# used to strip the input/output paths from the programs' output to
# make it more canonical and host independent.
ph.outFile('-') # To ensure that the out path is set.
transforms = [
app_tests.ReplaceTransform(os.path.join(ph.source_base_path, 'apps/razers3/tests') + os.sep, '', right=True),
app_tests.ReplaceTransform(ph.temp_dir + os.sep, '', right=True),
]
# Transforms for SAM output format only. Make VN field of @PG header canonical.
sam_transforms = [app_tests.RegexpReplaceTransform(r'\tVN:[^\t]*', r'\tVN:VERSION', right=True, left=True)]
# Transforms for RazerS output format only. Remove pair id column.
razers_transforms = [RemovePairIdColumn()]
# ============================================================
# Run Adeno Single-End Tests
# ============================================================
# We run the following for all read lengths we have reads for.
for rl in [36, 100]:
# Run with default options.
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('se-adeno-reads%d_1-tc%d.stdout' % (rl, num_threads)),
args=['-tc', str(num_threads),
ph.inFile('adeno-genome.fa'),
ph.inFile('adeno-reads%d_1.fa' % rl),
'-o', ph.outFile('se-adeno-reads%d_1-tc%d.razers' % (rl, num_threads))],
to_diff=[(ph.inFile('se-adeno-reads%d_1-tc%d.razers' % (rl, num_threads)),
ph.outFile('se-adeno-reads%d_1-tc%d.razers' % (rl, num_threads))),
(ph.inFile('se-adeno-reads%d_1-tc%d.stdout' % (rl, num_threads)),
ph.outFile('se-adeno-reads%d_1-tc%d.stdout' % (rl, num_threads)))])
conf_list.append(conf)
# Allow indels.
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('se-adeno-reads%d_1-ng-tc%d.stdout' % (rl, num_threads)),
args=['-tc', str(num_threads),
'-ng',
ph.inFile('adeno-genome.fa'),
ph.inFile('adeno-reads%d_1.fa' % rl),
'-o', ph.outFile('se-adeno-reads%d_1-ng-tc%d.razers' % (rl, num_threads))],
to_diff=[(ph.inFile('se-adeno-reads%d_1-ng-tc%d.razers' % (rl, num_threads)),
ph.outFile('se-adeno-reads%d_1-ng-tc%d.razers' % (rl, num_threads))),
(ph.inFile('se-adeno-reads%d_1-ng-tc%d.stdout' % (rl, num_threads)),
ph.outFile('se-adeno-reads%d_1-ng-tc%d.stdout' % (rl, num_threads)))])
conf_list.append(conf)
# Compute forward/reverse matches only.
for o in ['-r', '-f']:
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('se-adeno-reads%d_1%s-tc%d.stdout' % (rl, o, num_threads)),
args=['-tc', str(num_threads),
o,
ph.inFile('adeno-genome.fa'),
ph.inFile('adeno-reads%d_1.fa' % rl),
'-o', ph.outFile('se-adeno-reads%d_1%s-tc%d.razers' % (rl, o, num_threads))],
to_diff=[(ph.inFile('se-adeno-reads%d_1%s-tc%d.razers' % (rl, o, num_threads)),
ph.outFile('se-adeno-reads%d_1%s-tc%d.razers' % (rl, o, num_threads))),
(ph.inFile('se-adeno-reads%d_1%s-tc%d.stdout' % (rl, o, num_threads)),
ph.outFile('se-adeno-reads%d_1%s-tc%d.stdout' % (rl, o, num_threads)))])
conf_list.append(conf)
# Compute with different identity rates.
for i in range(90, 101):
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('se-adeno-reads%d_1-i%d-tc%d.stdout' % (rl, i, num_threads)),
args=['-tc', str(num_threads),
'-i', str(i),
ph.inFile('adeno-genome.fa'),
ph.inFile('adeno-reads%d_1.fa' % rl),
'-o', ph.outFile('se-adeno-reads%d_1-i%d-tc%d.razers' % (rl, i, num_threads))],
to_diff=[(ph.inFile('se-adeno-reads%d_1-i%d-tc%d.razers' % (rl, i, num_threads)),
ph.outFile('se-adeno-reads%d_1-i%d-tc%d.razers' % (rl, i, num_threads))),
(ph.inFile('se-adeno-reads%d_1-i%d-tc%d.stdout' % (rl, i, num_threads)),
ph.outFile('se-adeno-reads%d_1-i%d-tc%d.stdout' % (rl, i, num_threads)))])
conf_list.append(conf)
# Compute with different output formats.
for of, suffix in enumerate(['razers', 'fa', 'eland', 'gff', 'sam', 'afg']):
this_transforms = list(transforms)
if suffix == 'razers':
this_transforms += razers_transforms
elif suffix == 'sam':
this_transforms += sam_transforms
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('se-adeno-reads%d_1-of%d-tc%d.stdout' % (rl, of, num_threads)),
args=['-tc', str(num_threads),
ph.inFile('adeno-genome.fa'),
ph.inFile('adeno-reads%d_1.fa' % rl),
'-o', ph.outFile('se-adeno-reads%d_1-of%d-tc%d.%s' % (rl, of, num_threads, suffix))],
to_diff=[(ph.inFile('se-adeno-reads%d_1-of%d-tc%d.%s' % (rl, of, num_threads, suffix)),
ph.outFile('se-adeno-reads%d_1-of%d-tc%d.%s' % (rl, of, num_threads, suffix)),
this_transforms),
(ph.inFile('se-adeno-reads%d_1-of%d-tc%d.stdout' % (rl, of, num_threads)),
ph.outFile('se-adeno-reads%d_1-of%d-tc%d.stdout' % (rl, of, num_threads)),
transforms)])
conf_list.append(conf)
# Compute with different sort orders.
for so in [0, 1]:
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('se-adeno-reads%d_1-so%d-tc%d.stdout' % (rl, so, num_threads)),
args=['-tc', str(num_threads),
'-so', str(so),
ph.inFile('adeno-genome.fa'),
ph.inFile('adeno-reads%d_1.fa' % rl),
'-o', ph.outFile('se-adeno-reads%d_1-so%d-tc%d.razers' % (rl, so, num_threads))],
to_diff=[(ph.inFile('se-adeno-reads%d_1-so%d-tc%d.razers' % (rl, so, num_threads)),
ph.outFile('se-adeno-reads%d_1-so%d-tc%d.razers' % (rl, so, num_threads))),
(ph.inFile('se-adeno-reads%d_1-so%d-tc%d.stdout' % (rl, so, num_threads)),
ph.outFile('se-adeno-reads%d_1-so%d-tc%d.stdout' % (rl, so, num_threads)))])
conf_list.append(conf)
# ============================================================
# Run Adeno Paired-End Tests
# ============================================================
# We run the following for all read lengths we have reads for.
for rl in [36, 100]:
# Run with default options.
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('pe-adeno-reads%d_2-tc%d.stdout' % (rl, num_threads)),
args=['-tc', str(num_threads),
ph.inFile('adeno-genome.fa'),
ph.inFile('adeno-reads%d_1.fa' % rl),
ph.inFile('adeno-reads%d_2.fa' % rl),
'-o', ph.outFile('pe-adeno-reads%d_2-tc%d.razers' % (rl, num_threads))],
to_diff=[(ph.inFile('pe-adeno-reads%d_2-tc%d.razers' % (rl, num_threads)),
ph.outFile('pe-adeno-reads%d_2-tc%d.razers' % (rl, num_threads)),
razers_transforms),
(ph.inFile('pe-adeno-reads%d_2-tc%d.stdout' % (rl, num_threads)),
ph.outFile('pe-adeno-reads%d_2-tc%d.stdout' % (rl, num_threads)))])
conf_list.append(conf)
# Allow indels.
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('pe-adeno-reads%d_2-tc%d.stdout' % (rl, num_threads)),
args=['-tc', str(num_threads),
ph.inFile('adeno-genome.fa'),
ph.inFile('adeno-reads%d_1.fa' % rl),
ph.inFile('adeno-reads%d_2.fa' % rl),
'-o', ph.outFile('pe-adeno-reads%d_2-tc%d.razers' % (rl, num_threads))],
to_diff=[(ph.inFile('pe-adeno-reads%d_2-tc%d.razers' % (rl, num_threads)),
ph.outFile('pe-adeno-reads%d_2-tc%d.razers' % (rl, num_threads)),
razers_transforms),
(ph.inFile('pe-adeno-reads%d_2-tc%d.stdout' % (rl, num_threads)),
ph.outFile('pe-adeno-reads%d_2-tc%d.stdout' % (rl, num_threads)))])
conf_list.append(conf)
# Compute forward/reverse matches only.
for o in ['-r', '-f']:
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('pe-adeno-reads%d_2%s-tc%d.stdout' % (rl, o, num_threads)),
args=['-tc', str(num_threads),
o,
ph.inFile('adeno-genome.fa'),
ph.inFile('adeno-reads%d_1.fa' % rl),
ph.inFile('adeno-reads%d_2.fa' % rl),
'-o', ph.outFile('pe-adeno-reads%d_2%s-tc%d.razers' % (rl, o, num_threads))],
to_diff=[(ph.inFile('pe-adeno-reads%d_2%s-tc%d.razers' % (rl, o, num_threads)),
ph.outFile('pe-adeno-reads%d_2%s-tc%d.razers' % (rl, o, num_threads)),
razers_transforms),
(ph.inFile('pe-adeno-reads%d_2%s-tc%d.stdout' % (rl, o, num_threads)),
ph.outFile('pe-adeno-reads%d_2%s-tc%d.stdout' % (rl, o, num_threads)))])
conf_list.append(conf)
# Compute with different identity rates.
for i in range(90, 101):
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('pe-adeno-reads%d_2-i%d-tc%d.stdout' % (rl, i, num_threads)),
args=['-tc', str(num_threads),
'-i', str(i),
ph.inFile('adeno-genome.fa'),
ph.inFile('adeno-reads%d_1.fa' % rl),
ph.inFile('adeno-reads%d_2.fa' % rl),
'-o', ph.outFile('pe-adeno-reads%d_2-i%d-tc%d.razers' % (rl, i, num_threads))],
to_diff=[(ph.inFile('pe-adeno-reads%d_2-i%d-tc%d.razers' % (rl, i, num_threads)),
ph.outFile('pe-adeno-reads%d_2-i%d-tc%d.razers' % (rl, i, num_threads)),
razers_transforms),
(ph.inFile('pe-adeno-reads%d_2-i%d-tc%d.stdout' % (rl, i, num_threads)),
ph.outFile('pe-adeno-reads%d_2-i%d-tc%d.stdout' % (rl, i, num_threads)))])
conf_list.append(conf)
# Compute with different output formats.
for of, suffix in enumerate(['razers', 'fa', 'eland', 'gff', 'sam', 'afg']):
this_transforms = list(transforms)
if suffix == 'razers':
this_transforms += razers_transforms
elif suffix == 'sam':
this_transforms += sam_transforms
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('pe-adeno-reads%d_2-of%d-tc%d.stdout' % (rl, of, num_threads)),
args=['-tc', str(num_threads),
ph.inFile('adeno-genome.fa'),
ph.inFile('adeno-reads%d_1.fa' % rl),
ph.inFile('adeno-reads%d_2.fa' % rl),
'-o', ph.outFile('pe-adeno-reads%d_2-of%d-tc%d.%s' % (rl, of, num_threads, suffix))],
to_diff=[(ph.inFile('pe-adeno-reads%d_2-of%d-tc%d.%s' % (rl, of, num_threads, suffix)),
ph.outFile('pe-adeno-reads%d_2-of%d-tc%d.%s' % (rl, of, num_threads, suffix)),
this_transforms),
(ph.inFile('pe-adeno-reads%d_2-of%d-tc%d.stdout' % (rl, of, num_threads)),
ph.outFile('pe-adeno-reads%d_2-of%d-tc%d.stdout' % (rl, of, num_threads)),
this_transforms)])
conf_list.append(conf)
# Compute with different sort orders.
for so in [0, 1]:
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('pe-adeno-reads%d_2-so%d-tc%d.stdout' % (rl, so, num_threads)),
args=['-tc', str(num_threads),
'-so', str(so),
ph.inFile('adeno-genome.fa'),
ph.inFile('adeno-reads%d_1.fa' % rl),
ph.inFile('adeno-reads%d_2.fa' % rl),
'-o', ph.outFile('pe-adeno-reads%d_2-so%d-tc%d.razers' % (rl, so, num_threads))],
to_diff=[(ph.inFile('pe-adeno-reads%d_2-so%d-tc%d.razers' % (rl, so, num_threads)),
ph.outFile('pe-adeno-reads%d_2-so%d-tc%d.razers' % (rl, so, num_threads)),
razers_transforms),
(ph.inFile('pe-adeno-reads%d_2-so%d-tc%d.stdout' % (rl, so, num_threads)),
ph.outFile('pe-adeno-reads%d_2-so%d-tc%d.stdout' % (rl, so, num_threads)))])
conf_list.append(conf)
# Execute the tests.
failures = 0
for conf in conf_list:
res = app_tests.runTest(conf)
# Output to the user.
print ' '.join(['razers3'] + conf.args),
if res:
print 'OK'
else:
failures += 1
print 'FAILED'
# Cleanup.
ph.deleteTempDir()
print '=============================='
print ' total tests: %d' % len(conf_list)
print ' failed tests: %d' % failures
print 'successful tests: %d' % (len(conf_list) - failures)
print '=============================='
# Compute and return return code.
return failures != 0
def main(source_base, binary_base):
"""Main entry point of the script."""
if platform.machine().startswith('mips') or platform.machine().startswith(
's390'):
print 'Skipping tests for seqan_tcoffee on mips* and s390*'
print '==================================================='
return 0
print 'Executing test for seqan_tcoffee'
print '================================'
print
ph = app_tests.TestPathHelper(source_base, binary_base,
'apps/seqan_tcoffee/tests') # tests dir
# ============================================================
# Auto-detect the binary path.
# ============================================================
path_to_program = app_tests.autolocateBinary(binary_base,
'apps/seqan_tcoffee',
'seqan_tcoffee')
# ============================================================
# Built TestConf list.
# ============================================================
# Build list with TestConf objects, analoguely to how the output
# was generated in generate_outputs.sh.
conf_list = []
# ============================================================
# Run on Proteins (Balibase).
# ============================================================
# Run with defaults for all non-mandatory options.
for fname in ['1aab', '1ad2', '2trx']:
conf = app_tests.TestConf(program=path_to_program,
args=[
'-s',
ph.inFile('%s.fa' % fname), '-o',
ph.outFile('%s.fasta' % fname)
],
to_diff=[(ph.inFile('%s.fasta' % fname),
ph.outFile('%s.fasta' % fname))])
conf_list.append(conf)
# Run with explicit alphabet.
for fname in ['1aab', '1ad2', '2trx']:
conf = app_tests.TestConf(program=path_to_program,
args=[
'-a', 'protein', '-s',
ph.inFile('%s.fa' % fname), '-o',
ph.outFile('%s.protein.fasta' % fname)
],
to_diff=[
(ph.inFile('%s.protein.fasta' % fname),
ph.outFile('%s.protein.fasta' % fname))
])
conf_list.append(conf)
# Run with different segment match generation options. We run
# with with single values and combinations of neighbours
for fname in ['1aab', '1ad2', '2trx']:
for m in ['global', 'local', 'overlap', 'lcs']:
conf = app_tests.TestConf(
program=path_to_program,
args=[
'-m', m, '-s',
ph.inFile('%s.fa' % fname), '-o',
ph.outFile('%s.m%s.fasta' % (fname, m))
],
to_diff=[(ph.inFile('%s.m%s.fasta' % (fname, m)),
ph.outFile('%s.m%s.fasta' % (fname, m)))])
conf_list.append(conf)
m1 = 'global'
m2 = 'local'
conf = app_tests.TestConf(
program=path_to_program,
args=[
'-m', m1, '-m', m2, '-s',
ph.inFile('%s.fa' % fname), '-o',
ph.outFile('%s.m%s.m%s.fasta' % (fname, m1, m2))
],
to_diff=[(ph.inFile('%s.m%s.m%s.fasta' % (fname, m1, m2)),
ph.outFile('%s.m%s.m%s.fasta' % (fname, m1, m2)))])
conf_list.append(conf)
m1 = 'local'
m2 = 'overlap'
conf = app_tests.TestConf(
program=path_to_program,
args=[
'-m', m1, '-m', m2, '-s',
ph.inFile('%s.fa' % fname), '-o',
ph.outFile('%s.m%s.m%s.fasta' % (fname, m1, m2))
],
to_diff=[(ph.inFile('%s.m%s.m%s.fasta' % (fname, m1, m2)),
ph.outFile('%s.m%s.m%s.fasta' % (fname, m1, m2)))])
conf_list.append(conf)
m1 = 'overlap'
m2 = 'lcs'
conf = app_tests.TestConf(
program=path_to_program,
args=[
'-m', m1, '-m', m2, '-s',
ph.inFile('%s.fa' % fname), '-o',
ph.outFile('%s.m%s.m%s.fasta' % (fname, m1, m2))
],
to_diff=[(ph.inFile('%s.m%s.m%s.fasta' % (fname, m1, m2)),
ph.outFile('%s.m%s.m%s.fasta' % (fname, m1, m2)))])
m1 = 'global'
m2 = 'lcs'
conf = app_tests.TestConf(
program=path_to_program,
args=[
'-m', m1, '-m', m2, '-s',
ph.inFile('%s.fa' % fname), '-o',
ph.outFile('%s.m%s.m%s.fasta' % (fname, m1, m2))
],
to_diff=[(ph.inFile('%s.m%s.m%s.fasta' % (fname, m1, m2)),
ph.outFile('%s.m%s.m%s.fasta' % (fname, m1, m2)))])
# Run with different match files variations.
# TODO
# Run with different scoring options.
for fname in ['1aab', '1ad2', '2trx']:
conf = app_tests.TestConf(program=path_to_program,
args=[
'-g', '-20', '-s',
ph.inFile('%s.fa' % fname), '-o',
ph.outFile('%s.g-20.fasta' % fname)
],
to_diff=[
(ph.inFile('%s.g-20.fasta' % fname),
ph.outFile('%s.g-20.fasta' % fname))
])
conf_list.append(conf)
conf = app_tests.TestConf(program=path_to_program,
args=[
'-e', '-5', '-s',
ph.inFile('%s.fa' % fname), '-o',
ph.outFile('%s.e-5.fasta' % fname)
],
to_diff=[(ph.inFile('%s.e-5.fasta' % fname),
ph.outFile('%s.e-5.fasta' % fname))
])
conf_list.append(conf)
conf = app_tests.TestConf(program=path_to_program,
args=[
'-ms', '10', '-s',
ph.inFile('%s.fa' % fname), '-o',
ph.outFile('%s.ms10.fasta' % fname)
],
to_diff=[
(ph.inFile('%s.ms10.fasta' % fname),
ph.outFile('%s.ms10.fasta' % fname))
])
conf_list.append(conf)
conf = app_tests.TestConf(program=path_to_program,
args=[
'-mm', '-8', '-s',
ph.inFile('%s.fa' % fname), '-o',
ph.outFile('%s.mm-8.fasta' % fname)
],
to_diff=[
(ph.inFile('%s.mm-8.fasta' % fname),
ph.outFile('%s.mm-8.fasta' % fname))
])
conf_list.append(conf)
# Run with matrix file.
for fname in ['1aab', '1ad2', '2trx']:
conf = app_tests.TestConf(
program=path_to_program,
args=[
'-ma',
ph.inFile('VTML200I'), '-s',
ph.inFile('%s.fa' % fname), '-o',
ph.outFile('%s.maVTML200.fasta' % fname)
],
to_diff=[(ph.inFile('%s.maVTML200.fasta' % fname),
ph.outFile('%s.maVTML200.fasta' % fname))])
conf_list.append(conf)
# Run with manual guide tree.
for fname in ['1aab', '1ad2', '2trx']:
conf = app_tests.TestConf(program=path_to_program,
args=[
'-u',
ph.inFile('%s.newick' % fname), '-s',
ph.inFile('%s.fa' % fname), '-o',
ph.outFile('%s.u.fasta' % fname)
],
to_diff=[(ph.inFile('%s.u.fasta' % fname),
ph.outFile('%s.u.fasta' % fname))])
conf_list.append(conf)
# Run with different guide tree building options.
for fname in ['1aab', '1ad2', '2trx']:
for b in ['nj', 'min', 'max', 'avg', 'wavg']:
conf = app_tests.TestConf(
program=path_to_program,
args=[
'-b', b, '-s',
ph.inFile('%s.fa' % fname), '-o',
ph.outFile('%s.b%s.fasta' % (fname, b))
],
to_diff=[(ph.inFile('%s.b%s.fasta' % (fname, b)),
ph.outFile('%s.b%s.fasta' % (fname, b)))])
conf_list.append(conf)
# Run alignment evaluation.
for fname in ['1aab', '1ad2', '2trx']:
conf = app_tests.TestConf(program=path_to_program,
args=['-i',
ph.inFile('%s.fasta' % fname)],
redir_stdout=ph.outFile('%s.i.fasta' %
fname),
to_diff=[(ph.inFile('%s.i.fasta' % fname),
ph.outFile('%s.i.fasta' % fname))])
conf_list.append(conf)
# ============================================================
# Run on DNA (Adenoviruses).
# ============================================================
# Run with defaults for all non-mandatory options.
for i in [2, 3, 4]:
conf = app_tests.TestConf(program=path_to_program,
args=[
'-a', 'dna', '-s',
ph.inFile('adeno%d.fa' % i), '-o',
ph.outFile('adeno%d.fasta' % i)
],
to_diff=[(ph.inFile('adeno%d.fasta' % i),
ph.outFile('adeno%d.fasta' % i))])
conf_list.append(conf)
# ============================================================
# Run on RNA.
# ============================================================
# Run with defaults for all non-mandatory options.
for i in [2, 3, 4]:
conf = app_tests.TestConf(program=path_to_program,
args=[
'-a', 'rna', '-s',
ph.inFile('adeno%d-rna.fa' % i), '-o',
ph.outFile('adeno%d-rna.fasta' % i)
],
to_diff=[
(ph.inFile('adeno%d-rna.fasta' % i),
ph.outFile('adeno%d-rna.fasta' % i))
])
conf_list.append(conf)
# Execute the tests.
failures = 0
for conf in conf_list:
res = app_tests.runTest(conf)
# Output to the user.
print ' '.join(['seqan_tcoffee'] + conf.args),
if res:
print 'OK'
else:
failures += 1
print 'FAILED'
# Cleanup.
ph.deleteTempDir()
print '=============================='
print ' total tests: %d' % len(conf_list)
print ' failed tests: %d' % failures
print 'successful tests: %d' % (len(conf_list) - failures)
print '=============================='
# Compute and return return code.
return failures != 0
def main(source_base, binary_base):
"""Main entry point of the script."""
print 'Executing test for roi_intersect'
print '================================'
print
ph = app_tests.TestPathHelper(
source_base, binary_base,
'extras/apps/ngs_roi/tests') # tests dir
# ============================================================
# Auto-detect the binary path.
# ============================================================
path_to_project = app_tests.autolocateBinary(
binary_base, 'extras/apps/ngs_roi', 'roi_feature_projection')
path_to_bam2roi = app_tests.autolocateBinary(
binary_base, 'extras/apps/ngs_roi', 'bam2roi')
# ============================================================
# Built TestConf list.
# ============================================================
# Build list with TestConf objects, analoguely to how the output
# was generated in generate_outputs.sh.
conf_list = []
# We prepare a list of transforms to apply to the output files. This is
# used to strip the input/output paths from the programs' output to
# make it more canonical and host independent.
ph.outFile('-') # To ensure that the out path is set.
transforms = [
app_tests.ReplaceTransform(os.path.join(ph.source_base_path, 'extras/apps/ngs_roi/tests') + os.sep, '', right=True),
app_tests.ReplaceTransform(ph.temp_dir + os.sep, '', right=True),
]
# ------------------------------------------------------------
# Projection: Intersect with BED or GFF/GTF in BED style.
# ------------------------------------------------------------
for mode in ['projection', 'union', 'difference', 'intersection']:
for fmt in ['bed', 'gff', 'gtf']:
for ss_flag, ss_name in [('-ss', '_ss'), ('', '')]:
conf = app_tests.TestConf(
program=path_to_project,
redir_stderr=ph.outFile('out_small_%s_m%s%s.stderr' % (fmt, mode, ss_name)),
redir_stdout=ph.outFile('out_small_%s_m%s%s.stdout' % (fmt, mode, ss_name)),
args=['-m', mode, ss_flag,
'-ir', ph.inFile('small.roi'),
'-if', ph.inFile('small.%s' % fmt),
'-or', ph.outFile('out_small_%s_m%s%s.roi' % (fmt, mode, ss_name))],
to_diff=[(ph.inFile('out_small_%s_m%s%s.stderr' % (fmt, mode, ss_name)),
ph.outFile('out_small_%s_m%s%s.stderr' % (fmt, mode, ss_name)),
transforms),
(ph.inFile('out_small_%s_m%s%s.stdout' % (fmt, mode, ss_name)),
ph.outFile('out_small_%s_m%s%s.stdout' % (fmt, mode, ss_name)),
transforms),
(ph.inFile('out_small_%s_m%s%s.roi' % (fmt, mode, ss_name)),
ph.outFile('out_small_%s_m%s%s.roi' % (fmt, mode, ss_name)),
transforms),
])
conf_list.append(conf)
# TODO(holtgrew): Test with projection to transcripts.
# ------------------------------------------------------------
# BAM to ROI Conversion
# ------------------------------------------------------------
conf = app_tests.TestConf(
program=path_to_bam2roi,
redir_stderr=ph.outFile('out_mrna_2l_ss.roi.stderr'),
redir_stdout=ph.outFile('out_mrna_2l_ss.roi.stdout'),
args=['--strand-specific', '-if', ph.inFile('micro_rna_sorted_2l.bam'),
'-of', ph.outFile('out_mrna_2l_ss.roi')],
to_diff=[(ph.inFile('out_mrna_2l_ss.roi.stderr'), ph.outFile('out_mrna_2l_ss.roi.stderr'), transforms),
(ph.inFile('out_mrna_2l_ss.roi.stdout'), ph.outFile('out_mrna_2l_ss.roi.stdout'), transforms),
(ph.inFile('out_mrna_2l_ss.roi'), ph.outFile('out_mrna_2l_ss.roi'))
])
conf_list.append(conf)
conf = app_tests.TestConf(
program=path_to_bam2roi,
redir_stderr=ph.outFile('out_mrna_2l.roi.stderr'),
redir_stdout=ph.outFile('out_mrna_2l.roi.stdout'),
args=['-if', ph.inFile('micro_rna_sorted_2l.bam'),
'-of', ph.outFile('out_mrna_2l.roi')],
to_diff=[(ph.inFile('out_mrna_2l.roi.stderr'), ph.outFile('out_mrna_2l.roi.stderr'), transforms),
(ph.inFile('out_mrna_2l.roi.stdout'), ph.outFile('out_mrna_2l.roi.stdout'), transforms),
(ph.inFile('out_mrna_2l.roi'), ph.outFile('out_mrna_2l.roi'))
])
conf_list.append(conf)
# TODO(holtgrew): Test with paired-end data with/without ignoring pairing.
# Execute the tests.
failures = 0
for conf in conf_list:
res = app_tests.runTest(conf)
# Output to the user.
print ' '.join([os.path.basename(conf.program)] + conf.args),
if res:
print 'OK'
else:
failures += 1
print 'FAILED'
# Cleanup.
ph.deleteTempDir()
print '=============================='
print ' total tests: %d' % len(conf_list)
print ' failed tests: %d' % failures
print 'successful tests: %d' % (len(conf_list) - failures)
print '=============================='
# Compute and return return code.
return failures != 0
def main(source_base, binary_base):
"""Main entry point of the script."""
print 'Executing test for searchjoin'
print '==========================='
print
ph = app_tests.TestPathHelper(source_base, binary_base,
'apps/searchjoin/tests') # tests dir
# ============================================================
# Auto-detect the binary path.
# ============================================================
path_to_join = app_tests.autolocateBinary(binary_base, 'bin', 's4_join')
path_to_search = app_tests.autolocateBinary(binary_base, 'bin',
's4_search')
# ============================================================
# Built TestConf list.
# ============================================================
# Build list with TestConf objects, analoguely to how the output
# was generated in generate_outputs.sh.
conf_list = []
# ============================================================
# Define program parameters.
# ============================================================
# Seed length
SL = {'geo': ['5'], 'dna': ['10']}
# Errors
K = {'geo': ['0', '1', '3'], 'dna': ['0', '8', '16']}
# Threads
THREADS = '4'
# ============================================================
# Configure Join Tests.
# ============================================================
for alphabet in ['geo', 'dna']:
for k in K[alphabet]:
for sl in SL[alphabet]:
conf = app_tests.TestConf(
program=path_to_join,
# redir_stdout=ph.outFile('join_%s_%s_%s.stdout' % (alphabet, k, sl)),
args=[
ph.inFile('%s_database.csv' % alphabet), k, '-i',
alphabet, '-t', THREADS, '-sl', sl, '-o',
ph.outFile('join_%s_%s_%s.out' % (alphabet, k, sl))
],
to_diff=[
(ph.inFile('join_%s_%s.out' % (alphabet, k)),
ph.outFile('join_%s_%s_%s.out' % (alphabet, k, sl)),
transforms)
])
conf_list.append(conf)
# ============================================================
# Configure Search Tests.
# ============================================================
for alphabet in ['geo', 'dna']:
for sl in SL[alphabet]:
conf = app_tests.TestConf(
program=path_to_search,
# redir_stdout=ph.outFile('search_%s_%s.stdout' % (alphabet, sl)),
args=[
ph.inFile('%s_database.csv' % alphabet),
ph.inFile('%s_queries.csv' % alphabet), '--no-wait', '-i',
alphabet, '-t', THREADS, '-sl', sl, '-o',
ph.outFile('search_%s_%s.out' % (alphabet, sl))
],
to_diff=[(ph.inFile('search_%s.out' % (alphabet)),
ph.outFile('search_%s_%s.out' % (alphabet, sl)),
transforms)])
conf_list.append(conf)
# ============================================================
# Run Tests.
# ============================================================
# Execute the tests.
failures = 0
for conf in conf_list:
res = app_tests.runTest(conf)
# Output to the user.
print ' '.join([conf.program] + conf.args),
if res:
print 'OK'
else:
failures += 1
print 'FAILED'
# Cleanup.
ph.deleteTempDir()
print '=============================='
print ' total tests: %d' % len(conf_list)
print ' failed tests: %d' % failures
print 'successful tests: %d' % (len(conf_list) - failures)
print '=============================='
# Compute and return return code.
return failures != 0
def main(source_base, binary_base):
"""Main entry point of the script."""
print "Executing test for insegt"
print "========================="
print
ph = app_tests.TestPathHelper(source_base, binary_base, "apps/insegt/tests") # tests dir
# ============================================================
# Auto-detect the binary path.
# ============================================================
path_to_program = app_tests.autolocateBinary(binary_base, "bin", "insegt")
# ============================================================
# Built TestConf list.
# ============================================================
# Build list with TestConf objects, analoguely to how the output
# was generated in generate_outputs.sh.
conf_list = []
# ============================================================
# First Section.
# ============================================================
# App TestConf objects to conf_list, just like this for each
# test you want to run.
conf = app_tests.TestConf(
program=path_to_program,
args=[
"-ro",
ph.outFile("default_readOutput.gff"),
"-ao",
ph.outFile("default_annoOutput.gff"),
"-to",
ph.outFile("default_tupleOutput.gff"),
ph.inFile("alignments.sam"),
ph.inFile("annotations.gff"),
],
to_diff=[
(ph.inFile("default_annoOutput.gff"), ph.outFile("default_annoOutput.gff")),
(ph.inFile("default_readOutput.gff"), ph.outFile("default_readOutput.gff")),
(ph.inFile("default_tupleOutput.gff"), ph.outFile("default_tupleOutput.gff")),
],
)
conf_list.append(conf)
conf = app_tests.TestConf(
program=path_to_program,
args=[
"-c",
str(2),
"-ro",
ph.outFile("threshold-count2_readOutput.gff"),
"-ao",
ph.outFile("threshold-count2_annoOutput.gff"),
"-to",
ph.outFile("threshold-count2_tupleOutput.gff"),
ph.inFile("alignments.sam"),
ph.inFile("annotations.gff"),
],
to_diff=[
(ph.inFile("threshold-count2_annoOutput.gff"), ph.outFile("threshold-count2_annoOutput.gff")),
(ph.inFile("threshold-count2_readOutput.gff"), ph.outFile("threshold-count2_readOutput.gff")),
(ph.inFile("threshold-count2_tupleOutput.gff"), ph.outFile("threshold-count2_tupleOutput.gff")),
],
)
conf_list.append(conf)
conf = app_tests.TestConf(
program=path_to_program,
args=[
"-n",
str(3),
"-ro",
ph.outFile("ntuple3_readOutput.gff"),
"-ao",
ph.outFile("ntuple3_annoOutput.gff"),
"-to",
ph.outFile("ntuple3_tupleOutput.gff"),
ph.inFile("alignments.sam"),
ph.inFile("annotations.gff"),
],
to_diff=[
(ph.inFile("ntuple3_annoOutput.gff"), ph.outFile("ntuple3_annoOutput.gff")),
(ph.inFile("ntuple3_readOutput.gff"), ph.outFile("ntuple3_readOutput.gff")),
(ph.inFile("ntuple3_tupleOutput.gff"), ph.outFile("ntuple3_tupleOutput.gff")),
],
)
conf_list.append(conf)
conf = app_tests.TestConf(
program=path_to_program,
args=[
"-m",
"-ro",
ph.outFile("max-tuple_readOutput.gff"),
"-ao",
ph.outFile("max-tuple_annoOutput.gff"),
"-to",
ph.outFile("max-tuple_tupleOutput.gff"),
ph.inFile("alignments.sam"),
ph.inFile("annotations.gff"),
],
to_diff=[
(ph.inFile("max-tuple_annoOutput.gff"), ph.outFile("max-tuple_annoOutput.gff")),
(ph.inFile("max-tuple_readOutput.gff"), ph.outFile("max-tuple_readOutput.gff")),
(ph.inFile("max-tuple_tupleOutput.gff"), ph.outFile("max-tuple_tupleOutput.gff")),
],
)
conf_list.append(conf)
conf = app_tests.TestConf(
program=path_to_program,
args=[
"-e",
"-ro",
ph.outFile("exact-ntuple_readOutput.gff"),
"-ao",
ph.outFile("exact-ntuple_annoOutput.gff"),
"-to",
ph.outFile("exact-ntuple_tupleOutput.gff"),
ph.inFile("alignments.sam"),
ph.inFile("annotations.gff"),
],
to_diff=[
(ph.inFile("exact-ntuple_annoOutput.gff"), ph.outFile("exact-ntuple_annoOutput.gff")),
(ph.inFile("exact-ntuple_readOutput.gff"), ph.outFile("exact-ntuple_readOutput.gff")),
(ph.inFile("exact-ntuple_tupleOutput.gff"), ph.outFile("exact-ntuple_tupleOutput.gff")),
],
)
conf_list.append(conf)
# ============================================================
# Execute the tests.
# ============================================================
failures = 0
for conf in conf_list:
res = app_tests.runTest(conf)
# Output to the user.
print " ".join(["insegt"] + conf.args),
if res:
print "OK"
else:
failures += 1
print "FAILED"
# Cleanup.
ph.deleteTempDir()
print "=============================="
print " total tests: %d" % len(conf_list)
print " failed tests: %d" % failures
print "successful tests: %d" % (len(conf_list) - failures)
print "=============================="
# Compute and return return code.
return failures != 0
def main(source_base, binary_base):
"""Main entry point of the script."""
print 'Executing test for samcat'
print '========================='
print
ph = app_tests.TestPathHelper(source_base, binary_base,
'apps/samcat/tests') # tests dir
# ============================================================
# Auto-detect the binary path.
# ============================================================
path_to_program = app_tests.autolocateBinary(binary_base, 'apps/samcat',
'samcat')
# ============================================================
# Built TestConf list.
# ============================================================
# Build list with TestConf objects, analoguely to how the output
# was generated in generate_outputs.sh.
conf_list = []
# ============================================================
# Run on DNA (Adenoviruses).
# ============================================================
conf = app_tests.TestConf(program=path_to_program,
args=[
ph.inFile('ex1_a1.sam'),
ph.inFile('ex1_a2.sam'),
ph.inFile('ex1_a3.sam'), '-o',
ph.outFile('ex1_merged.sam')
],
to_diff=[(ph.inFile('ex1_merged.sam'),
ph.outFile('ex1_merged.sam'))])
conf_list.append(conf)
conf = app_tests.TestConf(program=path_to_program,
args=[
ph.inFile('ex1_a1.sam'),
ph.inFile('ex1_a2.sam'),
ph.inFile('ex1_a3.sam'), '-o',
ph.outFile('ex1_merged.bam')
],
to_diff=[(ph.inFile('ex1_merged.bam'),
ph.outFile('ex1_merged.bam'), "gunzip")
])
conf_list.append(conf)
# Execute the tests.
failures = 0
for conf in conf_list:
res = app_tests.runTest(conf)
# Output to the user.
print ' '.join(conf.commandLineArgs())
if res:
print 'OK'
else:
failures += 1
print 'FAILED'
# Cleanup.
ph.deleteTempDir()
print '=============================='
print ' total tests: %d' % len(conf_list)
print ' failed tests: %d' % failures
print 'successful tests: %d' % (len(conf_list) - failures)
print '=============================='
# Compute and return return code.
return failures != 0
def main(source_base, binary_base):
"""Main entry point of the script."""
print 'Executing test for rabema'
print '========================='
print
ph = app_tests.TestPathHelper(
source_base, binary_base,
'core/apps/rabema/tests') # tests dir
# ============================================================
# Auto-detect the binary path.
# ============================================================
path_to_prepare = app_tests.autolocateBinary(
binary_base, 'core/apps/rabema', 'rabema_prepare_sam')
path_to_build = app_tests.autolocateBinary(
binary_base, 'core/apps/rabema', 'rabema_build_gold_standard')
path_to_evaluate = app_tests.autolocateBinary(
binary_base, 'core/apps/rabema', 'rabema_evaluate')
# ============================================================
# Copy Files To Temp Dir.
# ============================================================
# We copy over the genome because an FAI file will be created.
shutil.copyfile(ph.inFile('adeno-genome.fa'),
ph.outFile('adeno-genome.fa'))
# ============================================================
# Build TestConf list.
# ============================================================
# Build list with TestConf objects, analoguely to how the output
# was generated in generate_outputs.sh.
conf_list = []
# ============================================================
# Prepare SAM
# ============================================================
conf = app_tests.TestConf(
program=path_to_prepare,
args=['-i', ph.inFile('gold-adeno-hamming-08.sam'),
'-o', ph.outFile('gold-adeno-hamming-08.by_qname.sam')],
to_diff=[(ph.inFile('gold-adeno-hamming-08.by_qname.sam'),
ph.outFile('gold-adeno-hamming-08.by_qname.sam'))])
conf_list.append(conf)
conf = app_tests.TestConf(
program=path_to_prepare,
args=['-i', ph.inFile('gold-adeno-edit-08.sam'),
'-o', ph.outFile('gold-adeno-edit-08.by_qname.sam')],
to_diff=[(ph.inFile('gold-adeno-edit-08.by_qname.sam'),
ph.outFile('gold-adeno-edit-08.by_qname.sam'))])
conf_list.append(conf)
# ============================================================
# Build Gold Standard
# ============================================================
conf = app_tests.TestConf(
program=path_to_build,
redir_stdout=ph.outFile('gold-adeno-hamming-08.stdout'),
args=['--distance-metric', 'hamming', '-e', '8',
'-o', ph.outFile('gold-adeno-hamming-08.gsi'),
'--reference', ph.outFile('adeno-genome.fa'),
'--in-sam', ph.inFile('gold-adeno-hamming-08.by_coordinate.sam')],
to_diff=[(ph.inFile('gold-adeno-hamming-08.stdout'),
ph.outFile('gold-adeno-hamming-08.stdout')),
(ph.inFile('gold-adeno-hamming-08.gsi'),
ph.outFile('gold-adeno-hamming-08.gsi'))])
conf_list.append(conf)
conf = app_tests.TestConf(
program=path_to_build,
redir_stdout=ph.outFile('gold-adeno-edit-08.stdout'),
args=['--distance-metric', 'edit', '-e', '8',
'-o', ph.outFile('gold-adeno-edit-08.gsi'),
'--reference', ph.outFile('adeno-genome.fa'),
'--in-sam', ph.inFile('gold-adeno-edit-08.by_coordinate.sam')],
to_diff=[(ph.inFile('gold-adeno-edit-08.stdout'),
ph.outFile('gold-adeno-edit-08.stdout')),
(ph.inFile('gold-adeno-edit-08.gsi'),
ph.outFile('gold-adeno-edit-08.gsi'))])
conf_list.append(conf)
# ============================================================
# Compare.
# ============================================================
conf = app_tests.TestConf(
program=path_to_evaluate,
redir_stdout=ph.outFile('razers2-adeno-hamming-08.stdout'),
args=['--distance-metric', 'hamming', '-e', '8',
'--reference', ph.outFile('adeno-genome.fa'),
'--in-sam', ph.inFile('razers2-adeno-hamming-08.sam'),
'--in-gsi', ph.inFile('gold-adeno-hamming-08.gsi')],
to_diff=[(ph.inFile('razers2-adeno-hamming-08.stdout'),
ph.outFile('razers2-adeno-hamming-08.stdout'))])
conf_list.append(conf)
conf = app_tests.TestConf(
program=path_to_evaluate,
redir_stdout=ph.outFile('razers2-adeno-hamming-04.stdout'),
args=['--distance-metric', 'hamming', '-e', '8',
'--reference', ph.outFile('adeno-genome.fa'),
'--in-sam', ph.inFile('razers2-adeno-hamming-04.sam'),
'--in-gsi', ph.inFile('gold-adeno-hamming-08.gsi')],
to_diff=[(ph.inFile('razers2-adeno-hamming-04.stdout'),
ph.outFile('razers2-adeno-hamming-04.stdout'))])
conf_list.append(conf)
conf = app_tests.TestConf(
program=path_to_evaluate,
redir_stdout=ph.outFile('razers2-adeno-edit-08.stdout'),
args=['--distance-metric', 'edit', '-e', '8',
'--reference', ph.outFile('adeno-genome.fa'),
'--in-sam', ph.inFile('razers2-adeno-edit-08.sam'),
'--in-gsi', ph.inFile('gold-adeno-edit-08.gsi')],
to_diff=[(ph.inFile('razers2-adeno-edit-08.stdout'),
ph.outFile('razers2-adeno-edit-08.stdout'))])
conf_list.append(conf)
conf = app_tests.TestConf(
program=path_to_evaluate,
redir_stdout=ph.outFile('razers2-adeno-edit-04.stdout'),
args=['--distance-metric', 'edit', '-e', '8',
'--reference', ph.outFile('adeno-genome.fa'),
'--in-sam', ph.inFile('razers2-adeno-edit-04.sam'),
'--in-gsi', ph.inFile('gold-adeno-edit-08.gsi')],
to_diff=[(ph.inFile('razers2-adeno-edit-04.stdout'),
ph.outFile('razers2-adeno-edit-04.stdout'))])
conf_list.append(conf)
# Execute the tests.
failures = 0
for conf in conf_list:
res = app_tests.runTest(conf)
# Output to the user.
print ' '.join([os.path.basename(conf.program)] + conf.args),
if res:
print 'OK'
else:
failures += 1
print 'FAILED'
# Cleanup.
ph.deleteTempDir()
print '=============================='
print ' total tests: %d' % len(conf_list)
print ' failed tests: %d' % failures
print 'successful tests: %d' % (len(conf_list) - failures)
print '=============================='
# Compute and return return code.
return failures != 0
def main(source_base, binary_base):
"""Main entry point of the script."""
print 'Executing test for insegt'
print '========================='
print
ph = app_tests.TestPathHelper(
source_base, binary_base,
'apps/insegt/tests') # tests dir
# ============================================================
# Auto-detect the binary path.
# ============================================================
path_to_program = app_tests.autolocateBinary(
binary_base, 'bin', 'insegt')
# ============================================================
# Built TestConf list.
# ============================================================
# Build list with TestConf objects, analoguely to how the output
# was generated in generate_outputs.sh.
conf_list = []
# ============================================================
# First Section.
# ============================================================
# App TestConf objects to conf_list, just like this for each
# test you want to run.
conf = app_tests.TestConf(
program=path_to_program,
args=['-ro', ph.outFile('default_readOutput.gff'),
'-ao', ph.outFile('default_annoOutput.gff'),
'-to', ph.outFile('default_tupleOutput.gff'),
ph.inFile('alignments.sam'),
ph.inFile('annotations.gff')],
to_diff=[(ph.inFile('default_annoOutput.gff'),
ph.outFile('default_annoOutput.gff')),
(ph.inFile('default_readOutput.gff'),
ph.outFile('default_readOutput.gff')),
(ph.inFile('default_tupleOutput.gff'),
ph.outFile('default_tupleOutput.gff'))])
conf_list.append(conf)
conf = app_tests.TestConf(
program=path_to_program,
args=['-c', str(2),
'-ro', ph.outFile('threshold-count2_readOutput.gff'),
'-ao', ph.outFile('threshold-count2_annoOutput.gff'),
'-to', ph.outFile('threshold-count2_tupleOutput.gff'),
ph.inFile('alignments.sam'),
ph.inFile('annotations.gff')],
to_diff=[(ph.inFile('threshold-count2_annoOutput.gff'),
ph.outFile('threshold-count2_annoOutput.gff')),
(ph.inFile('threshold-count2_readOutput.gff'),
ph.outFile('threshold-count2_readOutput.gff')),
(ph.inFile('threshold-count2_tupleOutput.gff'),
ph.outFile('threshold-count2_tupleOutput.gff'))])
conf_list.append(conf)
conf = app_tests.TestConf(
program=path_to_program,
args=['-n', str(3),
'-ro', ph.outFile('ntuple3_readOutput.gff'),
'-ao', ph.outFile('ntuple3_annoOutput.gff'),
'-to', ph.outFile('ntuple3_tupleOutput.gff'),
ph.inFile('alignments.sam'),
ph.inFile('annotations.gff')],
to_diff=[(ph.inFile('ntuple3_annoOutput.gff'),
ph.outFile('ntuple3_annoOutput.gff')),
(ph.inFile('ntuple3_readOutput.gff'),
ph.outFile('ntuple3_readOutput.gff')),
(ph.inFile('ntuple3_tupleOutput.gff'),
ph.outFile('ntuple3_tupleOutput.gff'))])
conf_list.append(conf)
conf = app_tests.TestConf(
program=path_to_program,
args=['-m',
'-ro', ph.outFile('max-tuple_readOutput.gff'),
'-ao', ph.outFile('max-tuple_annoOutput.gff'),
'-to', ph.outFile('max-tuple_tupleOutput.gff'),
ph.inFile('alignments.sam'),
ph.inFile('annotations.gff')],
to_diff=[(ph.inFile('max-tuple_annoOutput.gff'),
ph.outFile('max-tuple_annoOutput.gff')),
(ph.inFile('max-tuple_readOutput.gff'),
ph.outFile('max-tuple_readOutput.gff')),
(ph.inFile('max-tuple_tupleOutput.gff'),
ph.outFile('max-tuple_tupleOutput.gff'))])
conf_list.append(conf)
conf = app_tests.TestConf(
program=path_to_program,
args=['-e',
'-ro', ph.outFile('exact-ntuple_readOutput.gff'),
'-ao', ph.outFile('exact-ntuple_annoOutput.gff'),
'-to', ph.outFile('exact-ntuple_tupleOutput.gff'),
ph.inFile('alignments.sam'),
ph.inFile('annotations.gff')],
to_diff=[(ph.inFile('exact-ntuple_annoOutput.gff'),
ph.outFile('exact-ntuple_annoOutput.gff')),
(ph.inFile('exact-ntuple_readOutput.gff'),
ph.outFile('exact-ntuple_readOutput.gff')),
(ph.inFile('exact-ntuple_tupleOutput.gff'),
ph.outFile('exact-ntuple_tupleOutput.gff'))])
conf_list.append(conf)
# ============================================================
# Execute the tests.
# ============================================================
failures = 0
for conf in conf_list:
res = app_tests.runTest(conf)
# Output to the user.
print ' '.join(['insegt'] + conf.args),
if res:
print 'OK'
else:
failures += 1
print 'FAILED'
# Cleanup.
ph.deleteTempDir()
print '=============================='
print ' total tests: %d' % len(conf_list)
print ' failed tests: %d' % failures
print 'successful tests: %d' % (len(conf_list) - failures)
print '=============================='
# Compute and return return code.
return failures != 0
def main(source_base, binary_base):
"""Main entry point of the script."""
print 'Executing test for seqan_flexbar'
print '================================'
print
ph = app_tests.TestPathHelper(source_base, binary_base,
'apps/seqan_flexbar/tests') # tests dir
# ============================================================
# Auto-detect the binary path.
# ============================================================
path_to_program = []
path_to_program.append(
app_tests.autolocateBinary(binary_base, 'bin', 'sflexQC'))
path_to_program.append(
app_tests.autolocateBinary(binary_base, 'bin', 'sflexFilter'))
path_to_program.append(
app_tests.autolocateBinary(binary_base, 'bin', 'sflexAR'))
path_to_program.append(
app_tests.autolocateBinary(binary_base, 'bin', 'sflexDMulti'))
# ============================================================
# Built TestConf list.
# ============================================================
# Build list with TestConf objects, analoguely to how the output
# was generated in generate_outputs.sh.
conf_list = []
# ============================================================
# First Section.
# ============================================================
# App TestConf objects to conf_list, just like this for each
# test you want to run.
conf = app_tests.TestConf(program=path_to_program[0],
redir_stdout=ph.outFile('out.stdout'),
args=[
ph.inFile('testsample.fq'), '-q', '20', '-o',
ph.outFile('qc_test.fa'), '-t', '-ni'
],
to_diff=[(ph.inFile('qc_test.stdout'),
ph.outFile('out.stdout')),
(ph.inFile('gold_qc_test.fa'),
ph.outFile('qc_test.fa'))])
conf_list.append(conf)
conf = app_tests.TestConf(program=path_to_program[1],
redir_stdout=ph.outFile('out.stdout'),
args=[
ph.inFile('testsample.fq'), '-tl', '3',
'-tr', '4', '-ml', '70', '-u', '1', '-s',
'A', '-fl', '70', '-ni', '-o',
ph.outFile('filter_test.fq')
],
to_diff=[(ph.inFile('filter_test.stdout'),
ph.outFile('out.stdout')),
(ph.inFile('gold_filter_test.fq'),
ph.outFile('filter_test.fq'))])
conf_list.append(conf)
conf = app_tests.TestConf(program=path_to_program[2],
redir_stdout=ph.outFile('out.stdout'),
args=[
ph.inFile('testsample.fq'), '-a',
ph.inFile('adapter.fa'), '-o',
ph.outFile('ar_test.fq'), '-ni'
],
to_diff=[(ph.inFile('ar_test.stdout'),
ph.outFile('out.stdout')),
(ph.inFile('gold_ar_test.fq'),
ph.outFile('ar_test.fq'))])
conf_list.append(conf)
conf = app_tests.TestConf(program=path_to_program[3],
redir_stdout=ph.outFile('out.stdout'),
args=[
ph.inFile('testsample_multiplex.fq'), '-b',
ph.inFile('barcodes.fa'), '-o',
ph.outFile('test_de_multi.fq'), '-ni'
],
to_diff=[
(ph.inFile('gold_de_multi.stdout'),
ph.outFile('out.stdout')),
(ph.inFile('gold_de_multi_Sample-1.fq'),
ph.outFile('test_de_multi_Sample-1.fq')),
(ph.inFile('gold_de_multi_Sample26.fq'),
ph.outFile('test_de_multi_Sample26.fq')),
(ph.inFile('gold_de_multi_Sample-2.fq'),
ph.outFile('test_de_multi_Sample-2.fq')),
(ph.inFile('gold_de_multi_Sample0.fq'),
ph.outFile('test_de_multi_Sample0.fq')),
(ph.inFile('gold_de_multi_Sample1458.fq'),
ph.outFile('test_de_multi_Sample1458.fq')),
(ph.inFile('gold_de_multi_Sample37.fq'),
ph.outFile('test_de_multi_Sample37.fq')),
(ph.inFile('gold_de_multi_unidentified.fq'),
ph.outFile('test_de_multi_unidentified.fq'))
])
conf_list.append(conf)
# ============================================================
# Execute the tests.
# ============================================================
failures = 0
counter = 0
for conf in conf_list:
res = app_tests.runTest(conf)
# Output to the user.
print ' '.join([path_to_program[counter]] + conf.args),
if res:
print 'OK'
else:
failures += 1
print 'FAILED'
counter += 1
# Cleanup.
ph.deleteTempDir()
print '=============================='
print ' total tests: %d' % len(conf_list)
print ' failed tests: %d' % failures
print 'successful tests: %d' % (len(conf_list) - failures)
print '=============================='
# Compute and return return code.
return failures != 0
def main(source_base, binary_base):
"""Main entry point of the script."""
print 'Executing test for micro_razers'
print '==============================='
print
ph = app_tests.TestPathHelper(
source_base, binary_base,
'apps/micro_razers/tests') # tests dir
# ============================================================
# Auto-detect the binary path.
# ============================================================
path_to_program = app_tests.autolocateBinary(
binary_base, 'apps/micro_razers', 'micro_razers')
# ============================================================
# Built TestConf list.
# ============================================================
# Build list with TestConf objects, analoguely to how the output
# was generated in generate_outputs.sh.
conf_list = []
# ============================================================
# First Section.
# ============================================================
# Run with default options.
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('se-adeno-reads36_1_default.stdout'),
args=[ph.inFile('adeno-genome.fa'),
ph.inFile('adeno-reads36_1.fa'),
'-o', ph.outFile('se-adeno-reads36_1_default.razers' )],
to_diff=[(ph.inFile('se-adeno-reads36_1_default.razers' ),
ph.outFile('se-adeno-reads36_1_default.razers' )),
(ph.inFile('se-adeno-reads36_1_default.stdout' ),
ph.outFile('se-adeno-reads36_1_default.stdout' ))])
conf_list.append(conf)
# Run with different seed lengths
for sl in range(14,21):
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('se-adeno-reads36_1_sl%d.stdout' % sl),
args=['-sL', str(sl),
ph.inFile('adeno-genome.fa'),
ph.inFile('adeno-reads36_1.fa'),
'-o', ph.outFile('se-adeno-reads36_1_sl%d.razers' % sl)],
to_diff=[(ph.inFile('se-adeno-reads36_1_sl%d.razers' % sl),
ph.outFile('se-adeno-reads36_1_sl%d.razers' % sl)),
(ph.inFile('se-adeno-reads36_1_sl%d.stdout' % sl),
ph.outFile('se-adeno-reads36_1_sl%d.stdout' % sl))])
conf_list.append(conf)
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('se-adeno-reads36_1_sl%d_sam.stdout' % sl),
args=['-sL', str(sl),
ph.inFile('adeno-genome.fa'),
ph.inFile('adeno-reads36_1.fa'),
'-o', ph.outFile('se-adeno-reads36_1_sl%d.sam' % sl)],
to_diff=[(ph.inFile('se-adeno-reads36_1_sl%d.sam' % sl),
ph.outFile('se-adeno-reads36_1_sl%d.sam' % sl)),
(ph.inFile('se-adeno-reads36_1_sl%d_sam.stdout' % sl),
ph.outFile('se-adeno-reads36_1_sl%d_sam.stdout' % sl))])
conf_list.append(conf)
# allow error in seed
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('se-adeno-reads36_1_sl%d_se.stdout' % sl),
args=['-sL', str(sl), '-sE',
ph.inFile('adeno-genome.fa'),
ph.inFile('adeno-reads36_1.fa'),
'-o', ph.outFile('se-adeno-reads36_1_sl%d_se.razers' % sl)],
to_diff=[(ph.inFile('se-adeno-reads36_1_sl%d_se.razers' % sl),
ph.outFile('se-adeno-reads36_1_sl%d_se.razers' % sl)),
(ph.inFile('se-adeno-reads36_1_sl%d_se.stdout' % sl),
ph.outFile('se-adeno-reads36_1_sl%d_se.stdout' % sl))])
conf_list.append(conf)
# change maxhits parameter
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('se-adeno-reads36_1_sl18_m20_pa.stdout' ),
args=['-sL', str(18), '-m', str(20), '-pa',
ph.inFile('adeno-genome.fa'),
ph.inFile('adeno-reads36_1.fa'),
'-o', ph.outFile('se-adeno-reads36_1_sl18_m20_pa.razers' )],
to_diff=[(ph.inFile('se-adeno-reads36_1_sl18_m20_pa.razers' ),
ph.outFile('se-adeno-reads36_1_sl18_m20_pa.razers' )),
(ph.inFile('se-adeno-reads36_1_sl18_m20_pa.stdout' ),
ph.outFile('se-adeno-reads36_1_sl18_m20_pa.stdout' ))])
conf_list.append(conf)
# ============================================================
# Execute the tests.
# ============================================================
failures = 0
for conf in conf_list:
res = app_tests.runTest(conf)
# Output to the user.
print ' '.join(['micro_razers'] + conf.args),
if res:
print 'OK'
else:
failures += 1
print 'FAILED'
# Cleanup.
ph.deleteTempDir()
print '=============================='
print ' total tests: %d' % len(conf_list)
print ' failed tests: %d' % failures
print 'successful tests: %d' % (len(conf_list) - failures)
print '=============================='
# Compute and return return code.
return failures != 0
def main(source_base, binary_base):
"""Main entry point of the script."""
print 'Executing test for stellar'
print '========================='
print
ph = app_tests.TestPathHelper(source_base, binary_base,
'core/apps/stellar/tests') # tests dir
# ============================================================
# Auto-detect the binary path.
# ============================================================
path_to_program = app_tests.autolocateBinary(binary_base,
'core/apps/stellar',
'stellar')
# ============================================================
# Built TestConf list.
# ============================================================
# Build list with TestConf objects, analoguely to how the output
# was generated in generate_outputs.sh.
conf_list = []
# We prepare a list of transforms to apply to the output files. This is
# used to strip the input/output paths from the programs' output to
# make it more canonical and host independent.
ph.outFile('-') # To ensure that the out path is set.
transforms = [
app_tests.ReplaceTransform(
os.path.join(ph.source_base_path, 'core/apps/stellar/tests') +
os.sep,
'',
right=True),
app_tests.ReplaceTransform(ph.temp_dir + os.sep, '', right=True),
app_tests.NormalizeScientificExponentsTransform(),
]
# ============================================================
# Run STELLAR.
# ============================================================
# Error rate 0.1:
conf = app_tests.TestConf(program=path_to_program,
redir_stdout=ph.outFile('e-1.stdout'),
args=[
'-e', '0.1', '-l', '50', '-x', '10', '-k',
'7', '-n', '5000', '-s', '10000', '-f', '-v',
'-t', '-o',
ph.outFile('e-1.gff'),
ph.inFile('512_simSeq1_e-1.fa'),
ph.inFile('512_simSeq2_e-1.fa')
],
to_diff=[(ph.inFile('e-1.stdout'),
ph.outFile('e-1.stdout'), transforms),
(ph.inFile('e-1.gff'),
ph.outFile('e-1.gff'), transforms)])
conf_list.append(conf)
# Error rate 0.05:
conf = app_tests.TestConf(program=path_to_program,
redir_stdout=ph.outFile('5e-2.stdout'),
args=[
'-e', '0.05', '-l', '50', '-x', '10', '-k',
'7', '-n', '5000', '-s', '10000', '-f', '-v',
'-t', '-o',
ph.outFile('5e-2.gff'),
ph.inFile('512_simSeq1_5e-2.fa'),
ph.inFile('512_simSeq2_5e-2.fa')
],
to_diff=[(ph.inFile('5e-2.stdout'),
ph.outFile('5e-2.stdout'), transforms),
(ph.inFile('5e-2.gff'),
ph.outFile('5e-2.gff'), transforms)])
conf_list.append(conf)
# Error rate 0.25:
conf = app_tests.TestConf(program=path_to_program,
redir_stdout=ph.outFile('25e-3.stdout'),
args=[
'-e', '0.025', '-l', '50', '-x', '10', '-k',
'7', '-n', '5000', '-s', '10000', '-f', '-v',
'-t', '-o',
ph.outFile('25e-3.gff'),
ph.inFile('512_simSeq1_25e-3.fa'),
ph.inFile('512_simSeq2_25e-3.fa')
],
to_diff=[(ph.inFile('25e-3.stdout'),
ph.outFile('25e-3.stdout'),
transforms),
(ph.inFile('25e-3.gff'),
ph.outFile('25e-3.gff'), transforms)])
conf_list.append(conf)
# Error rate 0.75:
conf = app_tests.TestConf(program=path_to_program,
redir_stdout=ph.outFile('75e-3.stdout'),
args=[
'-e', '0.075', '-l', '50', '-x', '10', '-k',
'7', '-n', '5000', '-s', '10000', '-f', '-v',
'-t', '-o',
ph.outFile('75e-3.gff'),
ph.inFile('512_simSeq1_75e-3.fa'),
ph.inFile('512_simSeq2_75e-3.fa')
],
to_diff=[(ph.inFile('75e-3.stdout'),
ph.outFile('75e-3.stdout'),
transforms),
(ph.inFile('75e-3.gff'),
ph.outFile('75e-3.gff'), transforms)])
conf_list.append(conf)
# Error rate 0.0001:
conf = app_tests.TestConf(program=path_to_program,
redir_stdout=ph.outFile('e-4.stdout'),
args=[
'-e', '0.0001', '-l', '50', '-x', '10', '-k',
'7', '-n', '5000', '-s', '10000', '-f', '-v',
'-t', '-o',
ph.outFile('e-4.gff'),
ph.inFile('512_simSeq1_e-4.fa'),
ph.inFile('512_simSeq2_e-4.fa')
],
to_diff=[(ph.inFile('e-4.stdout'),
ph.outFile('e-4.stdout'), transforms),
(ph.inFile('e-4.gff'),
ph.outFile('e-4.gff'), transforms)])
conf_list.append(conf)
# Minimal length: 20, Error rate 0.05:
conf = app_tests.TestConf(program=path_to_program,
redir_stdout=ph.outFile('minLen20.stdout'),
args=[
'-e', '0.05', '-l', '20', '-x', '10', '-k',
'7', '-n', '5000', '-s', '10000', '-f', '-v',
'-t', '-o',
ph.outFile('minLen20.gff'),
ph.inFile('512_simSeq1_5e-2.fa'),
ph.inFile('512_simSeq2_5e-2.fa')
],
to_diff=[
(ph.inFile('minLen20.stdout'),
ph.outFile('minLen20.stdout'), transforms),
(ph.inFile('minLen20.gff'),
ph.outFile('minLen20.gff'), transforms)
])
conf_list.append(conf)
# Minimal length: 150, Error rate 0.05:
conf = app_tests.TestConf(program=path_to_program,
redir_stdout=ph.outFile('minLen150.stdout'),
args=[
'-e', '0.05', '-l', '150', '-x', '10', '-k',
'7', '-n', '5000', '-s', '10000', '-f', '-v',
'-t', '-o',
ph.outFile('minLen150.gff'),
ph.inFile('512_simSeq1_5e-2.fa'),
ph.inFile('512_simSeq2_5e-2.fa')
],
to_diff=[
(ph.inFile('minLen150.stdout'),
ph.outFile('minLen150.stdout'), transforms),
(ph.inFile('minLen150.gff'),
ph.outFile('minLen150.gff'), transforms)
])
conf_list.append(conf)
# Output format text:
conf = app_tests.TestConf(program=path_to_program,
redir_stdout=ph.outFile('5e-2txt.stdout'),
args=[
'-e', '0.05', '-l', '50', '-x', '10', '-k',
'7', '-n', '5000', '-s', '10000', '-f', '-v',
'-t', '-o',
ph.outFile('5e-2.txt'),
ph.inFile('512_simSeq1_5e-2.fa'),
ph.inFile('512_simSeq2_5e-2.fa')
],
to_diff=[(ph.inFile('5e-2txt.stdout'),
ph.outFile('5e-2txt.stdout'),
transforms),
(ph.inFile('5e-2.txt'),
ph.outFile('5e-2.txt'), transforms)])
conf_list.append(conf)
# ============================================================
# Execute the tests.
# ============================================================
failures = 0
for conf in conf_list:
res = app_tests.runTest(conf)
# Output to the user.
print ' '.join(['stellar'] + conf.args),
if res:
print 'OK'
else:
failures += 1
print 'FAILED'
print '=============================='
print ' total tests: %d' % len(conf_list)
print ' failed tests: %d' % failures
print 'successful tests: %d' % (len(conf_list) - failures)
print '=============================='
# Compute and return return code.
return failures != 0
def main(source_base, binary_base):
"""Main entry point of the script."""
print 'Executing test for stellar'
print '========================='
print
ph = app_tests.TestPathHelper(
source_base, binary_base,
'core/apps/stellar/tests') # tests dir
# ============================================================
# Auto-detect the binary path.
# ============================================================
path_to_program = app_tests.autolocateBinary(
binary_base, 'core/apps/stellar', 'stellar')
# ============================================================
# Built TestConf list.
# ============================================================
# Build list with TestConf objects, analoguely to how the output
# was generated in generate_outputs.sh.
conf_list = []
# We prepare a list of transforms to apply to the output files. This is
# used to strip the input/output paths from the programs' output to
# make it more canonical and host independent.
ph.outFile('-') # To ensure that the out path is set.
transforms = [
app_tests.ReplaceTransform(os.path.join(ph.source_base_path, 'core/apps/stellar/tests') + os.sep, '', right=True),
app_tests.ReplaceTransform(ph.temp_dir + os.sep, '', right=True),
app_tests.NormalizeScientificExponentsTransform(),
]
# ============================================================
# Run STELLAR.
# ============================================================
# Error rate 0.1:
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('e-1.stdout'),
args=['-e', '0.1', '-l', '50', '-x', '10', '-k', '7', '-n', '5000',
'-s', '10000', '-f', '-v', '-t',
'-o', ph.outFile('e-1.gff'),
ph.inFile('512_simSeq1_e-1.fa'),
ph.inFile('512_simSeq2_e-1.fa')],
to_diff=[(ph.inFile('e-1.stdout'),
ph.outFile('e-1.stdout'),
transforms),
(ph.inFile('e-1.gff'),
ph.outFile('e-1.gff'),
transforms)])
conf_list.append(conf)
# Error rate 0.05:
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('5e-2.stdout'),
args=['-e', '0.05', '-l', '50', '-x', '10', '-k', '7', '-n', '5000',
'-s', '10000', '-f', '-v', '-t',
'-o', ph.outFile('5e-2.gff'),
ph.inFile('512_simSeq1_5e-2.fa'),
ph.inFile('512_simSeq2_5e-2.fa')],
to_diff=[(ph.inFile('5e-2.stdout'),
ph.outFile('5e-2.stdout'),
transforms),
(ph.inFile('5e-2.gff'),
ph.outFile('5e-2.gff'),
transforms)])
conf_list.append(conf)
# Error rate 0.25:
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('25e-3.stdout'),
args=['-e', '0.025', '-l', '50', '-x', '10', '-k', '7', '-n', '5000',
'-s', '10000', '-f', '-v', '-t',
'-o', ph.outFile('25e-3.gff'),
ph.inFile('512_simSeq1_25e-3.fa'),
ph.inFile('512_simSeq2_25e-3.fa')],
to_diff=[(ph.inFile('25e-3.stdout'),
ph.outFile('25e-3.stdout'),
transforms),
(ph.inFile('25e-3.gff'),
ph.outFile('25e-3.gff'),
transforms)])
conf_list.append(conf)
# Error rate 0.75:
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('75e-3.stdout'),
args=['-e', '0.075', '-l', '50', '-x', '10', '-k', '7', '-n', '5000',
'-s', '10000', '-f', '-v', '-t',
'-o', ph.outFile('75e-3.gff'),
ph.inFile('512_simSeq1_75e-3.fa'),
ph.inFile('512_simSeq2_75e-3.fa')],
to_diff=[(ph.inFile('75e-3.stdout'),
ph.outFile('75e-3.stdout'),
transforms),
(ph.inFile('75e-3.gff'),
ph.outFile('75e-3.gff'),
transforms)])
conf_list.append(conf)
# Error rate 0.0001:
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('e-4.stdout'),
args=['-e', '0.0001', '-l', '50', '-x', '10', '-k', '7', '-n', '5000',
'-s', '10000', '-f', '-v', '-t',
'-o', ph.outFile('e-4.gff'),
ph.inFile('512_simSeq1_e-4.fa'),
ph.inFile('512_simSeq2_e-4.fa')],
to_diff=[(ph.inFile('e-4.stdout'),
ph.outFile('e-4.stdout'),
transforms),
(ph.inFile('e-4.gff'),
ph.outFile('e-4.gff'),
transforms)])
conf_list.append(conf)
# Minimal length: 20, Error rate 0.05:
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('minLen20.stdout'),
args=['-e', '0.05', '-l', '20',
'-x', '10', '-k', '7', '-n', '5000', '-s', '10000', '-f', '-v',
'-t',
'-o', ph.outFile('minLen20.gff'),
ph.inFile('512_simSeq1_5e-2.fa'),
ph.inFile('512_simSeq2_5e-2.fa')],
to_diff=[(ph.inFile('minLen20.stdout'),
ph.outFile('minLen20.stdout'),
transforms),
(ph.inFile('minLen20.gff'),
ph.outFile('minLen20.gff'),
transforms)])
conf_list.append(conf)
# Minimal length: 150, Error rate 0.05:
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('minLen150.stdout'),
args=['-e', '0.05', '-l', '150', '-x', '10', '-k', '7', '-n', '5000',
'-s', '10000', '-f', '-v', '-t',
'-o', ph.outFile('minLen150.gff'),
ph.inFile('512_simSeq1_5e-2.fa'),
ph.inFile('512_simSeq2_5e-2.fa')],
to_diff=[(ph.inFile('minLen150.stdout'),
ph.outFile('minLen150.stdout'),
transforms),
(ph.inFile('minLen150.gff'),
ph.outFile('minLen150.gff'),
transforms)])
conf_list.append(conf)
# Output format text:
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('5e-2txt.stdout'),
args=['-e', '0.05', '-l', '50', '-x', '10', '-k', '7', '-n', '5000',
'-s', '10000', '-f', '-v', '-t',
'-o', ph.outFile('5e-2.txt'),
ph.inFile('512_simSeq1_5e-2.fa'),
ph.inFile('512_simSeq2_5e-2.fa')],
to_diff=[(ph.inFile('5e-2txt.stdout'),
ph.outFile('5e-2txt.stdout'),
transforms),
(ph.inFile('5e-2.txt'),
ph.outFile('5e-2.txt'),
transforms)])
conf_list.append(conf)
# ============================================================
# Execute the tests.
# ============================================================
failures = 0
for conf in conf_list:
res = app_tests.runTest(conf)
# Output to the user.
print ' '.join(['stellar'] + conf.args),
if res:
print 'OK'
else:
failures += 1
print 'FAILED'
print '=============================='
print ' total tests: %d' % len(conf_list)
print ' failed tests: %d' % failures
print 'successful tests: %d' % (len(conf_list) - failures)
print '=============================='
# Compute and return return code.
return failures != 0
def main(source_base, binary_base):
"""Main entry point of the script."""
# gold standard binary files created on little endian
if sys.byteorder != 'little':
print('Skipping tests for DREAM-Yara on big endian')
print('=====================================')
return 0
print('Executing test for DREAM-Yara')
print('====================================')
ph = app_tests.TestPathHelper(source_base, binary_base,
'test') # tests dir
# ============================================================
# Auto-detect the binary path.
# ============================================================
path_to_dream_indexer = app_tests.autolocateBinary(binary_base, 'bin',
'dream_yara_indexer')
path_to_ibf_filter = app_tests.autolocateBinary(binary_base, 'bin',
'dream_yara_build_filter')
path_to_dream_mapper = app_tests.autolocateBinary(binary_base, 'bin',
'dream_yara_mapper')
# ============================================================
# Built TestConf list.
# ============================================================
# Build list with TestConf objects, analoguely to how the output
# was generated in generate_outputs.sh.
conf_list = []
# ============================================================
# Run Distributed indexer Tests
# ============================================================
for organism in ['64-viral']:
# ============================================================
# Split the genomes in to 64 bins.
# ============================================================
tempFastaDir = ph.outFile('%s-binned-genomes/' % organism)
if not os.path.exists(tempFastaDir):
os.makedirs(tempFastaDir)
binFastaLen = 101 # each fasta entry is 100 lines long (101 including the header)
inputFasta = open(ph.inFile('data/input/%s-genomes.fa' % organism),
'r').read().split('\n')
for b in range(64):
# First, get the slice
binFasta = inputFasta[b * binFastaLen:(b + 1) * binFastaLen]
# Now open one file per bin and dump the part
outputFasta = open(tempFastaDir + '/' + str(b) + '.fa', 'w')
outputFasta.write('\n'.join(binFasta))
outputFasta.close()
# Get file extensions for the fm index files
exts = [
os.path.basename(fname).split('.', 1)[-1] for fname in glob.glob(
ph.inFile('data/gold/%s-genomes.*' % organism))
]
outFileDir = ph.outFile('data/input/%s-binned-indices/' % organism)
InfileNames = [tempFastaDir + str(b) + '.fa' for b in range(64)]
fileNames = [str(b) + '.' + e for b in range(64) for e in exts]
if not os.path.exists(outFileDir):
os.makedirs(outFileDir)
conf = app_tests.TestConf(
program=path_to_dream_indexer,
args=['--verbose', '-o', outFileDir] + InfileNames,
to_diff=[(ph.inFile('data/gold/%s-binned-indices/%s' %
(organism, fileName)),
ph.outFile(outFileDir + fileName), 'md5')
for fileName in fileNames])
conf_list.append(conf)
# ============================================================
# Run DREAM-yara IBF Filter Tests compute
# ============================================================
ibf_args = ['-t', '4', '-k', '19', '-nh', ' 2', '-bs', '1']
for organism in ['64-viral']:
conf = app_tests.TestConf(
program=path_to_ibf_filter,
args=[
'--verbose', '-o',
ph.outFile('%s-binned-genomes.filter' % organism)
] + ibf_args + InfileNames)
conf_list.append(conf)
# ============================================================
# Run Single-End DREAM-Yara Tests
# ============================================================
dis_mapper_args = [
['-e', '0.03', '--threads', '1'],
['-e', '0.03', '--threads', '1', '-sm', 'record', '-s', '10'],
['-e', '0.03', '--threads', '1', '-sm', 'tag', '-s', '10']
]
dis_mapper_suffix = ['t1', 'rec.t1', 'tag.t1']
for organism in ['64-viral']:
for i in range(0, len(dis_mapper_args)):
basic = app_tests.TestConf(
program=path_to_dream_mapper,
args=[
'--verbose',
ph.inFile('data/gold/%s-binned-indices/' % organism),
ph.inFile('data/input/%s-reads.fa' % organism), '-fi',
ph.outFile('%s-binned-genomes.filter' % organism), '-o',
ph.outFile('%s-reads.%s.sam' %
(organism, dis_mapper_suffix[i]))
] + dis_mapper_args[i],
to_diff=[(ph.inFile('data/gold/%s-reads.%s.sam' %
(organism, dis_mapper_suffix[i])),
ph.outFile('%s-reads.%s.sam' %
(organism, dis_mapper_suffix[i])),
sam_transforms)])
conf_list.append(basic)
# ============================================================
# Execute the tests
# ============================================================
failures = 0
try:
for conf in conf_list:
# Output to the user.
print('Executing: {}'.format(' '.join([conf.program] + conf.args)))
res = app_tests.runTest(conf)
if res:
print('OK\n==============================\n')
else:
failures += 1
print('FAILED\n==============================\n')
except Exception as e:
raise e # This exception is saved, then finally is executed, and then the exception is raised.
finally:
# Cleanup.
ph.deleteTempDir()
print('==============================')
print(' total tests: %d' % len(conf_list))
print(' failed tests: %d' % failures)
print('successful tests: %d' % (len(conf_list) - failures))
print('==============================')
# Compute and return return code.
return failures != 0
def main(source_base, binary_base):
"""Main entry point of the script."""
print 'Executing test for mason_variator'
print '======================'
print
ph = app_tests.TestPathHelper(source_base, binary_base,
'extras/apps/mason2/tests') # tests dir
# ============================================================
# Auto-detect the binary path.
# ============================================================
path_to_genome = app_tests.autolocateBinary(binary_base, 'bin',
'mason_genome')
path_to_methylation = app_tests.autolocateBinary(binary_base, 'bin',
'mason_methylation')
path_to_variator = app_tests.autolocateBinary(binary_base, 'bin',
'mason_variator')
path_to_materializer = app_tests.autolocateBinary(binary_base, 'bin',
'mason_materializer')
path_to_simulator = app_tests.autolocateBinary(binary_base, 'bin',
'mason_simulator')
# ============================================================
# Built TestConf list.
# ============================================================
# Build list with TestConf objects, analoguely to how the output
# was generated in generate_outputs.sh.
conf_list = []
# We prepare a list of transforms to apply to the output files. This is
# used to strip the input/output paths from the programs' output to
# make it more canonical and host independent.
ph.outFile('-') # To ensure that the out path is set.
transforms = [
app_tests.ReplaceTransform(
os.path.join(ph.source_base_path, 'extras/apps/mason2/tests') +
os.sep,
'',
right=True),
app_tests.ReplaceTransform(ph.temp_dir + os.sep, '', right=True),
app_tests.NormalizeScientificExponentsTransform(),
]
# ============================================================
# Test mason_genome
# ============================================================
conf = app_tests.TestConf(program=path_to_genome,
args=[
'-l',
'1000',
'-o',
ph.outFile('genome.test1.fasta'),
],
redir_stdout=ph.outFile('genome.test1.stdout'),
redir_stderr=ph.outFile('genome.test1.stderr'),
to_diff=[
(ph.inFile('genome.test1.fasta'),
ph.outFile('genome.test1.fasta')),
(ph.inFile('genome.test1.stdout'),
ph.outFile('genome.test1.stdout'),
transforms),
(ph.inFile('genome.test1.stderr'),
ph.outFile('genome.test1.stderr'),
transforms),
])
conf_list.append(conf)
conf = app_tests.TestConf(program=path_to_genome,
args=[
'-s',
'1',
'-l',
'1000',
'-l',
'100',
'-o',
ph.outFile('genome.test2.fasta'),
],
redir_stdout=ph.outFile('genome.test2.stdout'),
redir_stderr=ph.outFile('genome.test2.stderr'),
to_diff=[
(ph.inFile('genome.test2.fasta'),
ph.outFile('genome.test2.fasta')),
(ph.inFile('genome.test2.stdout'),
ph.outFile('genome.test2.stdout'),
transforms),
(ph.inFile('genome.test2.stderr'),
ph.outFile('genome.test2.stderr'),
transforms),
])
conf_list.append(conf)
# ============================================================
# Test mason_methylation
# ============================================================
conf = app_tests.TestConf(
program=path_to_methylation,
args=[
'--seed',
'33',
'-i',
ph.inFile('random.fasta'),
'-o',
ph.outFile('random_meth1.fasta'),
],
redir_stdout=ph.outFile('methylation.test1.stdout'),
redir_stderr=ph.outFile('methylation.test1.stderr'),
to_diff=[
(ph.inFile('methylation.test1.fasta'),
ph.outFile('methylation.test1.fasta')),
(ph.inFile('methylation.test1.stdout'),
ph.outFile('methylation.test1.stdout'), transforms),
(ph.inFile('methylation.test1.stderr'),
ph.outFile('methylation.test1.stderr'), transforms),
])
# ============================================================
# Test mason_variator
# ============================================================
# Generation methylation in variator.
conf = app_tests.TestConf(
program=path_to_variator,
args=[
'-ir',
ph.inFile('random.fasta'),
'-n',
'2',
'-ov',
ph.outFile('random_var1.vcf'),
'-of',
ph.outFile('random_var1.fasta'),
'--snp-rate',
'0.001',
'--small-indel-rate',
'0.001',
'--sv-indel-rate',
'0.001',
'--sv-inversion-rate',
'0.001',
'--sv-translocation-rate',
'0.001',
'--sv-duplication-rate',
'0.001',
'--min-sv-size',
'50',
'--max-sv-size',
'100',
'--methylation-levels',
'--meth-fasta-out',
ph.outFile('random_var1_meth.fasta'),
'--out-breakpoints',
ph.outFile('random_var1_bp.txt'),
],
redir_stdout=ph.outFile('random_var1.vcf.stdout'),
redir_stderr=ph.outFile('random_var1.vcf.stderr'),
to_diff=[
(ph.inFile('random_var1.vcf'), ph.outFile('random_var1.vcf'),
transforms),
(ph.inFile('random_var1.fasta'), ph.outFile('random_var1.fasta')),
(ph.inFile('random_var1_bp.txt'),
ph.outFile('random_var1_bp.txt')),
(ph.inFile('random_var1_meth.fasta'),
ph.outFile('random_var1_meth.fasta')),
(ph.inFile('random_var1.vcf.stderr'),
ph.outFile('random_var1.vcf.stderr'), transforms),
(ph.inFile('random_var1.vcf.stdout'),
ph.outFile('random_var1.vcf.stdout'), transforms),
])
conf_list.append(conf)
# Generation methylation in variator.
conf = app_tests.TestConf(
program=path_to_variator,
args=[
'-ir',
ph.inFile('random.fasta'),
'-n',
'2',
'-ov',
ph.outFile('random_var2.vcf'),
'-of',
ph.outFile('random_var2.fasta'),
'--snp-rate',
'0.001',
'--small-indel-rate',
'0.001',
'--sv-indel-rate',
'0.001',
'--sv-inversion-rate',
'0.001',
'--sv-translocation-rate',
'0.001',
'--sv-duplication-rate',
'0.001',
'--min-sv-size',
'50',
'--max-sv-size',
'100',
'--methylation-levels',
'--meth-fasta-in',
ph.inFile('random_meth1.fasta'),
'--meth-fasta-out',
ph.outFile('random_var2_meth.fasta'),
'--out-breakpoints',
ph.outFile('random_var2_bp.txt'),
],
redir_stdout=ph.outFile('random_var2.vcf.stdout'),
redir_stderr=ph.outFile('random_var2.vcf.stderr'),
to_diff=[
(ph.inFile('random_var2.vcf'), ph.outFile('random_var2.vcf'),
transforms),
(ph.inFile('random_var2.fasta'), ph.outFile('random_var2.fasta')),
(ph.inFile('random_var2_bp.txt'),
ph.outFile('random_var2_bp.txt')),
(ph.inFile('random_var2_meth.fasta'),
ph.outFile('random_var2_meth.fasta')),
(ph.inFile('random_var2.vcf.stderr'),
ph.outFile('random_var2.vcf.stderr'), transforms),
(ph.inFile('random_var2.vcf.stdout'),
ph.outFile('random_var2.vcf.stdout'), transforms),
])
conf_list.append(conf)
# Variation without methylation levels.
conf = app_tests.TestConf(
program=path_to_variator,
args=[
'-ir',
ph.inFile('random.fasta'),
'-n',
'2',
'-ov',
ph.outFile('random_var3.vcf'),
'-of',
ph.outFile('random_var3.fasta'),
'--snp-rate',
'0.001',
'--small-indel-rate',
'0.001',
'--sv-indel-rate',
'0.001',
'--sv-inversion-rate',
'0.001',
'--sv-translocation-rate',
'0.001',
'--sv-duplication-rate',
'0.001',
'--min-sv-size',
'50',
'--max-sv-size',
'100',
'--out-breakpoints',
ph.outFile('random_var3_bp.txt'),
],
redir_stdout=ph.outFile('random_var3.vcf.stdout'),
redir_stderr=ph.outFile('random_var3.vcf.stderr'),
to_diff=[
(ph.inFile('random_var3.vcf'), ph.outFile('random_var3.vcf'),
transforms),
(ph.inFile('random_var3.fasta'), ph.outFile('random_var3.fasta')),
(ph.inFile('random_var3_bp.txt'),
ph.outFile('random_var3_bp.txt')),
(ph.inFile('random_var3.vcf.stderr'),
ph.outFile('random_var3.vcf.stderr'), transforms),
(ph.inFile('random_var3.vcf.stdout'),
ph.outFile('random_var3.vcf.stdout'), transforms),
])
conf_list.append(conf)
# Previously crashing test
conf = app_tests.TestConf(
program=path_to_variator,
args=[
'-ir',
ph.inFile('adeno_virus.fa'),
'-ov',
ph.outFile('random_var9.vcf'),
'-of',
ph.outFile('random_var9.fasta'),
'--sv-indel-rate',
'0.01',
'--sv-duplication-rate',
'0.01',
'--sv-inversion-rate',
'0.01',
'--min-sv-size',
'20',
'--max-sv-size',
'300',
],
redir_stdout=ph.outFile('random_var9.vcf.stdout'),
redir_stderr=ph.outFile('random_var9.vcf.stderr'),
to_diff=[
(ph.inFile('random_var9.vcf'), ph.outFile('random_var9.vcf'),
transforms),
(ph.inFile('random_var9.vcf.stderr'),
ph.outFile('random_var9.vcf.stderr'), transforms),
(ph.inFile('random_var9.vcf.stdout'),
ph.outFile('random_var9.vcf.stdout'), transforms),
])
conf_list.append(conf)
# ============================================================
# Test mason_materializer
# ============================================================
# Without methylation levels.
conf = app_tests.TestConf(
program=path_to_materializer,
args=[
'-ir',
ph.inFile('random.fasta'),
'-iv',
ph.inFile('random_var1.vcf'),
'-o',
ph.outFile('materializer.random_var1.fasta'),
],
redir_stdout=ph.outFile('materializer.random_var1.stdout'),
redir_stderr=ph.outFile('materializer.random_var1.stderr'),
to_diff=[
(ph.inFile('random_var1.fasta'),
ph.outFile('materializer.random_var1.fasta')),
(ph.inFile('materializer.random_var1.stdout'),
ph.outFile('materializer.random_var1.stdout'), transforms),
(ph.inFile('materializer.random_var1.stderr'),
ph.outFile('materializer.random_var1.stderr'), transforms),
])
conf_list.append(conf)
# With methylation levels.
conf = app_tests.TestConf(
program=path_to_materializer,
args=[
'-ir',
ph.inFile('random.fasta'),
'-iv',
ph.inFile('random_var2.vcf'),
'-o',
ph.outFile('materializer.random_var2.fasta'),
'--meth-fasta-in',
ph.inFile('random_meth1.fasta'),
'--meth-fasta-out',
ph.outFile('materializer.random_meth2.fasta'),
],
redir_stdout=ph.outFile('materializer.random_var2.stdout'),
redir_stderr=ph.outFile('materializer.random_var2.stderr'),
to_diff=[
(ph.inFile('random_var1.fasta'),
ph.outFile('materializer.random_var1.fasta')),
(ph.inFile('random_var2_meth.fasta'),
ph.outFile('materializer.random_meth2.fasta'), transforms),
(ph.inFile('materializer.random_var2.stdout'),
ph.outFile('materializer.random_var2.stdout'), transforms),
(ph.inFile('materializer.random_var2.stderr'),
ph.outFile('materializer.random_var2.stderr'), transforms),
])
conf_list.append(conf)
# ============================================================
# Test mason_simulator
# ============================================================
# Illumina Model
conf = app_tests.TestConf(program=path_to_simulator,
args=[
'-n',
'1000',
'-ir',
ph.inFile('random.fasta'),
'-o',
ph.outFile('simulator.left1.fq'),
'-or',
ph.outFile('simulator.right1.fq'),
'-oa',
ph.outFile('simulator.out1.sam'),
],
redir_stdout=ph.outFile('simulator.out1.stdout'),
redir_stderr=ph.outFile('simulator.out1.stderr'),
to_diff=[
(ph.inFile('simulator.left1.fq'),
ph.outFile('simulator.left1.fq')),
(ph.inFile('simulator.right1.fq'),
ph.outFile('simulator.right1.fq')),
(ph.inFile('simulator.out1.sam'),
ph.outFile('simulator.out1.sam')),
(ph.inFile('simulator.out1.stdout'),
ph.outFile('simulator.out1.stdout'),
transforms),
(ph.inFile('simulator.out1.stderr'),
ph.outFile('simulator.out1.stderr'),
transforms),
])
conf_list.append(conf)
conf = app_tests.TestConf(program=path_to_simulator,
args=[
'-n',
'1000',
'-ir',
ph.inFile('random.fasta'),
'-iv',
ph.inFile('random_var1.vcf'),
'-o',
ph.outFile('simulator.left2.fq'),
'-or',
ph.outFile('simulator.right2.fq'),
'-oa',
ph.outFile('simulator.out2.sam'),
],
redir_stdout=ph.outFile('simulator.out2.stdout'),
redir_stderr=ph.outFile('simulator.out2.stderr'),
to_diff=[
(ph.inFile('simulator.left2.fq'),
ph.outFile('simulator.left2.fq')),
(ph.inFile('simulator.right2.fq'),
ph.outFile('simulator.right2.fq')),
(ph.inFile('simulator.out2.sam'),
ph.outFile('simulator.out2.sam')),
(ph.inFile('simulator.out2.stdout'),
ph.outFile('simulator.out2.stdout'),
transforms),
(ph.inFile('simulator.out2.stderr'),
ph.outFile('simulator.out2.stderr'),
transforms),
])
conf_list.append(conf)
conf = app_tests.TestConf(program=path_to_simulator,
args=[
'-n',
'1000',
'-ir',
ph.inFile('random.fasta'),
'-o',
ph.outFile('simulator.left3.fa'),
'-or',
ph.outFile('simulator.right3.fa'),
],
redir_stdout=ph.outFile('simulator.out3.stdout'),
redir_stderr=ph.outFile('simulator.out3.stderr'),
to_diff=[
(ph.inFile('simulator.left3.fa'),
ph.outFile('simulator.left3.fa')),
(ph.inFile('simulator.right3.fa'),
ph.outFile('simulator.right3.fa')),
(ph.inFile('simulator.out3.stdout'),
ph.outFile('simulator.out3.stdout'),
transforms),
(ph.inFile('simulator.out3.stderr'),
ph.outFile('simulator.out3.stderr'),
transforms),
])
conf_list.append(conf)
conf = app_tests.TestConf(program=path_to_simulator,
args=[
'-n',
'1000',
'-ir',
ph.inFile('random.fasta'),
'-iv',
ph.inFile('random_var1.vcf'),
'-o',
ph.outFile('simulator.left7.fa'),
'-oa',
ph.outFile('simulator.out7.sam'),
],
redir_stdout=ph.outFile('simulator.out7.stdout'),
redir_stderr=ph.outFile('simulator.out7.stderr'),
to_diff=[
(ph.inFile('simulator.left7.fa'),
ph.outFile('simulator.left7.fa')),
(ph.inFile('simulator.out7.sam'),
ph.outFile('simulator.out7.sam')),
(ph.inFile('simulator.out7.stdout'),
ph.outFile('simulator.out7.stdout'),
transforms),
(ph.inFile('simulator.out7.stderr'),
ph.outFile('simulator.out7.stderr'),
transforms),
])
conf_list.append(conf)
conf = app_tests.TestConf(program=path_to_simulator,
args=[
'-n',
'1000',
'-ir',
ph.inFile('random.fasta'),
'-o',
ph.outFile('simulator.left4.fa'),
'-oa',
ph.outFile('simulator.out4.sam'),
],
redir_stdout=ph.outFile('simulator.out4.stdout'),
redir_stderr=ph.outFile('simulator.out4.stderr'),
to_diff=[
(ph.inFile('simulator.left4.fa'),
ph.outFile('simulator.left4.fa')),
(ph.inFile('simulator.out4.sam'),
ph.outFile('simulator.out4.sam')),
(ph.inFile('simulator.out4.stdout'),
ph.outFile('simulator.out4.stdout'),
transforms),
(ph.inFile('simulator.out4.stderr'),
ph.outFile('simulator.out4.stderr'),
transforms),
])
conf_list.append(conf)
conf = app_tests.TestConf(program=path_to_simulator,
args=[
'-n',
'1000',
'-ir',
ph.inFile('random.fasta'),
'--meth-fasta-in',
ph.inFile('random_meth1.fasta'),
'--methylation-levels',
'--enable-bs-seq',
'-o',
ph.outFile('simulator.left5.fq'),
'-or',
ph.outFile('simulator.right5.fq'),
],
redir_stdout=ph.outFile('simulator.out5.stdout'),
redir_stderr=ph.outFile('simulator.out5.stderr'),
to_diff=[
(ph.inFile('simulator.left5.fq'),
ph.outFile('simulator.left5.fq')),
(ph.inFile('simulator.right5.fq'),
ph.outFile('simulator.right5.fq')),
(ph.inFile('simulator.out5.stdout'),
ph.outFile('simulator.out5.stdout'),
transforms),
(ph.inFile('simulator.out5.stderr'),
ph.outFile('simulator.out5.stderr'),
transforms),
])
conf_list.append(conf)
conf = app_tests.TestConf(program=path_to_simulator,
args=[
'-n',
'1000',
'-ir',
ph.inFile('random.fasta'),
'-iv',
ph.inFile('random_var1.vcf'),
'--meth-fasta-in',
ph.inFile('random_meth1.fasta'),
'--methylation-levels',
'--enable-bs-seq',
'-o',
ph.outFile('simulator.left6.fq'),
'-or',
ph.outFile('simulator.right6.fq'),
],
redir_stdout=ph.outFile('simulator.out6.stdout'),
redir_stderr=ph.outFile('simulator.out6.stderr'),
to_diff=[
(ph.inFile('simulator.left6.fq'),
ph.outFile('simulator.left6.fq')),
(ph.inFile('simulator.right6.fq'),
ph.outFile('simulator.right6.fq')),
(ph.inFile('simulator.out6.stdout'),
ph.outFile('simulator.out6.stdout'),
transforms),
(ph.inFile('simulator.out6.stderr'),
ph.outFile('simulator.out6.stderr'),
transforms),
])
conf_list.append(conf)
# 454 Model
conf = app_tests.TestConf(program=path_to_simulator,
args=[
'--seq-technology',
'454',
'--fragment-mean-size',
'800',
'--454-read-length-mean',
'200',
'--454-read-length-stddev',
'20',
'-n',
'1000',
'-v',
'-ir',
ph.inFile('random.fasta'),
'-o',
ph.outFile('simulator.left8.fq'),
'-oa',
ph.outFile('simulator.out8.sam'),
],
redir_stdout=ph.outFile('simulator.out8.stdout'),
redir_stderr=ph.outFile('simulator.out8.stderr'),
to_diff=[
(ph.inFile('simulator.left8.fq'),
ph.outFile('simulator.left8.fq')),
(ph.inFile('simulator.out8.sam'),
ph.outFile('simulator.out8.sam')),
(ph.inFile('simulator.out8.stdout'),
ph.outFile('simulator.out8.stdout'),
transforms),
(ph.inFile('simulator.out8.stderr'),
ph.outFile('simulator.out8.stderr'),
transforms),
])
conf_list.append(conf)
# Execute the tests.
failures = 0
for conf in conf_list:
res = app_tests.runTest(conf)
# Output to the user.
print ' '.join([os.path.basename(conf.program)] + conf.args),
if res:
print 'OK'
else:
failures += 1
print 'FAILED'
# Cleanup.
ph.deleteTempDir()
print '=============================='
print ' total tests: %d' % len(conf_list)
print ' failed tests: %d' % failures
print 'successful tests: %d' % (len(conf_list) - failures)
print '=============================='
# Compute and return return code.
return failures != 0
def main(source_base, binary_base):
"""Main entry point of the script."""
print 'Executing test for seqcons2'
print '==========================='
print
ph = app_tests.TestPathHelper(
source_base, binary_base,
'apps/seqcons2/tests') # tests dir
# ============================================================
# Auto-detect the binary path.
# ============================================================
path_to_seqcons = app_tests.autolocateBinary(
binary_base, 'bin', 'seqcons2')
# ============================================================
# Built TestConf list.
# ============================================================
# Build list with TestConf objects, analoguely to how the output
# was generated in generate_outputs.sh.
conf_list = []
# We prepare a list of transforms to apply to the output files. This is
# used to strip the input/output paths from the programs' output to
# make it more canonical and host independent.
ph.outFile('-') # To ensure that the out path is set.
transforms = [
app_tests.ReplaceTransform(
os.path.join(ph.source_base_path,
'apps/seqcons2/tests') + os.sep,
'', right=True),
app_tests.ReplaceTransform(ph.temp_dir + os.sep, '', right=True),
app_tests.RegexpReplaceTransform(r'Overall time: .*s', r'Overall time: <removed>s', right=True, left=True),
app_tests.NormalizeScientificExponentsTransform(),
]
# ============================================================
# Test seqcons2
# ============================================================
# overlap_consensus and nop for FASTA input
for method in ['overlap_consensus', 'nop']:
conf = app_tests.TestConf(
program=path_to_seqcons,
args=['-m', method,
'-i', ph.inFile('alns1.sam'),
'-oc', ph.outFile('alns1.%s.fa' % method),
'-oa', ph.outFile('alns1.%s.sam' % method),
],
redir_stdout=ph.outFile('alns1.%s.sam.stdout' % method),
redir_stderr=ph.outFile('alns1.%s.sam.stderr' % method),
to_diff=[(ph.inFile('alns1.%s.fa' % method),
ph.outFile('alns1.%s.fa' % method)),
(ph.inFile('alns1.%s.sam' % method),
ph.outFile('alns1.%s.sam' % method)),
(ph.inFile('alns1.%s.sam.stderr' % method),
ph.outFile('alns1.%s.sam.stderr' % method),
transforms),
(ph.inFile('alns1.%s.sam.stdout' % method),
ph.outFile('alns1.%s.sam.stdout' % method),
transforms),
])
conf_list.append(conf)
# all consensus variants (except for align) for SAM input
for oa_ext in ['.sam', '.txt']:
for method in ['overlap_consensus', 'pos_consensus',
'contig_consensus', 'realign', 'nop']:
args = ['-m', method,
'-i', ph.inFile('alns1.sam'),
'-oa', ph.outFile('alns1.%s%s' % (method, oa_ext)),
]
to_diff = [(ph.inFile('alns1.%s.fa' % method),
ph.outFile('alns1.%s.fa' % method)),
(ph.inFile('alns1.%s%s' % (method, oa_ext)),
ph.outFile('alns1.%s%s' % (method, oa_ext))),
(ph.inFile('alns1.%s%s.stderr' % (method, oa_ext)),
ph.outFile('alns1.%s%s.stderr' % (method, oa_ext)),
transforms),
(ph.inFile('alns1.%s%s.stdout' % (method, oa_ext)),
ph.outFile('alns1.%s%s.stdout' % (method, oa_ext)),
transforms)
]
if oa_ext != '.txt':
args += ['-oc', ph.outFile('alns1.%s.fa' % method),]
to_diff += [(ph.inFile('alns1.%s.fa' % method),
ph.outFile('alns1.%s.fa' % method))]
conf = app_tests.TestConf(
program=path_to_seqcons,
args=args,
redir_stdout=ph.outFile('alns1.%s%s.stdout' % (method, oa_ext)),
redir_stderr=ph.outFile('alns1.%s%s.stderr' % (method, oa_ext)),
to_diff=to_diff)
conf_list.append(conf)
# align_consensus for longer sequences that are roughly globally similar
for oa_ext in ['.sam', '.txt']:
for method in ['align_consensus']:
args = ['-m', method,
'-i', ph.inFile('seqs2.fa'),
'-oa', ph.outFile('seqs2.%s%s' % (method, oa_ext)),
]
to_diff = [(ph.inFile('seqs2.%s.fa' % method),
ph.outFile('seqs2.%s.fa' % method)),
(ph.inFile('seqs2.%s%s' % (method, oa_ext)),
ph.outFile('seqs2.%s%s' % (method, oa_ext))),
(ph.inFile('seqs2.%s%s.stderr' % (method, oa_ext)),
ph.outFile('seqs2.%s%s.stderr' % (method, oa_ext)),
transforms),
(ph.inFile('seqs2.%s%s.stdout' % (method, oa_ext)),
ph.outFile('seqs2.%s%s.stdout' % (method, oa_ext)),
transforms)
]
if oa_ext != '.txt':
args += ['-oc', ph.outFile('seqs2.%s.fa' % method),]
to_diff += [(ph.inFile('seqs2.%s.fa' % method),
ph.outFile('seqs2.%s.fa' % method))]
conf = app_tests.TestConf(
program=path_to_seqcons,
args=args,
redir_stdout=ph.outFile('seqs2.%s%s.stdout' % (method, oa_ext)),
redir_stderr=ph.outFile('seqs2.%s%s.stderr' % (method, oa_ext)),
to_diff=to_diff)
conf_list.append(conf)
# Execute the tests.
failures = 0
for conf in conf_list:
res = app_tests.runTest(conf)
# Output to the user.
print ' '.join([os.path.basename(conf.program)] + conf.args),
if res:
print 'OK'
else:
failures += 1
print 'FAILED'
# Cleanup.
ph.deleteTempDir()
print '=============================='
print ' total tests: %d' % len(conf_list)
print ' failed tests: %d' % failures
print 'successful tests: %d' % (len(conf_list) - failures)
print '=============================='
# Compute and return return code.
return failures != 0
def main(source_base, binary_base):
"""Main entry point of the script."""
print 'Executing test for searchjoin'
print '==========================='
print
ph = app_tests.TestPathHelper(
source_base, binary_base,
'apps/searchjoin/tests') # tests dir
# ============================================================
# Auto-detect the binary path.
# ============================================================
path_to_join = app_tests.autolocateBinary(
binary_base, 'bin', 's4_join')
path_to_search = app_tests.autolocateBinary(
binary_base, 'bin', 's4_search')
# ============================================================
# Built TestConf list.
# ============================================================
# Build list with TestConf objects, analoguely to how the output
# was generated in generate_outputs.sh.
conf_list = []
# ============================================================
# Define program parameters.
# ============================================================
# Seed length
SL = {
'geo': ['5'],
'dna': ['10']
}
# Errors
K = {
'geo': ['0', '1', '3'],
'dna': ['0', '8', '16']
}
# Threads
THREADS = '4'
# ============================================================
# Configure Join Tests.
# ============================================================
for alphabet in ['geo', 'dna']:
for k in K[alphabet]:
for sl in SL[alphabet]:
conf = app_tests.TestConf(
program=path_to_join,
# redir_stdout=ph.outFile('join_%s_%s_%s.stdout' % (alphabet, k, sl)),
args=[ph.inFile('%s_database.csv' % alphabet), k,
'-i', alphabet,
'-t', THREADS,
'-sl', sl,
'-o', ph.outFile('join_%s_%s_%s.out' % (alphabet, k, sl))],
to_diff=[(ph.inFile('join_%s_%s.out' % (alphabet, k)),
ph.outFile('join_%s_%s_%s.out' % (alphabet, k, sl)),
transforms)])
conf_list.append(conf)
# ============================================================
# Configure Search Tests.
# ============================================================
for alphabet in ['geo', 'dna']:
for sl in SL[alphabet]:
conf = app_tests.TestConf(
program=path_to_search,
# redir_stdout=ph.outFile('search_%s_%s.stdout' % (alphabet, sl)),
args=[ph.inFile('%s_database.csv' % alphabet),
ph.inFile('%s_queries.csv' % alphabet),
'--no-wait',
'-i', alphabet,
'-t', THREADS,
'-sl', sl,
'-o', ph.outFile('search_%s_%s.out' % (alphabet, sl))],
to_diff=[(ph.inFile('search_%s.out' % (alphabet)),
ph.outFile('search_%s_%s.out' % (alphabet, sl)),
transforms)])
conf_list.append(conf)
# ============================================================
# Run Tests.
# ============================================================
# Execute the tests.
failures = 0
for conf in conf_list:
res = app_tests.runTest(conf)
# Output to the user.
print ' '.join([conf.program] + conf.args),
if res:
print 'OK'
else:
failures += 1
print 'FAILED'
# Cleanup.
ph.deleteTempDir()
print '=============================='
print ' total tests: %d' % len(conf_list)
print ' failed tests: %d' % failures
print 'successful tests: %d' % (len(conf_list) - failures)
print '=============================='
# Compute and return return code.
return failures != 0
def main(source_base, binary_base):
"""Main entry point of the script."""
# gold standard binary files created on little endian
if sys.byteorder != 'little':
print 'Skipping tests for Yara on big endian'
print '====================================='
return 0
print 'Executing test for Yara'
print '=============================='
print
ph = app_tests.TestPathHelper(source_base, binary_base,
'apps/yara/tests') # tests dir
# ============================================================
# Auto-detect the binary path.
# ============================================================
path_to_indexer = app_tests.autolocateBinary(binary_base, 'bin',
'yara_indexer')
path_to_mapper = app_tests.autolocateBinary(binary_base, 'bin',
'yara_mapper')
# ============================================================
# Built TestConf list.
# ============================================================
# Build list with TestConf objects, analoguely to how the output
# was generated in generate_outputs.sh.
conf_list = []
# ============================================================
# Run Indexer Tests
# ============================================================
for organism in ['adeno']:
# Get file extensions for the fm index files
exts = [
os.path.basename(fname).split('.', 1)[-1]
for fname in glob.glob(ph.inFile('gold/%s-genome.*' % organism))
]
conf = app_tests.TestConf(
program=path_to_indexer,
args=[
ph.inFile('input/%s-genome.fa' % organism), '-o',
ph.outFile('%s-genome' % organism)
],
to_diff=[(ph.inFile('gold/%s-genome.%s' % (organism, ext)),
ph.outFile('%s-genome.%s' % (organism, ext)), 'md5')
for ext in exts])
conf_list.append(conf)
# ============================================================
# Run Single-End Mapper Tests
# ============================================================
# mapper_args = [
# ['--threads', '1' ]],
# ['--threads', '8' ]
# ]
# mapper_suffix = ['t1', 't8']
mapper_args = [['--threads', '1']]
mapper_suffix = ['t1']
for organism in ['adeno']:
for i in range(0, len(mapper_args)):
conf = app_tests.TestConf(
program=path_to_mapper,
args=[
ph.inFile('gold/%s-genome' % organism),
ph.inFile('input/%s-reads_1.fa' % organism), '-o',
ph.outFile('%s-reads_1.%s.sam' %
(organism, mapper_suffix[i]))
] + mapper_args[i],
to_diff=[(ph.inFile('gold/%s-reads_1.%s.sam' %
(organism, mapper_suffix[i])),
ph.outFile('%s-reads_1.%s.sam' %
(organism, mapper_suffix[i])),
sam_transforms)])
conf_list.append(conf)
# ============================================================
# Execute the tests
# ============================================================
failures = 0
for conf in conf_list:
res = app_tests.runTest(conf)
# Output to the user.
print ' '.join([conf.program] + conf.args),
if res:
print 'OK'
else:
failures += 1
print 'FAILED'
# Cleanup.
ph.deleteTempDir()
print '=============================='
print ' total tests: %d' % len(conf_list)
print ' failed tests: %d' % failures
print 'successful tests: %d' % (len(conf_list) - failures)
print '=============================='
# Compute and return return code.
return failures != 0
def main(source_base, binary_base):
"""Main entry point of the script."""
print 'Executing test for sak'
print '======================'
print
ph = app_tests.TestPathHelper(source_base, binary_base,
'core/apps/sak/tests') # tests dir
# ============================================================
# Auto-detect the binary path.
# ============================================================
path_to_program = app_tests.autolocateBinary(binary_base, 'core/apps/sak',
'sak')
# ============================================================
# Built TestConf list.
# ============================================================
# Build list with TestConf objects, analoguely to how the output
# was generated in generate_outputs.sh.
conf_list = []
# ============================================================
# Run on DNA (Adenoviruses).
# ============================================================
conf = app_tests.TestConf(
program=path_to_program,
args=[
ph.inFile('adeno.fasta'),
# '-ll', '1000',
'-o',
ph.outFile('adeno.all.fa')
],
to_diff=[(ph.inFile('adeno.all.fa'), ph.outFile('adeno.all.fa'))])
conf_list.append(conf)
conf = app_tests.TestConf(
program=path_to_program,
args=[
ph.inFile('adeno.fasta'),
# '-ll', '1000',
'-s',
'1',
'-o',
ph.outFile('adeno.seq1.fa')
],
to_diff=[(ph.inFile('adeno.seq1.fa'), ph.outFile('adeno.seq1.fa'))])
conf_list.append(conf)
conf = app_tests.TestConf(
program=path_to_program,
args=[
ph.inFile('adeno.fasta'),
# '-ll', '1000',
'-ss',
'1-2',
'-o',
ph.outFile('adeno.seq1-2.fa')
],
to_diff=[(ph.inFile('adeno.seq1-2.fa'), ph.outFile('adeno.seq1-2.fa'))
])
conf_list.append(conf)
conf = app_tests.TestConf(
program=path_to_program,
args=[
ph.inFile('adeno.fasta'),
# '-ll', '1000',
'-s',
'3',
'-o',
ph.outFile('adeno.seq3.fa')
],
to_diff=[(ph.inFile('adeno.seq3.fa'), ph.outFile('adeno.seq3.fa'))])
conf_list.append(conf)
conf = app_tests.TestConf(
program=path_to_program,
args=[
ph.inFile('adeno.fasta'),
# '-ll', '1000',
'-sn',
'gi|9626621',
'-o',
ph.outFile('adeno.sn.fa')
],
to_diff=[(ph.inFile('adeno.sn.fa'), ph.outFile('adeno.sn.fa'))])
conf_list.append(conf)
conf = app_tests.TestConf(
program=path_to_program,
args=[
ph.inFile('adeno.fasta'),
# '-ll', '1000',
'-s',
'1',
'-i',
'5-25',
'-o',
ph.outFile('adeno.s1i5-25.fa')
],
to_diff=[(ph.inFile('adeno.s1i5-25.fa'),
ph.outFile('adeno.s1i5-25.fa'))])
conf_list.append(conf)
conf = app_tests.TestConf(
program=path_to_program,
args=[
ph.inFile('adeno.fasta'),
# '-ll', '1000',
'-ss',
'1-2',
'-i',
'5-25',
'-o',
ph.outFile('adeno.s1-2i5-25.fa')
],
to_diff=[(ph.inFile('adeno.s1-2i5-25.fa'),
ph.outFile('adeno.s1-2i5-25.fa'))])
conf_list.append(conf)
conf = app_tests.TestConf(
program=path_to_program,
args=[
ph.inFile('adeno.fasta'),
# '-ll', '1000',
'-s',
'1',
'-rc',
'-o',
ph.outFile('adeno.s1rc.fa')
],
to_diff=[(ph.inFile('adeno.s1rc.fa'), ph.outFile('adeno.s1rc.fa'))])
conf_list.append(conf)
# Execute the tests.
failures = 0
for conf in conf_list:
res = app_tests.runTest(conf)
# Output to the user.
print ' '.join(['sak'] + conf.args),
if res:
print 'OK'
else:
failures += 1
print 'FAILED'
# Cleanup.
ph.deleteTempDir()
print '=============================='
print ' total tests: %d' % len(conf_list)
print ' failed tests: %d' % failures
print 'successful tests: %d' % (len(conf_list) - failures)
print '=============================='
# Compute and return return code.
return failures != 0
def main(source_base, binary_base):
"""Main entry point of the script."""
print 'Executing test for cuda mapper'
print '=============================='
print
ph = app_tests.TestPathHelper(source_base, binary_base,
'core/apps/cuda_mapper/tests') # tests dir
# ============================================================
# Auto-detect the binary path.
# ============================================================
path_to_indexer = app_tests.autolocateBinary(binary_base, 'bin',
'cuda_indexer')
path_to_mapper = app_tests.autolocateBinary(binary_base, 'bin',
'cuda_mapper')
# ============================================================
# Built TestConf list.
# ============================================================
# Build list with TestConf objects, analoguely to how the output
# was generated in generate_outputs.sh.
conf_list = []
# ============================================================
# Run Indexer Tests
# ============================================================
# for organism in ['celegans', 'hg18']:
for organism in []:
# Get file extensions for the fm index files
exts = [
os.path.basename(fname).split('.', 2)[-1] for fname in glob.glob(
ph.inFile('datasets/%s/genome.fasta.*' % organism))
]
conf = app_tests.TestConf(
program=path_to_indexer,
args=[
ph.inFile('datasets/%s/genome.fasta' % organism), '-xp',
ph.outFile('%s.fm' % organism)
],
redir_stdout=ph.outFile('indexer.%s.stdout' % organism),
to_diff=[(ph.inFile('datasets/%s/genome.fm.%s' % (organism, ext)),
ph.outFile('%s.fm.%s' % (organism, ext)), 'md5')
for ext in exts] +
[(ph.inFile('logs/indexer.%s.stdout' % organism),
ph.outFile('indexer.%s.stdout' % organism), transforms)])
conf_list.append(conf)
# ============================================================
# Run Single-End Mapper Tests
# ============================================================
mapper_args = [['--no-cuda', '--threads', '1'],
['--no-cuda', '--threads', '8'], []]
log_suffix = ['t1', 't8', 'cuda']
for organism in ['celegans', 'hg18']:
for i in range(0, len(mapper_args)):
conf = app_tests.TestConf(
program=path_to_mapper,
args=[
ph.inFile('datasets/%s/genome.fasta' % organism),
ph.inFile('datasets/%s/reads.fastq' % organism), '-xp',
ph.inFile('datasets/%s/genome.fm' % organism)
] + mapper_args[i],
redir_stdout=ph.outFile('mapper.%s.%s.stdout' %
(organism, log_suffix[i])),
to_diff=[(ph.inFile('logs/mapper.%s.%s.stdout' %
(organism, log_suffix[i])),
ph.outFile('mapper.%s.%s.stdout' %
(organism, log_suffix[i])), transforms)])
conf_list.append(conf)
# ============================================================
# Execute the tests
# ============================================================
failures = 0
for conf in conf_list:
res = app_tests.runTest(conf)
# Output to the user.
print ' '.join([conf.program] + conf.args),
if res:
print 'OK'
else:
failures += 1
print 'FAILED'
# Cleanup.
ph.deleteTempDir()
print '=============================='
print ' total tests: %d' % len(conf_list)
print ' failed tests: %d' % failures
print 'successful tests: %d' % (len(conf_list) - failures)
print '=============================='
# Compute and return return code.
return failures != 0
def main(source_base, binary_base):
"""Main entry point of the script."""
print 'Executing test for tree_recomb'
print '=============================='
print
ph = app_tests.TestPathHelper(source_base, binary_base,
'apps/tree_recon/tests') # tests dir
# ============================================================
# Auto-detect the binary path.
# ============================================================
path_to_program = app_tests.autolocateBinary(binary_base,
'apps/tree_recon',
'tree_recon')
# ============================================================
# Built TestConf list.
# ============================================================
# Build list with TestConf objects, analoguely to how the output
# was generated in generate_outputs.sh.
conf_list = []
for i in [1, 2, 3]:
conf = app_tests.TestConf(program=path_to_program,
args=[
'-m',
ph.inFile('example%d.dist' % i), '-o',
ph.outFile('example%d.dot' % i)
],
to_diff=[(ph.inFile('example%d.dot' % i),
ph.outFile('example%d.dot' % i))])
conf_list.append(conf)
for i in [1, 2, 3]:
for b in ['nj', 'min', 'max', 'avg', 'wavg']:
if i == 1 and b == 'avg':
continue # Skip, rounding problems MSVC vs GCC.
conf = app_tests.TestConf(
program=path_to_program,
args=[
'-b', b, '-m',
ph.inFile('example%d.dist' % i), '-o',
ph.outFile('example%d.%s.dot' % (i, b))
],
to_diff=[(ph.inFile('example%d.%s.dot' % (i, b)),
ph.outFile('example%d.%s.dot' % (i, b)))])
conf_list.append(conf)
for i in [1, 2, 3]:
for f in ['dot', 'newick']:
conf = app_tests.TestConf(program=path_to_program,
args=[
'-m',
ph.inFile('example%d.dist' % i),
'-o',
ph.outFile('example%d.%s' % (i, f))
],
to_diff=[
(ph.inFile('example%d.%s' % (i, f)),
ph.outFile('example%d.%s' % (i, f)))
])
conf_list.append(conf)
# Execute the tests.
failures = 0
for conf in conf_list:
res = app_tests.runTest(conf)
# Output to the user.
print ' '.join(['tree_recomb'] + conf.args),
if res:
print 'OK'
else:
failures += 1
print 'FAILED'
# Cleanup.
ph.deleteTempDir()
print '=============================='
print ' total tests: %d' % len(conf_list)
print ' failed tests: %d' % failures
print 'successful tests: %d' % (len(conf_list) - failures)
print '=============================='
# Compute and return return code.
return failures != 0
def main(source_base, binary_base):
"""Main entry point of the script."""
print 'Executing test for %(APP_NAME)s'
print '========================='
print
ph = app_tests.TestPathHelper(
source_base, binary_base,
'%(LOCATION)s/tests') # tests dir
# ============================================================
# Auto-detect the binary path.
# ============================================================
path_to_program = app_tests.autolocateBinary(
binary_base, '%(LOCATION)s', '%(APP_NAME)s')
# ============================================================
# Built TestConf list.
# ============================================================
# Build list with TestConf objects, analoguely to how the output
# was generated in generate_outputs.sh.
conf_list = []
# ============================================================
# First Section.
# ============================================================
# App TestConf objects to conf_list, just like this for each
# test you want to run.
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('STDOUT_FILE'),
args=['ARGS', 'MUST', 'BE', 'STRINGS', str(1), str(99),
ph.inFile('INPUT_FILE1'),
ph.inFile('INPUT_FILE2')],
to_diff=[(ph.inFile('STDOUT_FILE'),
ph.outFile('STDOUT_FILE')),
(ph.inFile('INPUT_FILE1'),
ph.outFile('INPUT_FILE1'))])
conf_list.append(conf)
# ============================================================
# Execute the tests.
# ============================================================
failures = 0
for conf in conf_list:
res = app_tests.runTest(conf)
# Output to the user.
print ' '.join(['%(APP_NAME)s'] + conf.args),
if res:
print 'OK'
else:
failures += 1
print 'FAILED'
# Cleanup.
ph.deleteTempDir()
print '=============================='
print ' total tests: %%d' %% len(conf_list)
print ' failed tests: %%d' %% failures
print 'successful tests: %%d' %% (len(conf_list) - failures)
print '=============================='
# Compute and return return code.
return failures != 0
def main(source_base, binary_base):
"""Main entry point of the script."""
print 'Executing test for seqcons2'
print '==========================='
print
ph = app_tests.TestPathHelper(source_base, binary_base,
'apps/seqcons2/tests') # tests dir
# ============================================================
# Auto-detect the binary path.
# ============================================================
path_to_seqcons = app_tests.autolocateBinary(binary_base, 'bin',
'seqcons2')
# ============================================================
# Built TestConf list.
# ============================================================
# Build list with TestConf objects, analoguely to how the output
# was generated in generate_outputs.sh.
conf_list = []
# We prepare a list of transforms to apply to the output files. This is
# used to strip the input/output paths from the programs' output to
# make it more canonical and host independent.
ph.outFile('-') # To ensure that the out path is set.
transforms = [
app_tests.ReplaceTransform(
os.path.join(ph.source_base_path, 'apps/seqcons2/tests') + os.sep,
'',
right=True),
app_tests.ReplaceTransform(ph.temp_dir + os.sep, '', right=True),
app_tests.RegexpReplaceTransform(r'Overall time: .*s',
r'Overall time: <removed>s',
right=True,
left=True),
app_tests.NormalizeScientificExponentsTransform(),
]
# ============================================================
# Test seqcons2
# ============================================================
# overlap_consensus and nop for FASTA input
for method in ['overlap_consensus', 'nop']:
conf = app_tests.TestConf(
program=path_to_seqcons,
args=[
'-m',
method,
'-i',
ph.inFile('alns1.sam'),
'-oc',
ph.outFile('alns1.%s.fa' % method),
'-oa',
ph.outFile('alns1.%s.sam' % method),
],
redir_stdout=ph.outFile('alns1.%s.sam.stdout' % method),
redir_stderr=ph.outFile('alns1.%s.sam.stderr' % method),
to_diff=[
(ph.inFile('alns1.%s.fa' % method),
ph.outFile('alns1.%s.fa' % method)),
(ph.inFile('alns1.%s.sam' % method),
ph.outFile('alns1.%s.sam' % method)),
(ph.inFile('alns1.%s.sam.stderr' % method),
ph.outFile('alns1.%s.sam.stderr' % method), transforms),
(ph.inFile('alns1.%s.sam.stdout' % method),
ph.outFile('alns1.%s.sam.stdout' % method), transforms),
])
conf_list.append(conf)
# all consensus variants (except for align) for SAM input
for oa_ext in ['.sam', '.txt']:
for method in [
'overlap_consensus', 'pos_consensus', 'contig_consensus',
'realign', 'nop'
]:
args = [
'-m',
method,
'-i',
ph.inFile('alns1.sam'),
'-oa',
ph.outFile('alns1.%s%s' % (method, oa_ext)),
]
to_diff = [(ph.inFile('alns1.%s.fa' % method),
ph.outFile('alns1.%s.fa' % method)),
(ph.inFile('alns1.%s%s' % (method, oa_ext)),
ph.outFile('alns1.%s%s' % (method, oa_ext))),
(ph.inFile('alns1.%s%s.stderr' % (method, oa_ext)),
ph.outFile('alns1.%s%s.stderr' % (method, oa_ext)),
transforms),
(ph.inFile('alns1.%s%s.stdout' % (method, oa_ext)),
ph.outFile('alns1.%s%s.stdout' % (method, oa_ext)),
transforms)]
if oa_ext != '.txt':
args += [
'-oc',
ph.outFile('alns1.%s.fa' % method),
]
to_diff += [(ph.inFile('alns1.%s.fa' % method),
ph.outFile('alns1.%s.fa' % method))]
conf = app_tests.TestConf(
program=path_to_seqcons,
args=args,
redir_stdout=ph.outFile('alns1.%s%s.stdout' %
(method, oa_ext)),
redir_stderr=ph.outFile('alns1.%s%s.stderr' %
(method, oa_ext)),
to_diff=to_diff)
conf_list.append(conf)
# align_consensus for longer sequences that are roughly globally similar
for oa_ext in ['.sam', '.txt']:
for method in ['align_consensus']:
args = [
'-m',
method,
'-i',
ph.inFile('seqs2.fa'),
'-oa',
ph.outFile('seqs2.%s%s' % (method, oa_ext)),
]
to_diff = [(ph.inFile('seqs2.%s.fa' % method),
ph.outFile('seqs2.%s.fa' % method)),
(ph.inFile('seqs2.%s%s' % (method, oa_ext)),
ph.outFile('seqs2.%s%s' % (method, oa_ext))),
(ph.inFile('seqs2.%s%s.stderr' % (method, oa_ext)),
ph.outFile('seqs2.%s%s.stderr' % (method, oa_ext)),
transforms),
(ph.inFile('seqs2.%s%s.stdout' % (method, oa_ext)),
ph.outFile('seqs2.%s%s.stdout' % (method, oa_ext)),
transforms)]
if oa_ext != '.txt':
args += [
'-oc',
ph.outFile('seqs2.%s.fa' % method),
]
to_diff += [(ph.inFile('seqs2.%s.fa' % method),
ph.outFile('seqs2.%s.fa' % method))]
conf = app_tests.TestConf(
program=path_to_seqcons,
args=args,
redir_stdout=ph.outFile('seqs2.%s%s.stdout' %
(method, oa_ext)),
redir_stderr=ph.outFile('seqs2.%s%s.stderr' %
(method, oa_ext)),
to_diff=to_diff)
conf_list.append(conf)
# Execute the tests.
failures = 0
for conf in conf_list:
res = app_tests.runTest(conf)
# Output to the user.
print ' '.join([os.path.basename(conf.program)] + conf.args),
if res:
print 'OK'
else:
failures += 1
print 'FAILED'
# Cleanup.
ph.deleteTempDir()
print '=============================='
print ' total tests: %d' % len(conf_list)
print ' failed tests: %d' % failures
print 'successful tests: %d' % (len(conf_list) - failures)
print '=============================='
# Compute and return return code.
return failures != 0
def main(source_base, binary_base):
"""Main entry point of the script."""
print 'Executing test for %(APP_NAME)s'
print '========================='
print
ph = app_tests.TestPathHelper(
source_base, binary_base,
'%(LOCATION)s/tests') # tests dir
# ============================================================
# Auto-detect the binary path.
# ============================================================
path_to_program = app_tests.autolocateBinary(
binary_base, '%(LOCATION)s', '%(APP_NAME)s')
# ============================================================
# Built TestConf list.
# ============================================================
# Build list with TestConf objects, analoguely to how the output
# was generated in generate_outputs.sh.
conf_list = []
# ============================================================
# First Section.
# ============================================================
# App TestConf objects to conf_list, just like this for each
# test you want to run.
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('STDOUT_FILE'),
args=['ARGS', 'MUST', 'BE', 'STRINGS', str(1), str(99),
ph.inFile('INPUT_FILE1'),
ph.inFile('INPUT_FILE2')],
to_diff=[(ph.inFile('STDOUT_FILE'),
ph.outFile('STDOUT_FILE')),
(ph.inFile('INPUT_FILE1'),
ph.outFile('INPUT_FILE1'))])
conf_list.append(conf)
# ============================================================
# Execute the tests.
# ============================================================
failures = 0
for conf in conf_list:
res = app_tests.runTest(conf)
# Output to the user.
print ' '.join(['%(APP_NAME)s'] + conf.args),
if res:
print 'OK'
else:
failures += 1
print 'FAILED'
# Cleanup.
ph.deleteTempDir()
print '=============================='
print ' total tests: %%d' %% len(conf_list)
print ' failed tests: %%d' %% failures
print 'successful tests: %%d' %% (len(conf_list) - failures)
print '=============================='
# Compute and return return code.
return failures != 0
def main(source_base, binary_base):
"""Main entry point of the script."""
print 'Executing test for dfi'
print '======================'
print
ph = app_tests.TestPathHelper(source_base, binary_base,
'apps/dfi/tests') # tests dir
# ============================================================
# Auto-detect the binary path.
# ============================================================
path_to_program = app_tests.autolocateBinary(binary_base, 'apps/dfi',
'dfi')
# ============================================================
# Built TestConf list.
# ============================================================
# Build list with TestConf objects, analoguely to how the output
# was generated in generate_outputs.sh.
conf_list = []
paramsFile = open(ph.inFile("params.txt"), "r")
# unzip datasets into test directory
unzip_file_into_dir(ph.inFile("datasets.zip"), ph.outFile('', 'datasets'))
unzip_file_into_dir(ph.inFile("results.zip"), ph.outFile('', 'expected'))
# We run the following for all read lengths we have reads for.
for paramLine in paramsFile.readlines():
params = paramLine.split()
# Run with options parsed from params file.
conf = app_tests.TestConf(program=path_to_program,
redir_stdout=ph.outFile(params[0]),
args=[
ph.outFile(params[1], 'datasets'),
ph.outFile(params[2], 'datasets')
] + params[3:],
to_diff=[(ph.outFile(params[0], 'expected'),
ph.outFile(params[0]))])
conf_list.append(conf)
# Execute the tests.
failures = 0
for conf in conf_list:
res = app_tests.runTest(conf)
# Output to the user.
print ' '.join(['dfi'] + conf.args),
if res:
print 'OK'
else:
failures += 1
print 'FAILED'
# Cleanup.
ph.deleteTempDir()
print '=============================='
print ' total tests: %d' % len(conf_list)
print ' failed tests: %d' % failures
print 'successful tests: %d' % (len(conf_list) - failures)
print '=============================='
# Compute and return return code.
return failures != 0
def main(source_base, binary_base):
"""Main entry point of the script."""
print 'Executing test for gustaf'
print '==============================='
print
ph = app_tests.TestPathHelper(
source_base, binary_base,
'extras/apps/gustaf/tests') # tests dir
# ============================================================
# Auto-detect the binary path.
# ============================================================
path_to_program = app_tests.autolocateBinary(
binary_base, 'bin', 'gustaf')
# ============================================================
# Built TestConf list.
# ============================================================
# Build list with TestConf objects, analoguely to how the output
# was generated in generate_outputs.sh.
conf_list = []
# We prepare a list of transforms to apply to the output files. This is
# used to strip the input/output paths from the programs' output to
# make it more canonical and host independent.
ph.outFile('-') # To ensure that the out path is set.
transforms = [
app_tests.ReplaceTransform(
os.path.join(ph.source_base_path,
'extras/apps/gustaf/tests') + os.sep,
'', right=True),
app_tests.ReplaceTransform(ph.temp_dir + os.sep, '', right=True),
app_tests.NormalizeScientificExponentsTransform(),
]
# ============================================================
# Adeno Tests
# ============================================================
# ============================================================
# Sanity check with default values and empty output file
# ============================================================
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('st2_l100.stdout'),
redir_stderr=ph.outFile('st2_l100.stderr'),
args=[ph.inFile('adeno.fa'),
ph.inFile('adeno_modified_reads.fa'),
'-gff', ph.outFile('st2_l100.gff'),
'-vcf', ph.outFile('st2_l100.vcf'),
],
to_diff=[(ph.inFile('st2_l100.vcf'),
ph.outFile('st2_l100.vcf'),
transforms),
(ph.inFile('st2_l100.gff'),
ph.outFile('st2_l100.gff'))])
conf_list.append(conf)
#out="st2_l100"
#${GUSTAF} adeno.fa adeno_modified_reads.fa -gff ${out}.gff -vcf ${out}.vcf > ${out}.stdout 2> ${out}.stderr
# ============================================================
# -st 1 -l 30
# ============================================================
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('st1_l30.stdout'),
redir_stderr=ph.outFile('st1_l30.stderr'),
args=[ph.inFile('adeno.fa'),
ph.inFile('adeno_modified_reads.fa'),
'-gff', ph.outFile('st1_l30.gff'),
'-vcf', ph.outFile('st1_l30.vcf'),
'-st', str(1),
'-l', str(30),
],
to_diff=[(ph.inFile('st1_l30.vcf'),
ph.outFile('st1_l30.vcf'),
transforms),
(ph.inFile('st1_l30.gff'),
ph.outFile('st1_l30.gff'))])
conf_list.append(conf)
#out="st1_l30"
#${GUSTAF} adeno.fa adeno_modified_reads.fa -st 1 -l 30 -gff ${out}.gff -vcf ${out}.vcf > ${out}.stdout 2> ${out}.stderr
# ============================================================
# -st 1 -m stellar.gff
# ============================================================
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('st1_l30_m.stdout'),
redir_stderr=ph.outFile('st1_l30_m.stderr'),
args=[ph.inFile('adeno.fa'),
ph.inFile('adeno_modified_reads.fa'),
'-m', ph.inFile('stellar.gff'),
'-gff', ph.outFile('st1_l30_m.gff'),
'-vcf', ph.outFile('st1_l30_m.vcf'),
'-st', str(1),
],
to_diff=[(ph.inFile('st1_l30_m.vcf'),
ph.outFile('st1_l30_m.vcf'),
transforms),
(ph.inFile('st1_l30_m.gff'),
ph.outFile('st1_l30_m.gff'))])
conf_list.append(conf)
#out="st1_l30_m"
#${GUSTAF} adeno.fa adeno_modified_reads.fa -st 1 -m stellar.gff -gff ${out}.gff -vcf ${out}.vcf > ${out}.stdout 2> ${out}.stderr
# ============================================================
# -st 1 -l 30 -ith 5
# ============================================================
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('st1_l30_ith5.stdout'),
redir_stderr=ph.outFile('st1_l30_ith5.stderr'),
args=[ph.inFile('adeno.fa'),
ph.inFile('adeno_modified_reads.fa'),
'-gff', ph.outFile('st1_l30_ith5.gff'),
'-vcf', ph.outFile('st1_l30_ith5.vcf'),
'-st', str(1),
'-l', str(30),
'-ith', str(5),
],
to_diff=[(ph.inFile('st1_l30_m.vcf'),
ph.outFile('st1_l30_m.vcf'),
transforms),
(ph.inFile('st1_l30_ith5.gff'),
ph.outFile('st1_l30_ith5.gff'))])
conf_list.append(conf)
#out="st1_l30_ith5"
#${GUSTAF} adeno.fa adeno_modified_reads.fa -st 1 -l 30 -ith 5 -gff ${out}.gff -vcf ${out}.vcf > ${out}.stdout 2> ${out}.stderr
# ============================================================
# -st 1 -l 30 -gth 3
# ============================================================
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('st1_l30_gth3.stdout'),
redir_stderr=ph.outFile('st1_l30_gth3.stderr'),
args=[ph.inFile('adeno.fa'),
ph.inFile('adeno_modified_reads.fa'),
'-gff', ph.outFile('st1_l30_gth3.gff'),
'-vcf', ph.outFile('st1_l30_gth3.vcf'),
'-st', str(1),
'-l', str(30),
'-gth', str(3),
],
to_diff=[(ph.inFile('st1_l30_m.vcf'),
ph.outFile('st1_l30_m.vcf'),
transforms),
(ph.inFile('st1_l30_gth3.gff'),
ph.outFile('st1_l30_gth3.gff'))])
conf_list.append(conf)
#out="st1_l30_gth3"
#${GUSTAF} adeno.fa adeno_modified_reads.fa -st 1 -l 30 -gth 3 -gff ${out}.gff -vcf ${out}.vcf > ${out}.stdout 2> ${out}.stderr
# ============================================================
# Execute the tests.
# ============================================================
failures = 0
for conf in conf_list:
res = app_tests.runTest(conf)
# Output to the user.
print ' '.join(['gustaf'] + conf.args),
if res:
print 'OK'
else:
failures += 1
print 'FAILED'
# Cleanup.
ph.deleteTempDir()
print '=============================='
print ' total tests: %d' % len(conf_list)
print ' failed tests: %d' % failures
print 'successful tests: %d' % (len(conf_list) - failures)
print '=============================='
# Compute and return return code.
return failures != 0
def main(source_base, binary_base):
"""Main entry point of the script."""
print('Executing test for gustaf')
print('===============================')
print()
ph = app_tests.TestPathHelper(source_base, binary_base,
'apps/gustaf/tests') # tests dir
# ============================================================
# Auto-detect the binary path.
# ============================================================
path_to_program = app_tests.autolocateBinary(binary_base, 'bin', 'gustaf')
path_to_snd_program = app_tests.autolocateBinary(binary_base, 'bin',
'gustaf_mate_joining')
# ============================================================
# Built TestConf list.
# ============================================================
# Build list with TestConf objects, analoguely to how the output
# was generated in generate_outputs.sh.
conf_list = []
# We prepare a list of transforms to apply to the output files. This is
# used to strip the input/output paths from the programs' output to
# make it more canonical and host independent.
ph.outFile('-') # To ensure that the out path is set.
transforms = [
app_tests.ReplaceTransform(
os.path.join(ph.source_base_path, 'apps/gustaf/tests') + os.sep,
'',
right=True),
app_tests.ReplaceTransform(ph.temp_dir + os.sep, '', right=True),
app_tests.NormalizeScientificExponentsTransform(),
]
# ============================================================
# Gustaf_mate_joining Tests
# ============================================================
# ============================================================
# Simple gustaf_mate_joining app test
# ============================================================
conf = app_tests.TestConf(
program=path_to_snd_program,
redir_stdout=ph.outFile('gustaf_mate_joining.stdout'),
redir_stderr=ph.outFile('gustaf_mate_joining.stderr'),
args=[
ph.inFile('adeno_modified_reads_mates1.fa'),
ph.inFile('adeno_modified_reads_mates2.fa'),
'-o',
ph.outFile('adeno_modified_reads_joinedMates.fa'),
'-rc',
],
to_diff=[ #(ph.inFile('st2_l100.vcf'),
#ph.outFile('st2_l100.vcf'),
#transforms),
(ph.inFile('adeno_modified_reads_joinedMates.fa'),
ph.outFile('adeno_modified_reads_joinedMates.fa'))
])
conf_list.append(conf)
# ${JOINMATES} adeno_modified_reads_mates1.fa adeno_modified_reads_mates2.fa \
# -o adeno_modified_reads_joinedMates.fa -rc 1 \
# > gustaf_mate_joining.stdout 2> gustaf_mate_joining.stderr
# ============================================================
# Read joining, reverse complement
# ============================================================
conf = app_tests.TestConf(
program=path_to_snd_program,
redir_stdout=ph.outFile('gustaf_mate_joining.stdout'),
redir_stderr=ph.outFile('gustaf_mate_joining.stderr'),
args=[
ph.inFile('reads_simulated_mates1_gold.fa'),
ph.inFile('reads_simulated_mates2_gold.fa'),
'-o',
ph.outFile('reads_simulated_joined_rc.fa'),
'-rc',
],
to_diff=[ #(ph.inFile('st2_l100.vcf'),
#ph.outFile('st2_l100.vcf'),
#transforms),
(ph.inFile('reads_simulated_joined_rc.fa'),
ph.outFile('reads_simulated_joined_rc.fa'))
])
conf_list.append(conf)
# ${JOINMATES} reads_simulated_mates1_gold.fa reads_simulated_mates2_gold.fa \
# -o reads_simulated_joined_rc.fa -rc 1 \
# > gustaf_mate_joining.stdout 2> gustaf_mate_joining.stderr
# ============================================================
# Read joining, no reverse complement
# ============================================================
conf = app_tests.TestConf(
program=path_to_snd_program,
redir_stdout=ph.outFile('gustaf_mate_joining.stdout'),
redir_stderr=ph.outFile('gustaf_mate_joining.stderr'),
args=[
ph.inFile('reads_simulated_mates1_gold.fa'),
ph.inFile('reads_simulated_mates2_gold.fa'),
'-o',
ph.outFile('reads_simulated_joined.fa'),
],
to_diff=[ #(ph.inFile('st2_l100.vcf'),
#ph.outFile('st2_l100.vcf'),
#transforms),
(ph.inFile('reads_simulated_joined.fa'),
ph.outFile('reads_simulated_joined.fa'))
])
conf_list.append(conf)
# ${JOINMATES} reads_simulated_mates1_gold.fa reads_simulated_mates2_gold.fa \
# -o reads_simulated_joined.fa \
# > gustaf_mate_joining.stdout 2> gustaf_mate_joining.stderr
# ============================================================
# Read splitting, reverse complement
# ============================================================
conf = app_tests.TestConf(
program=path_to_snd_program,
redir_stdout=ph.outFile('gustaf_mate_joining.stdout'),
redir_stderr=ph.outFile('gustaf_mate_joining.stderr'),
args=[
ph.inFile('reads_simulated_joined_gold.fa'),
'-o',
ph.outFile('reads_simulated_mates1_rc.fa'),
'-o',
ph.outFile('reads_simulated_mates2_rc.fa'),
'-rc',
],
to_diff=[(ph.inFile('reads_simulated_mates1_rc.fa'),
ph.outFile('reads_simulated_mates1_rc.fa'), transforms),
(ph.inFile('reads_simulated_mates2_rc.fa'),
ph.outFile('reads_simulated_mates2_rc.fa'))])
conf_list.append(conf)
# ${JOINMATES} reads_simulated_joined_gold.fa \
# -o reads_simulated_mates1_rc.fa -o reads_simulated_mates2_rc.fa -rc 1 \
# > gustaf_mate_joining.stdout 2> gustaf_mate_joining.stderr
# ============================================================
# Read splitting, no reverse complement
# ============================================================
conf = app_tests.TestConf(
program=path_to_snd_program,
redir_stdout=ph.outFile('gustaf_mate_joining.stdout'),
redir_stderr=ph.outFile('gustaf_mate_joining.stderr'),
args=[
ph.inFile('reads_simulated_joined_gold.fa'),
'-o',
ph.outFile('reads_simulated_mates1.fa'),
'-o',
ph.outFile('reads_simulated_mates2.fa'),
],
to_diff=[(ph.inFile('reads_simulated_mates1.fa'),
ph.outFile('reads_simulated_mates1.fa'), transforms),
(ph.inFile('reads_simulated_mates2.fa'),
ph.outFile('reads_simulated_mates2.fa'))])
conf_list.append(conf)
# ${JOINMATES} reads_simulated_joined_gold.fa \
# -o reads_simulated_mates1.fa -o reads_simulated_mates2.fa \
# > gustaf_mate_joining.stdout 2> gustaf_mate_joining.stderr
# ============================================================
# Gustaf Tests
# ============================================================
# ============================================================
# Sanity check with default values and empty output file
# ============================================================
conf = app_tests.TestConf(program=path_to_program,
redir_stdout=ph.outFile('st2_l100.stdout'),
redir_stderr=ph.outFile('st2_l100.stderr'),
args=[
ph.inFile('adeno.fa'),
ph.inFile('adeno_modified_reads.fa'),
'-gff',
ph.outFile('st2_l100.gff'),
'-vcf',
ph.outFile('st2_l100.vcf'),
],
to_diff=[]) #(ph.inFile('st2_l100.vcf'),
# ph.outFile('st2_l100.vcf'),
# transforms),
#(ph.inFile('st2_l100.gff'),
# ph.outFile('st2_l100.gff'))])
conf_list.append(conf)
#out="st2_l100"
#${GUSTAF} adeno.fa adeno_modified_reads.fa -gff ${out}.gff -vcf ${out}.vcf > ${out}.stdout 2> ${out}.stderr
# ============================================================
# -st 1 -l 30
# ============================================================
conf = app_tests.TestConf(program=path_to_program,
redir_stdout=ph.outFile('st1_l30.stdout'),
redir_stderr=ph.outFile('st1_l30.stderr'),
args=[
ph.inFile('adeno.fa'),
ph.inFile('adeno_modified_reads.fa'),
'-gff',
ph.outFile('st1_l30.gff'),
'-vcf',
ph.outFile('st1_l30.vcf'),
'-st',
str(1),
'-l',
str(30),
],
to_diff=[(ph.inFile('st1_l30.vcf'),
ph.outFile('st1_l30.vcf'), transforms),
(ph.inFile('st1_l30.gff'),
ph.outFile('st1_l30.gff'))])
conf_list.append(conf)
#out="st1_l30"
#${GUSTAF} adeno.fa adeno_modified_reads.fa -st 1 -l 30 -gff ${out}.gff -vcf ${out}.vcf > ${out}.stdout 2> ${out}.stderr
# ============================================================
# -st 1 -m stellar.gff
# ============================================================
conf = app_tests.TestConf(program=path_to_program,
redir_stdout=ph.outFile('st1_l30_m.stdout'),
redir_stderr=ph.outFile('st1_l30_m.stderr'),
args=[
ph.inFile('adeno.fa'),
ph.inFile('adeno_modified_reads.fa'),
'-m',
ph.inFile('stellar.gff'),
'-gff',
ph.outFile('st1_l30_m.gff'),
'-vcf',
ph.outFile('st1_l30_m.vcf'),
'-st',
str(1),
],
to_diff=[(ph.inFile('st1_l30_m.vcf'),
ph.outFile('st1_l30_m.vcf'),
transforms),
(ph.inFile('st1_l30_m.gff'),
ph.outFile('st1_l30_m.gff'))])
conf_list.append(conf)
#out="st1_l30_m"
#${GUSTAF} adeno.fa adeno_modified_reads.fa -st 1 -m stellar.gff -gff ${out}.gff -vcf ${out}.vcf > ${out}.stdout 2> ${out}.stderr
# ============================================================
# -st 1 -l 30 -ith 5
# ============================================================
conf = app_tests.TestConf(program=path_to_program,
redir_stdout=ph.outFile('st1_l30_ith5.stdout'),
redir_stderr=ph.outFile('st1_l30_ith5.stderr'),
args=[
ph.inFile('adeno.fa'),
ph.inFile('adeno_modified_reads.fa'),
'-gff',
ph.outFile('st1_l30_ith5.gff'),
'-vcf',
ph.outFile('st1_l30_ith5.vcf'),
'-st',
str(1),
'-l',
str(30),
'-ith',
str(5),
'-bth',
str(5),
],
to_diff=[(ph.inFile('st1_l30_m.vcf'),
ph.outFile('st1_l30_m.vcf'),
transforms),
(ph.inFile('st1_l30_ith5.gff'),
ph.outFile('st1_l30_ith5.gff'))])
conf_list.append(conf)
#out="st1_l30_ith5"
#${GUSTAF} adeno.fa adeno_modified_reads.fa -st 1 -l 30 -ith 5 -bth 5 -gff ${out}.gff -vcf ${out}.vcf > ${out}.stdout 2> ${out}.stderr
# ============================================================
# -st 1 -l 30 -gth 3
# ============================================================
conf = app_tests.TestConf(program=path_to_program,
redir_stdout=ph.outFile('st1_l30_gth3.stdout'),
redir_stderr=ph.outFile('st1_l30_gth3.stderr'),
args=[
ph.inFile('adeno.fa'),
ph.inFile('adeno_modified_reads.fa'),
'-gff',
ph.outFile('st1_l30_gth3.gff'),
'-vcf',
ph.outFile('st1_l30_gth3.vcf'),
'-st',
str(1),
'-l',
str(30),
'-gth',
str(3),
],
to_diff=[(ph.inFile('st1_l30_m.vcf'),
ph.outFile('st1_l30_m.vcf'),
transforms),
(ph.inFile('st1_l30_gth3.gff'),
ph.outFile('st1_l30_gth3.gff'))])
conf_list.append(conf)
#out="st1_l30_gth3"
#${GUSTAF} adeno.fa adeno_modified_reads.fa -st 1 -l 30 -gth 3 -gff ${out}.gff -vcf ${out}.vcf > ${out}.stdout 2> ${out}.stderr
# ============================================================
# paired-end
# -st 1 -m stellar_joinedMates_l30.gff
# ============================================================
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('pairedEnd_st1_l30.stdout'),
redir_stderr=ph.outFile('pairedEnd_st1_l30.stderr'),
args=[
ph.inFile('adeno.fa'),
ph.inFile('adeno_modified_reads_mates1.fa'),
ph.inFile('adeno_modified_reads_mates2.fa'),
'-m',
ph.inFile('stellar_joinedMates_l30.gff'),
'-gff',
ph.outFile('pairedEnd_st1_l30.gff'),
'-vcf',
ph.outFile('pairedEnd_st1_l30.vcf'),
'-st',
str(1),
'-mst',
str(1),
'-ll',
str(1000),
'-le',
str(100),
'-rc',
],
to_diff=[(ph.inFile('pairedEnd_st1_l30.vcf'),
ph.outFile('pairedEnd_st1_l30.vcf'), transforms),
(ph.inFile('pairedEnd_st1_l30.gff'),
ph.outFile('pairedEnd_st1_l30.gff'))])
conf_list.append(conf)
#out="pairedEnd_st1_l30"
#${GUSTAF} adeno.fa adeno_modified_reads_mates1.fa adeno_modified_reads_mates2.fa -m stellar_joinedMates_l30.gff -st 1
#-mst 1 -ll 1000 -le 30 -rc -gff ${out}.gff -vcf ${out}.vcf > ${out}.stdout 2> ${out}.stderr
# ============================================================
# Sanity check multiple references
# -st 1 -l 30
# ============================================================
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('reference2_st1_l30.stdout'),
redir_stderr=ph.outFile('reference2_st1_l30.stderr'),
args=[
ph.inFile('adeno.fa'),
ph.inFile('read_reference2.fa'),
'-gff',
ph.outFile('reference2_st1_l30.gff'),
'-vcf',
ph.outFile('reference2_st1_l30.vcf'),
'-st',
str(1),
'-l',
str(30),
],
to_diff=[(ph.inFile('reference2_st1_l30.vcf'),
ph.outFile('reference2_st1_l30.vcf'), transforms),
(ph.inFile('reference2_st1_l30.gff'),
ph.outFile('reference2_st1_l30.gff'))])
conf_list.append(conf)
#out="reference2_st1_l30"
#${GUSTAF} adeno.fa read_reference2.fa -st 1 \
#-l 30 -gff ${out}.gff -vcf ${out}.vcf > ${out}.stdout 2> ${out}.stderr
# ============================================================
# Execute the tests.
# ============================================================
failures = 0
for conf in conf_list:
res = app_tests.runTest(conf)
# Output to the user.
print(' '.join(['gustaf'] + conf.args), end=' ')
if res:
print('OK')
else:
failures += 1
print('FAILED')
# Cleanup.
ph.deleteTempDir()
print('==============================')
print(' total tests: %d' % len(conf_list))
print(' failed tests: %d' % failures)
print('successful tests: %d' % (len(conf_list) - failures))
print('==============================')
# Compute and return return code.
return failures != 0
def main(source_base, binary_base):
"""Main entry point of the script."""
print 'Executing test for tree_recomb'
print '=============================='
print
ph = app_tests.TestPathHelper(
source_base, binary_base,
'core/apps/tree_recon/tests') # tests dir
# ============================================================
# Auto-detect the binary path.
# ============================================================
path_to_program = app_tests.autolocateBinary(
binary_base, 'core/apps/tree_recon', 'tree_recon')
# ============================================================
# Built TestConf list.
# ============================================================
# Build list with TestConf objects, analoguely to how the output
# was generated in generate_outputs.sh.
conf_list = []
for i in [1, 2, 3]:
conf = app_tests.TestConf(
program=path_to_program,
args=['-m', ph.inFile('example%d.dist' % i),
'-o', ph.outFile('example%d.out' % i)],
to_diff=[(ph.inFile('example%d.out' % i),
ph.outFile('example%d.out' % i))])
conf_list.append(conf)
for i in [1, 2, 3]:
for b in ['nj', 'min', 'max', 'avg', 'wavg']:
if i == 1 and b == 'avg':
continue # Skip, rounding problems MSVC vs GCC.
conf = app_tests.TestConf(
program=path_to_program,
args=['-b', b,
'-m', ph.inFile('example%d.dist' % i),
'-o', ph.outFile('example%d.%s.out' % (i, b))],
to_diff=[(ph.inFile('example%d.%s.out' % (i, b)),
ph.outFile('example%d.%s.out' % (i, b)))])
conf_list.append(conf)
for i in [1, 2, 3]:
for f in ['dot', 'newick']:
conf = app_tests.TestConf(
program=path_to_program,
args=['-f', f,
'-m', ph.inFile('example%d.dist' % i),
'-o', ph.outFile('example%d.%s.out' % (i, f))],
to_diff=[(ph.inFile('example%d.%s.out' % (i, f)),
ph.outFile('example%d.%s.out' % (i, f)))])
conf_list.append(conf)
# Execute the tests.
failures = 0
for conf in conf_list:
res = app_tests.runTest(conf)
# Output to the user.
print ' '.join(['tree_recomb'] + conf.args),
if res:
print 'OK'
else:
failures += 1
print 'FAILED'
# Cleanup.
ph.deleteTempDir()
print '=============================='
print ' total tests: %d' % len(conf_list)
print ' failed tests: %d' % failures
print 'successful tests: %d' % (len(conf_list) - failures)
print '=============================='
# Compute and return return code.
return failures != 0
def main(source_base, binary_base):
"""Main entry point of the script."""
print 'Executing test for mason'
print '========================'
print
ph = app_tests.TestPathHelper(
source_base, binary_base,
'core/apps/mason/tests') # tests dir
# ============================================================
# Auto-detect the binary path.
# ============================================================
path_to_program = app_tests.autolocateBinary(
binary_base, 'core/apps/mason', 'mason')
# ============================================================
# Built TestConf list.
# ============================================================
# Build list with TestConf objects, analoguely to how the output
# was generated in generate_outputs.sh.
conf_list = []
# We prepare a list of transforms to apply to the output files: Strip the
# running times from output.
transforms = [
app_tests.RegexpReplaceTransform(r'Finished haplotype creation in [^ ]+s',
r'Finished haplotype creation in <cut out>s',
left=True, right=True),
]
# ============================================================
# Run 454 Reads, Single-End
# ============================================================
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('454-se-random-N100-nm400-ne40-s0.stdout'),
args=['454', '-N', '100', '-nm', '400', '-ne', '40', '-s', '0', '-rnp', 'read',
'-o', ph.outFile('454-se-random-N100-nm400-ne40-s0.fasta'),
'random.fasta'],
to_diff=[(ph.inFile('454-se-random-N100-nm400-ne40-s0.fasta'),
ph.outFile('454-se-random-N100-nm400-ne40-s0.fasta')),
(ph.inFile('454-se-random-N100-nm400-ne40-s0.fasta.sam'),
ph.outFile('454-se-random-N100-nm400-ne40-s0.fasta.sam')),
(ph.inFile('454-se-random-N100-nm400-ne40-s0.stdout'),
ph.outFile('454-se-random-N100-nm400-ne40-s0.stdout'),
transforms)])
conf_list.append(conf)
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('454-se-random-N100-nm400-ne40-s0-sq.stdout'),
args=['454', '-N', '100', '-nm', '400', '-ne', '40', '-s', '0', '-sq', '-rnp', 'read',
'-o', ph.outFile('454-se-random-N100-nm400-ne40-s0-sq.fastq'),
'random.fasta'],
to_diff=[(ph.inFile('454-se-random-N100-nm400-ne40-s0-sq.fastq'),
ph.outFile('454-se-random-N100-nm400-ne40-s0-sq.fastq')),
(ph.inFile('454-se-random-N100-nm400-ne40-s0-sq.fastq.sam'),
ph.outFile('454-se-random-N100-nm400-ne40-s0-sq.fastq.sam')),
(ph.inFile('454-se-random-N100-nm400-ne40-s0-sq.stdout'),
ph.outFile('454-se-random-N100-nm400-ne40-s0-sq.stdout'),
transforms)])
conf_list.append(conf)
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('454-se-random-N100-nm200-ne20-s0.stdout'),
args=['454', '-N', '100', '-nm', '200', '-ne', '20', '-s', '0', '-rnp', 'read',
'-o', ph.outFile('454-se-random-N100-nm200-ne20-s0.fasta'),
'random.fasta'],
to_diff=[(ph.inFile('454-se-random-N100-nm200-ne20-s0.fasta'),
ph.outFile('454-se-random-N100-nm200-ne20-s0.fasta')),
(ph.inFile('454-se-random-N100-nm200-ne20-s0.fasta.sam'),
ph.outFile('454-se-random-N100-nm200-ne20-s0.fasta.sam')),
(ph.inFile('454-se-random-N100-nm200-ne20-s0.stdout'),
ph.outFile('454-se-random-N100-nm200-ne20-s0.stdout'),
transforms)])
conf_list.append(conf)
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('454-se-random-N100-nm200-ne20-s0-sq.stdout'),
args=['454', '-N', '100', '-nm', '200', '-ne', '20', '-s', '0', '-sq', '-rnp', 'read',
'-o', ph.outFile('454-se-random-N100-nm200-ne20-s0-sq.fastq'),
'random.fasta'],
to_diff=[(ph.inFile('454-se-random-N100-nm200-ne20-s0-sq.fastq'),
ph.outFile('454-se-random-N100-nm200-ne20-s0-sq.fastq')),
(ph.inFile('454-se-random-N100-nm200-ne20-s0-sq.fastq.sam'),
ph.outFile('454-se-random-N100-nm200-ne20-s0-sq.fastq.sam')),
(ph.inFile('454-se-random-N100-nm200-ne20-s0-sq.stdout'),
ph.outFile('454-se-random-N100-nm200-ne20-s0-sq.stdout'),
transforms)])
conf_list.append(conf)
# ============================================================
# Run Illumina Reads, Single-End
# ============================================================
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('illumina-se-random-N100-n36-s0.stdout'),
args=['illumina', '-N', '100', '-n', '36', '-s', '0', '-rnp', 'read',
'-o', ph.outFile('illumina-se-random-N100-n36-s0.fasta'),
'random.fasta'],
to_diff=[(ph.inFile('illumina-se-random-N100-n36-s0.fasta'),
ph.outFile('illumina-se-random-N100-n36-s0.fasta')),
(ph.inFile('illumina-se-random-N100-n36-s0.fasta.sam'),
ph.outFile('illumina-se-random-N100-n36-s0.fasta.sam')),
(ph.inFile('illumina-se-random-N100-n36-s0.stdout'),
ph.outFile('illumina-se-random-N100-n36-s0.stdout'),
transforms)])
conf_list.append(conf)
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('illumina-se-random-N100-n36-s0-sq.stdout'),
args=['illumina', '-N', '100', '-n', '36', '-s', '0', '-sq', '-rnp', 'read',
'-o', ph.outFile('illumina-se-random-N100-n36-s0-sq.fastq'),
'random.fasta'],
to_diff=[(ph.inFile('illumina-se-random-N100-n36-s0-sq.fastq'),
ph.outFile('illumina-se-random-N100-n36-s0-sq.fastq')),
(ph.inFile('illumina-se-random-N100-n36-s0-sq.fastq.sam'),
ph.outFile('illumina-se-random-N100-n36-s0-sq.fastq.sam')),
(ph.inFile('illumina-se-random-N100-n36-s0-sq.stdout'),
ph.outFile('illumina-se-random-N100-n36-s0-sq.stdout'),
transforms)])
conf_list.append(conf)
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('illumina-se-random-N100-n100-s0.stdout'),
args=['illumina', '-N', '100', '-n', '100', '-s', '0', '-rnp', 'read',
'-o', ph.outFile('illumina-se-random-N100-n100-s0.fasta'),
'random.fasta'],
to_diff=[(ph.inFile('illumina-se-random-N100-n100-s0.fasta'),
ph.outFile('illumina-se-random-N100-n100-s0.fasta')),
(ph.inFile('illumina-se-random-N100-n100-s0.fasta.sam'),
ph.outFile('illumina-se-random-N100-n100-s0.fasta.sam')),
(ph.inFile('illumina-se-random-N100-n100-s0.stdout'),
ph.outFile('illumina-se-random-N100-n100-s0.stdout'),
transforms)])
conf_list.append(conf)
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('illumina-se-random-N100-n100-s0-sq.stdout'),
args=['illumina', '-N', '100', '-n', '100', '-s', '0', '-sq', '-rnp', 'read',
'-o', ph.outFile('illumina-se-random-N100-n100-s0-sq.fastq'),
'random.fasta'],
to_diff=[(ph.inFile('illumina-se-random-N100-n100-s0-sq.fastq'),
ph.outFile('illumina-se-random-N100-n100-s0-sq.fastq')),
(ph.inFile('illumina-se-random-N100-n100-s0-sq.fastq.sam'),
ph.outFile('illumina-se-random-N100-n100-s0-sq.fastq.sam')),
(ph.inFile('illumina-se-random-N100-n100-s0-sq.stdout'),
ph.outFile('illumina-se-random-N100-n100-s0-sq.stdout'),
transforms)])
conf_list.append(conf)
# ============================================================
# Run Illumina Reads, Single-End, Existing Contig
# ============================================================
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('illumina-se-adeno-N100-n36-s0.stdout'),
args=['illumina', '-N', '100', '-n', '36', '-s', '0', '-rnp', 'read',
'-o', ph.outFile('illumina-se-adeno-N100-n36-s0.fasta'),
ph.inFile('adeno-genome.fa')],
to_diff=[(ph.inFile('illumina-se-adeno-N100-n36-s0.fasta'),
ph.outFile('illumina-se-adeno-N100-n36-s0.fasta')),
(ph.inFile('illumina-se-adeno-N100-n36-s0.fasta.sam'),
ph.outFile('illumina-se-adeno-N100-n36-s0.fasta.sam')),
(ph.inFile('illumina-se-adeno-N100-n36-s0.stdout'),
ph.outFile('illumina-se-adeno-N100-n36-s0.stdout'),
transforms)])
conf_list.append(conf)
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('illumina-se-adeno-N100-n36-s0-sq.stdout'),
args=['illumina', '-N', '100', '-n', '36', '-s', '0', '-sq', '-rnp', 'read',
'-o', ph.outFile('illumina-se-adeno-N100-n36-s0-sq.fastq'),
ph.inFile('adeno-genome.fa')],
to_diff=[(ph.inFile('illumina-se-adeno-N100-n36-s0-sq.fastq'),
ph.outFile('illumina-se-adeno-N100-n36-s0-sq.fastq')),
(ph.inFile('illumina-se-adeno-N100-n36-s0-sq.fastq.sam'),
ph.outFile('illumina-se-adeno-N100-n36-s0-sq.fastq.sam')),
(ph.inFile('illumina-se-adeno-N100-n36-s0-sq.stdout'),
ph.outFile('illumina-se-adeno-N100-n36-s0-sq.stdout'),
transforms)])
conf_list.append(conf)
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('illumina-se-adeno-N100-n100-s0.stdout'),
args=['illumina', '-N', '100', '-n', '100', '-s', '0', '-rnp', 'read',
'-o', ph.outFile('illumina-se-adeno-N100-n100-s0.fasta'),
ph.inFile('adeno-genome.fa')],
to_diff=[(ph.inFile('illumina-se-adeno-N100-n100-s0.fasta'),
ph.outFile('illumina-se-adeno-N100-n100-s0.fasta')),
(ph.inFile('illumina-se-adeno-N100-n100-s0.fasta.sam'),
ph.outFile('illumina-se-adeno-N100-n100-s0.fasta.sam')),
(ph.inFile('illumina-se-adeno-N100-n100-s0.stdout'),
ph.outFile('illumina-se-adeno-N100-n100-s0.stdout'),
transforms)])
conf_list.append(conf)
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('illumina-se-adeno-N100-n100-s0-sq.stdout'),
args=['illumina', '-N', '100', '-n', '100', '-s', '0', '-sq', '-rnp', 'read',
'-o', ph.outFile('illumina-se-adeno-N100-n100-s0-sq.fastq'),
ph.inFile('adeno-genome.fa')],
to_diff=[(ph.inFile('illumina-se-adeno-N100-n100-s0-sq.fastq'),
ph.outFile('illumina-se-adeno-N100-n100-s0-sq.fastq')),
(ph.inFile('illumina-se-adeno-N100-n100-s0-sq.fastq.sam'),
ph.outFile('illumina-se-adeno-N100-n100-s0-sq.fastq.sam')),
(ph.inFile('illumina-se-adeno-N100-n100-s0-sq.stdout'),
ph.outFile('illumina-se-adeno-N100-n100-s0-sq.stdout'),
transforms)])
conf_list.append(conf)
# ============================================================
# Run Illumina Reads, Paired-End
# ============================================================
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('illumina-pe-random-N100-n36-s0.stdout'),
args=['illumina', '-mp', '-N', '100', '-n', '36', '-s', '0', '-rnp', 'read',
'-o', ph.outFile('illumina-pe-random-N100-n36-s0.fasta'),
'random.fasta'],
to_diff=[(ph.inFile('illumina-pe-random-N100-n36-s0_1.fasta'),
ph.outFile('illumina-pe-random-N100-n36-s0_1.fasta')),
(ph.inFile('illumina-pe-random-N100-n36-s0_2.fasta'),
ph.outFile('illumina-pe-random-N100-n36-s0_2.fasta')),
(ph.inFile('illumina-pe-random-N100-n36-s0.fasta.sam'),
ph.outFile('illumina-pe-random-N100-n36-s0.fasta.sam')),
(ph.inFile('illumina-pe-random-N100-n36-s0.stdout'),
ph.outFile('illumina-pe-random-N100-n36-s0.stdout'),
transforms)])
conf_list.append(conf)
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('illumina-pe-random-N100-n36-s0-sq.stdout'),
args=['illumina', '-mp', '-N', '100', '-n', '36', '-s', '0', '-sq', '-rnp', 'read',
'-o', ph.outFile('illumina-pe-random-N100-n36-s0-sq.fastq'),
'random.fasta'],
to_diff=[(ph.inFile('illumina-pe-random-N100-n36-s0-sq_1.fastq'),
ph.outFile('illumina-pe-random-N100-n36-s0-sq_1.fastq')),
(ph.inFile('illumina-pe-random-N100-n36-s0-sq_2.fastq'),
ph.outFile('illumina-pe-random-N100-n36-s0-sq_2.fastq')),
(ph.inFile('illumina-pe-random-N100-n36-s0-sq.fastq.sam'),
ph.outFile('illumina-pe-random-N100-n36-s0-sq.fastq.sam')),
(ph.inFile('illumina-pe-random-N100-n36-s0-sq.stdout'),
ph.outFile('illumina-pe-random-N100-n36-s0-sq.stdout'),
transforms)])
conf_list.append(conf)
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('illumina-pe-random-N100-n100-s0.stdout'),
args=['illumina', '-mp', '-N', '100', '-n', '100', '-s', '0', '-rnp', 'read',
'-o', ph.outFile('illumina-pe-random-N100-n100-s0.fasta'),
'random.fasta'],
to_diff=[(ph.inFile('illumina-pe-random-N100-n100-s0_1.fasta'),
ph.outFile('illumina-pe-random-N100-n100-s0_1.fasta')),
(ph.inFile('illumina-pe-random-N100-n100-s0_2.fasta'),
ph.outFile('illumina-pe-random-N100-n100-s0_2.fasta')),
(ph.inFile('illumina-pe-random-N100-n100-s0.fasta.sam'),
ph.outFile('illumina-pe-random-N100-n100-s0.fasta.sam')),
(ph.inFile('illumina-pe-random-N100-n100-s0.stdout'),
ph.outFile('illumina-pe-random-N100-n100-s0.stdout'),
transforms)])
conf_list.append(conf)
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('illumina-pe-random-N100-n100-s0-sq.stdout'),
args=['illumina', '-mp', '-N', '100', '-n', '100', '-s', '0', '-sq', '-rnp', 'read',
'-o', ph.outFile('illumina-pe-random-N100-n100-s0-sq.fastq'),
'random.fasta'],
to_diff=[(ph.inFile('illumina-pe-random-N100-n100-s0-sq_1.fastq'),
ph.outFile('illumina-pe-random-N100-n100-s0-sq_1.fastq')),
(ph.inFile('illumina-pe-random-N100-n100-s0-sq_2.fastq'),
ph.outFile('illumina-pe-random-N100-n100-s0-sq_2.fastq')),
(ph.inFile('illumina-pe-random-N100-n100-s0-sq.fastq.sam'),
ph.outFile('illumina-pe-random-N100-n100-s0-sq.fastq.sam')),
(ph.inFile('illumina-pe-random-N100-n100-s0-sq.stdout'),
ph.outFile('illumina-pe-random-N100-n100-s0-sq.stdout'),
transforms)])
conf_list.append(conf)
# ============================================================
# Run Sanger Reads, Single-End
# ============================================================
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('sanger-se-random-N100-nm400-ne40-s0.stdout'),
args=['sanger', '-N', '100', '-nm', '400', '-ne', '40', '-s', '0', '-rnp', 'read',
'-o', ph.outFile('sanger-se-random-N100-nm400-ne40-s0.fasta'),
'random.fasta'],
to_diff=[(ph.inFile('sanger-se-random-N100-nm400-ne40-s0.fasta'),
ph.outFile('sanger-se-random-N100-nm400-ne40-s0.fasta')),
(ph.inFile('sanger-se-random-N100-nm400-ne40-s0.fasta.sam'),
ph.outFile('sanger-se-random-N100-nm400-ne40-s0.fasta.sam')),
(ph.inFile('sanger-se-random-N100-nm400-ne40-s0.stdout'),
ph.outFile('sanger-se-random-N100-nm400-ne40-s0.stdout'),
transforms)])
conf_list.append(conf)
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('sanger-se-random-N100-nm400-ne40-s0-sq.stdout'),
args=['sanger', '-N', '100', '-nm', '400', '-ne', '40', '-s', '0', '-sq', '-rnp', 'read',
'-o', ph.outFile('sanger-se-random-N100-nm400-ne40-s0-sq.fastq'),
'random.fasta'],
to_diff=[(ph.inFile('sanger-se-random-N100-nm400-ne40-s0-sq.fastq'),
ph.outFile('sanger-se-random-N100-nm400-ne40-s0-sq.fastq')),
(ph.inFile('sanger-se-random-N100-nm400-ne40-s0-sq.fastq.sam'),
ph.outFile('sanger-se-random-N100-nm400-ne40-s0-sq.fastq.sam')),
(ph.inFile('sanger-se-random-N100-nm400-ne40-s0-sq.stdout'),
ph.outFile('sanger-se-random-N100-nm400-ne40-s0-sq.stdout'),
transforms)])
conf_list.append(conf)
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('sanger-se-random-N100-nm200-ne20-s0.stdout'),
args=['sanger', '-N', '100', '-nm', '200', '-ne', '20', '-s', '0', '-rnp', 'read',
'-o', ph.outFile('sanger-se-random-N100-nm200-ne20-s0.fasta'),
'random.fasta'],
to_diff=[(ph.inFile('sanger-se-random-N100-nm200-ne20-s0.fasta'),
ph.outFile('sanger-se-random-N100-nm200-ne20-s0.fasta')),
(ph.inFile('sanger-se-random-N100-nm200-ne20-s0.fasta.sam'),
ph.outFile('sanger-se-random-N100-nm200-ne20-s0.fasta.sam')),
(ph.inFile('sanger-se-random-N100-nm200-ne20-s0.stdout'),
ph.outFile('sanger-se-random-N100-nm200-ne20-s0.stdout'),
transforms)])
conf_list.append(conf)
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('sanger-se-random-N100-nm200-ne20-s0-sq.stdout'),
args=['sanger', '-N', '100', '-nm', '200', '-ne', '20', '-s', '0', '-sq', '-rnp', 'read',
'-o', ph.outFile('sanger-se-random-N100-nm200-ne20-s0-sq.fastq'),
'random.fasta'],
to_diff=[(ph.inFile('sanger-se-random-N100-nm200-ne20-s0-sq.fastq'),
ph.outFile('sanger-se-random-N100-nm200-ne20-s0-sq.fastq')),
(ph.inFile('sanger-se-random-N100-nm200-ne20-s0-sq.fastq.sam'),
ph.outFile('sanger-se-random-N100-nm200-ne20-s0-sq.fastq.sam')),
(ph.inFile('sanger-se-random-N100-nm200-ne20-s0-sq.stdout'),
ph.outFile('sanger-se-random-N100-nm200-ne20-s0-sq.stdout'),
transforms)])
conf_list.append(conf)
# Execute the tests.
failures = 0
for conf in conf_list:
print ' '.join(['mason'] + conf.args),
sys.stdout.flush()
res = app_tests.runTest(conf)
# Output to the user.
print ' '.join(['mason'] + conf.args),
if res:
print 'OK'
else:
failures += 1
print 'FAILED'
# Cleanup.
ph.deleteTempDir()
print '=============================='
print ' total tests: %d' % len(conf_list)
print ' failed tests: %d' % failures
print 'successful tests: %d' % (len(conf_list) - failures)
print '=============================='
# Compute and return return code.
return failures != 0
def main(source_base, binary_base):
"""Main entry point of the script."""
print "Executing test for mason_variator"
print "======================"
print
ph = app_tests.TestPathHelper(source_base, binary_base, "apps/mason2/tests") # tests dir
# ============================================================
# Auto-detect the binary path.
# ============================================================
path_to_genome = app_tests.autolocateBinary(binary_base, "bin", "mason_genome")
path_to_methylation = app_tests.autolocateBinary(binary_base, "bin", "mason_methylation")
path_to_variator = app_tests.autolocateBinary(binary_base, "bin", "mason_variator")
path_to_materializer = app_tests.autolocateBinary(binary_base, "bin", "mason_materializer")
path_to_simulator = app_tests.autolocateBinary(binary_base, "bin", "mason_simulator")
# ============================================================
# Built TestConf list.
# ============================================================
# Build list with TestConf objects, analoguely to how the output
# was generated in generate_outputs.sh.
conf_list = []
# We prepare a list of transforms to apply to the output files. This is
# used to strip the input/output paths from the programs' output to
# make it more canonical and host independent.
ph.outFile("-") # To ensure that the out path is set.
transforms = [
app_tests.ReplaceTransform(os.path.join(ph.source_base_path, "apps/mason2/tests") + os.sep, "", right=True),
app_tests.ReplaceTransform(ph.temp_dir + os.sep, "", right=True),
app_tests.NormalizeScientificExponentsTransform(),
]
# ============================================================
# Test mason_genome
# ============================================================
conf = app_tests.TestConf(
program=path_to_genome,
args=["-l", "1000", "-o", ph.outFile("genome.test1.fasta")],
redir_stdout=ph.outFile("genome.test1.stdout"),
redir_stderr=ph.outFile("genome.test1.stderr"),
to_diff=[
(ph.inFile("genome.test1.fasta"), ph.outFile("genome.test1.fasta")),
(ph.inFile("genome.test1.stdout"), ph.outFile("genome.test1.stdout"), transforms),
(ph.inFile("genome.test1.stderr"), ph.outFile("genome.test1.stderr"), transforms),
],
)
conf_list.append(conf)
conf = app_tests.TestConf(
program=path_to_genome,
args=["-s", "1", "-l", "1000", "-l", "100", "-o", ph.outFile("genome.test2.fasta")],
redir_stdout=ph.outFile("genome.test2.stdout"),
redir_stderr=ph.outFile("genome.test2.stderr"),
to_diff=[
(ph.inFile("genome.test2.fasta"), ph.outFile("genome.test2.fasta")),
(ph.inFile("genome.test2.stdout"), ph.outFile("genome.test2.stdout"), transforms),
(ph.inFile("genome.test2.stderr"), ph.outFile("genome.test2.stderr"), transforms),
],
)
conf_list.append(conf)
# ============================================================
# Test mason_methylation
# ============================================================
conf = app_tests.TestConf(
program=path_to_methylation,
args=["--seed", "33", "-i", ph.inFile("random.fasta"), "-o", ph.outFile("random_meth1.fasta")],
redir_stdout=ph.outFile("methylation.test1.stdout"),
redir_stderr=ph.outFile("methylation.test1.stderr"),
to_diff=[
(ph.inFile("methylation.test1.fasta"), ph.outFile("methylation.test1.fasta")),
(ph.inFile("methylation.test1.stdout"), ph.outFile("methylation.test1.stdout"), transforms),
(ph.inFile("methylation.test1.stderr"), ph.outFile("methylation.test1.stderr"), transforms),
],
)
# ============================================================
# Test mason_variator
# ============================================================
# Generation methylation in variator.
conf = app_tests.TestConf(
program=path_to_variator,
args=[
"-ir",
ph.inFile("random.fasta"),
"-n",
"2",
"-ov",
ph.outFile("random_var1.vcf"),
"-of",
ph.outFile("random_var1.fasta"),
"--snp-rate",
"0.001",
"--small-indel-rate",
"0.001",
"--sv-indel-rate",
"0.001",
"--sv-inversion-rate",
"0.001",
"--sv-translocation-rate",
"0.001",
"--sv-duplication-rate",
"0.001",
"--min-sv-size",
"50",
"--max-sv-size",
"100",
"--methylation-levels",
"--meth-fasta-out",
ph.outFile("random_var1_meth.fasta"),
"--out-breakpoints",
ph.outFile("random_var1_bp.txt"),
],
redir_stdout=ph.outFile("random_var1.vcf.stdout"),
redir_stderr=ph.outFile("random_var1.vcf.stderr"),
to_diff=[
(ph.inFile("random_var1.vcf"), ph.outFile("random_var1.vcf"), transforms),
(ph.inFile("random_var1.fasta"), ph.outFile("random_var1.fasta")),
(ph.inFile("random_var1_bp.txt"), ph.outFile("random_var1_bp.txt")),
(ph.inFile("random_var1_meth.fasta"), ph.outFile("random_var1_meth.fasta")),
(ph.inFile("random_var1.vcf.stderr"), ph.outFile("random_var1.vcf.stderr"), transforms),
(ph.inFile("random_var1.vcf.stdout"), ph.outFile("random_var1.vcf.stdout"), transforms),
],
)
conf_list.append(conf)
# Generation methylation in variator.
conf = app_tests.TestConf(
program=path_to_variator,
args=[
"-ir",
ph.inFile("random.fasta"),
"-n",
"2",
"-ov",
ph.outFile("random_var2.vcf"),
"-of",
ph.outFile("random_var2.fasta"),
"--snp-rate",
"0.001",
"--small-indel-rate",
"0.001",
"--sv-indel-rate",
"0.001",
"--sv-inversion-rate",
"0.001",
"--sv-translocation-rate",
"0.001",
"--sv-duplication-rate",
"0.001",
"--min-sv-size",
"50",
"--max-sv-size",
"100",
"--methylation-levels",
"--meth-fasta-in",
ph.inFile("random_meth1.fasta"),
"--meth-fasta-out",
ph.outFile("random_var2_meth.fasta"),
"--out-breakpoints",
ph.outFile("random_var2_bp.txt"),
],
redir_stdout=ph.outFile("random_var2.vcf.stdout"),
redir_stderr=ph.outFile("random_var2.vcf.stderr"),
to_diff=[
(ph.inFile("random_var2.vcf"), ph.outFile("random_var2.vcf"), transforms),
(ph.inFile("random_var2.fasta"), ph.outFile("random_var2.fasta")),
(ph.inFile("random_var2_bp.txt"), ph.outFile("random_var2_bp.txt")),
(ph.inFile("random_var2_meth.fasta"), ph.outFile("random_var2_meth.fasta")),
(ph.inFile("random_var2.vcf.stderr"), ph.outFile("random_var2.vcf.stderr"), transforms),
(ph.inFile("random_var2.vcf.stdout"), ph.outFile("random_var2.vcf.stdout"), transforms),
],
)
conf_list.append(conf)
# Variation without methylation levels.
conf = app_tests.TestConf(
program=path_to_variator,
args=[
"-ir",
ph.inFile("random.fasta"),
"-n",
"2",
"-ov",
ph.outFile("random_var3.vcf"),
"-of",
ph.outFile("random_var3.fasta"),
"--snp-rate",
"0.001",
"--small-indel-rate",
"0.001",
"--sv-indel-rate",
"0.001",
"--sv-inversion-rate",
"0.001",
"--sv-translocation-rate",
"0.001",
"--sv-duplication-rate",
"0.001",
"--min-sv-size",
"50",
"--max-sv-size",
"100",
"--out-breakpoints",
ph.outFile("random_var3_bp.txt"),
],
redir_stdout=ph.outFile("random_var3.vcf.stdout"),
redir_stderr=ph.outFile("random_var3.vcf.stderr"),
to_diff=[
(ph.inFile("random_var3.vcf"), ph.outFile("random_var3.vcf"), transforms),
(ph.inFile("random_var3.fasta"), ph.outFile("random_var3.fasta")),
(ph.inFile("random_var3_bp.txt"), ph.outFile("random_var3_bp.txt")),
(ph.inFile("random_var3.vcf.stderr"), ph.outFile("random_var3.vcf.stderr"), transforms),
(ph.inFile("random_var3.vcf.stdout"), ph.outFile("random_var3.vcf.stdout"), transforms),
],
)
conf_list.append(conf)
# Previously crashing test
conf = app_tests.TestConf(
program=path_to_variator,
args=[
"-ir",
ph.inFile("adeno_virus.fa"),
"-ov",
ph.outFile("random_var9.vcf"),
"-of",
ph.outFile("random_var9.fasta"),
"--sv-indel-rate",
"0.01",
"--sv-duplication-rate",
"0.01",
"--sv-inversion-rate",
"0.01",
"--min-sv-size",
"20",
"--max-sv-size",
"300",
],
redir_stdout=ph.outFile("random_var9.vcf.stdout"),
redir_stderr=ph.outFile("random_var9.vcf.stderr"),
to_diff=[
(ph.inFile("random_var9.vcf"), ph.outFile("random_var9.vcf"), transforms),
(ph.inFile("random_var9.vcf.stderr"), ph.outFile("random_var9.vcf.stderr"), transforms),
(ph.inFile("random_var9.vcf.stdout"), ph.outFile("random_var9.vcf.stdout"), transforms),
],
)
conf_list.append(conf)
# ============================================================
# Test mason_materializer
# ============================================================
# Without methylation levels.
conf = app_tests.TestConf(
program=path_to_materializer,
args=[
"-ir",
ph.inFile("random.fasta"),
"-iv",
ph.inFile("random_var1.vcf"),
"-o",
ph.outFile("materializer.random_var1.fasta"),
],
redir_stdout=ph.outFile("materializer.random_var1.stdout"),
redir_stderr=ph.outFile("materializer.random_var1.stderr"),
to_diff=[
(ph.inFile("random_var1.fasta"), ph.outFile("materializer.random_var1.fasta")),
(ph.inFile("materializer.random_var1.stdout"), ph.outFile("materializer.random_var1.stdout"), transforms),
(ph.inFile("materializer.random_var1.stderr"), ph.outFile("materializer.random_var1.stderr"), transforms),
],
)
conf_list.append(conf)
# With methylation levels.
conf = app_tests.TestConf(
program=path_to_materializer,
args=[
"-ir",
ph.inFile("random.fasta"),
"-iv",
ph.inFile("random_var2.vcf"),
"-o",
ph.outFile("materializer.random_var2.fasta"),
"--meth-fasta-in",
ph.inFile("random_meth1.fasta"),
"--meth-fasta-out",
ph.outFile("materializer.random_meth2.fasta"),
],
redir_stdout=ph.outFile("materializer.random_var2.stdout"),
redir_stderr=ph.outFile("materializer.random_var2.stderr"),
to_diff=[
(ph.inFile("random_var1.fasta"), ph.outFile("materializer.random_var1.fasta")),
(ph.inFile("random_var2_meth.fasta"), ph.outFile("materializer.random_meth2.fasta"), transforms),
(ph.inFile("materializer.random_var2.stdout"), ph.outFile("materializer.random_var2.stdout"), transforms),
(ph.inFile("materializer.random_var2.stderr"), ph.outFile("materializer.random_var2.stderr"), transforms),
],
)
conf_list.append(conf)
# ============================================================
# Test mason_simulator
# ============================================================
# Illumina Model
conf = app_tests.TestConf(
program=path_to_simulator,
args=[
"-n",
"1000",
"-ir",
ph.inFile("random.fasta"),
"-o",
ph.outFile("simulator.left1.fq"),
"-or",
ph.outFile("simulator.right1.fq"),
"-oa",
ph.outFile("simulator.out1.sam"),
],
redir_stdout=ph.outFile("simulator.out1.stdout"),
redir_stderr=ph.outFile("simulator.out1.stderr"),
to_diff=[
(ph.inFile("simulator.left1.fq"), ph.outFile("simulator.left1.fq")),
(ph.inFile("simulator.right1.fq"), ph.outFile("simulator.right1.fq")),
(ph.inFile("simulator.out1.sam"), ph.outFile("simulator.out1.sam")),
(ph.inFile("simulator.out1.stdout"), ph.outFile("simulator.out1.stdout"), transforms),
(ph.inFile("simulator.out1.stderr"), ph.outFile("simulator.out1.stderr"), transforms),
],
)
conf_list.append(conf)
conf = app_tests.TestConf(
program=path_to_simulator,
args=[
"-n",
"1000",
"-ir",
ph.inFile("random.fasta"),
"-iv",
ph.inFile("random_var1.vcf"),
"-o",
ph.outFile("simulator.left2.fq"),
"-or",
ph.outFile("simulator.right2.fq"),
"-oa",
ph.outFile("simulator.out2.sam"),
],
redir_stdout=ph.outFile("simulator.out2.stdout"),
redir_stderr=ph.outFile("simulator.out2.stderr"),
to_diff=[
(ph.inFile("simulator.left2.fq"), ph.outFile("simulator.left2.fq")),
(ph.inFile("simulator.right2.fq"), ph.outFile("simulator.right2.fq")),
(ph.inFile("simulator.out2.sam"), ph.outFile("simulator.out2.sam")),
(ph.inFile("simulator.out2.stdout"), ph.outFile("simulator.out2.stdout"), transforms),
(ph.inFile("simulator.out2.stderr"), ph.outFile("simulator.out2.stderr"), transforms),
],
)
conf_list.append(conf)
conf = app_tests.TestConf(
program=path_to_simulator,
args=[
"-n",
"1000",
"-ir",
ph.inFile("random.fasta"),
"-o",
ph.outFile("simulator.left3.fa"),
"-or",
ph.outFile("simulator.right3.fa"),
],
redir_stdout=ph.outFile("simulator.out3.stdout"),
redir_stderr=ph.outFile("simulator.out3.stderr"),
to_diff=[
(ph.inFile("simulator.left3.fa"), ph.outFile("simulator.left3.fa")),
(ph.inFile("simulator.right3.fa"), ph.outFile("simulator.right3.fa")),
(ph.inFile("simulator.out3.stdout"), ph.outFile("simulator.out3.stdout"), transforms),
(ph.inFile("simulator.out3.stderr"), ph.outFile("simulator.out3.stderr"), transforms),
],
)
conf_list.append(conf)
conf = app_tests.TestConf(
program=path_to_simulator,
args=[
"-n",
"1000",
"-ir",
ph.inFile("random.fasta"),
"-iv",
ph.inFile("random_var1.vcf"),
"-o",
ph.outFile("simulator.left7.fa"),
"-oa",
ph.outFile("simulator.out7.sam"),
],
redir_stdout=ph.outFile("simulator.out7.stdout"),
redir_stderr=ph.outFile("simulator.out7.stderr"),
to_diff=[
(ph.inFile("simulator.left7.fa"), ph.outFile("simulator.left7.fa")),
(ph.inFile("simulator.out7.sam"), ph.outFile("simulator.out7.sam")),
(ph.inFile("simulator.out7.stdout"), ph.outFile("simulator.out7.stdout"), transforms),
(ph.inFile("simulator.out7.stderr"), ph.outFile("simulator.out7.stderr"), transforms),
],
)
conf_list.append(conf)
conf = app_tests.TestConf(
program=path_to_simulator,
args=[
"-n",
"1000",
"-ir",
ph.inFile("random.fasta"),
"-o",
ph.outFile("simulator.left4.fa"),
"-oa",
ph.outFile("simulator.out4.sam"),
],
redir_stdout=ph.outFile("simulator.out4.stdout"),
redir_stderr=ph.outFile("simulator.out4.stderr"),
to_diff=[
(ph.inFile("simulator.left4.fa"), ph.outFile("simulator.left4.fa")),
(ph.inFile("simulator.out4.sam"), ph.outFile("simulator.out4.sam")),
(ph.inFile("simulator.out4.stdout"), ph.outFile("simulator.out4.stdout"), transforms),
(ph.inFile("simulator.out4.stderr"), ph.outFile("simulator.out4.stderr"), transforms),
],
)
conf_list.append(conf)
conf = app_tests.TestConf(
program=path_to_simulator,
args=[
"-n",
"1000",
"-ir",
ph.inFile("random.fasta"),
"--meth-fasta-in",
ph.inFile("random_meth1.fasta"),
"--methylation-levels",
"--enable-bs-seq",
"-o",
ph.outFile("simulator.left5.fq"),
"-or",
ph.outFile("simulator.right5.fq"),
],
redir_stdout=ph.outFile("simulator.out5.stdout"),
redir_stderr=ph.outFile("simulator.out5.stderr"),
to_diff=[
(ph.inFile("simulator.left5.fq"), ph.outFile("simulator.left5.fq")),
(ph.inFile("simulator.right5.fq"), ph.outFile("simulator.right5.fq")),
(ph.inFile("simulator.out5.stdout"), ph.outFile("simulator.out5.stdout"), transforms),
(ph.inFile("simulator.out5.stderr"), ph.outFile("simulator.out5.stderr"), transforms),
],
)
conf_list.append(conf)
conf = app_tests.TestConf(
program=path_to_simulator,
args=[
"-n",
"1000",
"-ir",
ph.inFile("random.fasta"),
"-iv",
ph.inFile("random_var1.vcf"),
"--meth-fasta-in",
ph.inFile("random_meth1.fasta"),
"--methylation-levels",
"--enable-bs-seq",
"-o",
ph.outFile("simulator.left6.fq"),
"-or",
ph.outFile("simulator.right6.fq"),
],
redir_stdout=ph.outFile("simulator.out6.stdout"),
redir_stderr=ph.outFile("simulator.out6.stderr"),
to_diff=[
(ph.inFile("simulator.left6.fq"), ph.outFile("simulator.left6.fq")),
(ph.inFile("simulator.right6.fq"), ph.outFile("simulator.right6.fq")),
(ph.inFile("simulator.out6.stdout"), ph.outFile("simulator.out6.stdout"), transforms),
(ph.inFile("simulator.out6.stderr"), ph.outFile("simulator.out6.stderr"), transforms),
],
)
conf_list.append(conf)
# 454 Model
conf = app_tests.TestConf(
program=path_to_simulator,
args=[
"--seq-technology",
"454",
"--fragment-mean-size",
"800",
"--454-read-length-mean",
"200",
"--454-read-length-stddev",
"20",
"-n",
"1000",
"-v",
"-ir",
ph.inFile("random.fasta"),
"-o",
ph.outFile("simulator.left8.fq"),
"-oa",
ph.outFile("simulator.out8.sam"),
],
redir_stdout=ph.outFile("simulator.out8.stdout"),
redir_stderr=ph.outFile("simulator.out8.stderr"),
to_diff=[
(ph.inFile("simulator.left8.fq"), ph.outFile("simulator.left8.fq")),
(ph.inFile("simulator.out8.sam"), ph.outFile("simulator.out8.sam")),
(ph.inFile("simulator.out8.stdout"), ph.outFile("simulator.out8.stdout"), transforms),
(ph.inFile("simulator.out8.stderr"), ph.outFile("simulator.out8.stderr"), transforms),
],
)
conf_list.append(conf)
# Execute the tests.
failures = 0
for conf in conf_list:
res = app_tests.runTest(conf)
# Output to the user.
print " ".join([os.path.basename(conf.program)] + conf.args),
if res:
print "OK"
else:
failures += 1
print "FAILED"
# Cleanup.
ph.deleteTempDir()
print "=============================="
print " total tests: %d" % len(conf_list)
print " failed tests: %d" % failures
print "successful tests: %d" % (len(conf_list) - failures)
print "=============================="
# Compute and return return code.
return failures != 0
def main(source_base, binary_base):
"""Main entry point of the script."""
print 'Executing test for Yara'
print '=============================='
print
ph = app_tests.TestPathHelper(
source_base, binary_base,
'apps/yara/tests') # tests dir
# ============================================================
# Auto-detect the binary path.
# ============================================================
path_to_indexer = app_tests.autolocateBinary(
binary_base, 'bin', 'yara_indexer')
path_to_mapper = app_tests.autolocateBinary(
binary_base, 'bin', 'yara_mapper')
# ============================================================
# Built TestConf list.
# ============================================================
# Build list with TestConf objects, analoguely to how the output
# was generated in generate_outputs.sh.
conf_list = []
# ============================================================
# Run Indexer Tests
# ============================================================
for organism in ['adeno']:
# Get file extensions for the fm index files
exts = [os.path.basename(fname).split('.', 1)[-1]
for fname in glob.glob(ph.inFile('gold/%s-genome.*' % organism))]
conf = app_tests.TestConf(
program=path_to_indexer,
args=[ph.inFile('input/%s-genome.fa' % organism),
'-o', ph.outFile('%s-genome' % organism)],
to_diff=[(ph.inFile('gold/%s-genome.%s' % (organism, ext)),
ph.outFile('%s-genome.%s' % (organism, ext)), 'md5') for ext in exts])
conf_list.append(conf)
# ============================================================
# Run Single-End Mapper Tests
# ============================================================
# mapper_args = [
# ['--threads', '1' ]],
# ['--threads', '8' ]
# ]
# mapper_suffix = ['t1', 't8']
mapper_args = [[]]
mapper_suffix = ['t1']
for organism in ['adeno']:
for i in range(0, len(mapper_args)):
conf = app_tests.TestConf(
program=path_to_mapper,
args=[ph.inFile('gold/%s-genome' % organism),
ph.inFile('input/%s-reads_1.fa' % organism),
'-o', ph.outFile('%s-reads_1.%s.sam' % (organism, mapper_suffix[i]))] +
mapper_args[i],
to_diff=[(ph.inFile('gold/%s-reads_1.%s.sam' % (organism, mapper_suffix[i])),
ph.outFile('%s-reads_1.%s.sam' % (organism, mapper_suffix[i])),
sam_transforms)])
conf_list.append(conf)
# ============================================================
# Execute the tests
# ============================================================
failures = 0
for conf in conf_list:
res = app_tests.runTest(conf)
# Output to the user.
print ' '.join([conf.program] + conf.args),
if res:
print 'OK'
else:
failures += 1
print 'FAILED'
# Cleanup.
ph.deleteTempDir()
print '=============================='
print ' total tests: %d' % len(conf_list)
print ' failed tests: %d' % failures
print 'successful tests: %d' % (len(conf_list) - failures)
print '=============================='
# Compute and return return code.
return failures != 0
def main(source_base, binary_base):
"""Main entry point of the script."""
print 'Executing test for gustaf'
print '==============================='
print
ph = app_tests.TestPathHelper(source_base, binary_base,
'extras/apps/gustaf/tests') # tests dir
# ============================================================
# Auto-detect the binary path.
# ============================================================
path_to_program = app_tests.autolocateBinary(binary_base, 'bin', 'gustaf')
# ============================================================
# Built TestConf list.
# ============================================================
# Build list with TestConf objects, analoguely to how the output
# was generated in generate_outputs.sh.
conf_list = []
# We prepare a list of transforms to apply to the output files. This is
# used to strip the input/output paths from the programs' output to
# make it more canonical and host independent.
ph.outFile('-') # To ensure that the out path is set.
transforms = [
app_tests.ReplaceTransform(
os.path.join(ph.source_base_path, 'extras/apps/gustaf/tests') +
os.sep,
'',
right=True),
app_tests.ReplaceTransform(ph.temp_dir + os.sep, '', right=True),
app_tests.NormalizeScientificExponentsTransform(),
]
# ============================================================
# Adeno Tests
# ============================================================
# ============================================================
# Sanity check with default values and empty output file
# ============================================================
conf = app_tests.TestConf(program=path_to_program,
redir_stdout=ph.outFile('st2_l100.stdout'),
redir_stderr=ph.outFile('st2_l100.stderr'),
args=[
ph.inFile('adeno.fa'),
ph.inFile('adeno_modified_reads.fa'),
'-gff',
ph.outFile('st2_l100.gff'),
'-vcf',
ph.outFile('st2_l100.vcf'),
],
to_diff=[(ph.inFile('st2_l100.vcf'),
ph.outFile('st2_l100.vcf'),
transforms),
(ph.inFile('st2_l100.gff'),
ph.outFile('st2_l100.gff'))])
conf_list.append(conf)
#out="st2_l100"
#${GUSTAF} adeno.fa adeno_modified_reads.fa -gff ${out}.gff -vcf ${out}.vcf > ${out}.stdout 2> ${out}.stderr
# ============================================================
# -st 1 -l 30
# ============================================================
conf = app_tests.TestConf(program=path_to_program,
redir_stdout=ph.outFile('st1_l30.stdout'),
redir_stderr=ph.outFile('st1_l30.stderr'),
args=[
ph.inFile('adeno.fa'),
ph.inFile('adeno_modified_reads.fa'),
'-gff',
ph.outFile('st1_l30.gff'),
'-vcf',
ph.outFile('st1_l30.vcf'),
'-st',
str(1),
'-l',
str(30),
],
to_diff=[(ph.inFile('st1_l30.vcf'),
ph.outFile('st1_l30.vcf'), transforms),
(ph.inFile('st1_l30.gff'),
ph.outFile('st1_l30.gff'))])
conf_list.append(conf)
#out="st1_l30"
#${GUSTAF} adeno.fa adeno_modified_reads.fa -st 1 -l 30 -gff ${out}.gff -vcf ${out}.vcf > ${out}.stdout 2> ${out}.stderr
# ============================================================
# -st 1 -m stellar.gff
# ============================================================
conf = app_tests.TestConf(program=path_to_program,
redir_stdout=ph.outFile('st1_l30_m.stdout'),
redir_stderr=ph.outFile('st1_l30_m.stderr'),
args=[
ph.inFile('adeno.fa'),
ph.inFile('adeno_modified_reads.fa'),
'-m',
ph.inFile('stellar.gff'),
'-gff',
ph.outFile('st1_l30_m.gff'),
'-vcf',
ph.outFile('st1_l30_m.vcf'),
'-st',
str(1),
],
to_diff=[(ph.inFile('st1_l30_m.vcf'),
ph.outFile('st1_l30_m.vcf'),
transforms),
(ph.inFile('st1_l30_m.gff'),
ph.outFile('st1_l30_m.gff'))])
conf_list.append(conf)
#out="st1_l30_m"
#${GUSTAF} adeno.fa adeno_modified_reads.fa -st 1 -m stellar.gff -gff ${out}.gff -vcf ${out}.vcf > ${out}.stdout 2> ${out}.stderr
# ============================================================
# -st 1 -l 30 -ith 5
# ============================================================
conf = app_tests.TestConf(program=path_to_program,
redir_stdout=ph.outFile('st1_l30_ith5.stdout'),
redir_stderr=ph.outFile('st1_l30_ith5.stderr'),
args=[
ph.inFile('adeno.fa'),
ph.inFile('adeno_modified_reads.fa'),
'-gff',
ph.outFile('st1_l30_ith5.gff'),
'-vcf',
ph.outFile('st1_l30_ith5.vcf'),
'-st',
str(1),
'-l',
str(30),
'-ith',
str(5),
],
to_diff=[(ph.inFile('st1_l30_m.vcf'),
ph.outFile('st1_l30_m.vcf'),
transforms),
(ph.inFile('st1_l30_ith5.gff'),
ph.outFile('st1_l30_ith5.gff'))])
conf_list.append(conf)
#out="st1_l30_ith5"
#${GUSTAF} adeno.fa adeno_modified_reads.fa -st 1 -l 30 -ith 5 -gff ${out}.gff -vcf ${out}.vcf > ${out}.stdout 2> ${out}.stderr
# ============================================================
# -st 1 -l 30 -gth 3
# ============================================================
conf = app_tests.TestConf(program=path_to_program,
redir_stdout=ph.outFile('st1_l30_gth3.stdout'),
redir_stderr=ph.outFile('st1_l30_gth3.stderr'),
args=[
ph.inFile('adeno.fa'),
ph.inFile('adeno_modified_reads.fa'),
'-gff',
ph.outFile('st1_l30_gth3.gff'),
'-vcf',
ph.outFile('st1_l30_gth3.vcf'),
'-st',
str(1),
'-l',
str(30),
'-gth',
str(3),
],
to_diff=[(ph.inFile('st1_l30_m.vcf'),
ph.outFile('st1_l30_m.vcf'),
transforms),
(ph.inFile('st1_l30_gth3.gff'),
ph.outFile('st1_l30_gth3.gff'))])
conf_list.append(conf)
#out="st1_l30_gth3"
#${GUSTAF} adeno.fa adeno_modified_reads.fa -st 1 -l 30 -gth 3 -gff ${out}.gff -vcf ${out}.vcf > ${out}.stdout 2> ${out}.stderr
# ============================================================
# Execute the tests.
# ============================================================
failures = 0
for conf in conf_list:
res = app_tests.runTest(conf)
# Output to the user.
print ' '.join(['gustaf'] + conf.args),
if res:
print 'OK'
else:
failures += 1
print 'FAILED'
# Cleanup.
ph.deleteTempDir()
print '=============================='
print ' total tests: %d' % len(conf_list)
print ' failed tests: %d' % failures
print 'successful tests: %d' % (len(conf_list) - failures)
print '=============================='
# Compute and return return code.
return failures != 0
def main(source_base, binary_base):
"""Main entry point of the script."""
print 'Executing test for snp_store'
print '========================='
print
ph = app_tests.TestPathHelper(
source_base, binary_base,
'core/apps/snp_store/tests') # tests dir
# ============================================================
# Auto-detect the binary path.
# ============================================================
path_to_program = app_tests.autolocateBinary(
binary_base, 'core/apps/snp_store', 'snp_store')
# ============================================================
# Built TestConf list.
# ============================================================
# Build list with TestConf objects, analoguely to how the output
# was generated in generate_outputs.sh.
conf_list = []
# ============================================================
# First Section.
# ============================================================
# App TestConf objects to conf_list, just like this for each
# test you want to run.
# default
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('snp_store_default.stdout'),
args=[ph.inFile('human-chr22-inf2.fa'),
ph.inFile('human-reads2.gff'),
'-id', ph.outFile('indels_default.out'),
'-o', ph.outFile('snps_default.out')],
to_diff=[(ph.inFile('snp_store_default.stdout'),
ph.outFile('snp_store_default.stdout')),
# (ph.inFile('snps_default.out'),
# ph.outFile('snps_default.out')),
(ph.inFile('indels_default.out'),
ph.outFile('indels_default.out'))])
conf_list.append(conf)
# test 2
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('snp_store_realign.stdout'),
args=[ph.inFile('human-chr22-inf2.fa'),
ph.inFile('human-reads2.sam'),
'-re', '-if', str(1),
'-id', ph.outFile('indels_realign.out'),
'-o', ph.outFile('snps_realign.out')],
to_diff=[(ph.inFile('snp_store_realign.stdout'),
ph.outFile('snp_store_realign.stdout')),
# (ph.inFile('snps_realign.out'),
# ph.outFile('snps_realign.out')),
(ph.inFile('indels_realign.out'),
ph.outFile('indels_realign.out'))])
conf_list.append(conf)
# test 3
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('snp_store_realign_m0mp1oa.stdout'),
args=[ph.inFile('human-chr22-inf2.fa'),
ph.inFile('human-reads2.sam'),
'-re', '-if', str(1), '-oa', '-hq', '-it', str(1), '-mp', str(1), '-m', str(1),
'-id', ph.outFile('indels_realign_m0mp1oa.out'),
'-o', ph.outFile('snps_realign_m0mp1oa.out')],
to_diff=[(ph.inFile('snp_store_realign_m0mp1oa.stdout'),
ph.outFile('snp_store_realign_m0mp1oa.stdout')),
# (ph.inFile('snps_realign_m0mp1oa.out'),
# ph.outFile('snps_realign_m0mp1oa.out')),
(ph.inFile('indels_realign_m0mp1oa.out'),
ph.outFile('indels_realign_m0mp1oa.out'))])
conf_list.append(conf)
# ============================================================
# Execute the tests.
# ============================================================
failures = 0
for conf in conf_list:
res = app_tests.runTest(conf)
# Output to the user.
print ' '.join(['snp_store'] + conf.args),
if res:
print 'OK'
else:
failures += 1
print 'FAILED'
# Cleanup.
ph.deleteTempDir()
print '=============================='
print ' total tests: %d' % len(conf_list)
print ' failed tests: %d' % failures
print 'successful tests: %d' % (len(conf_list) - failures)
print '=============================='
# Compute and return return code.
return failures != 0
def main(source_base, binary_base):
"""Main entry point of the script."""
print 'Executing test for dfi'
print '======================'
print
ph = app_tests.TestPathHelper(
source_base, binary_base,
'apps/dfi/tests') # tests dir
# ============================================================
# Auto-detect the binary path.
# ============================================================
path_to_program = app_tests.autolocateBinary(
binary_base, 'apps/dfi', 'dfi')
# ============================================================
# Built TestConf list.
# ============================================================
# Build list with TestConf objects, analoguely to how the output
# was generated in generate_outputs.sh.
conf_list = []
paramsFile = open(ph.inFile("params.txt"), "r")
# unzip datasets into test directory
unzip_file_into_dir(ph.inFile("datasets.zip"), ph.outFile('', 'datasets'))
unzip_file_into_dir(ph.inFile("results.zip"), ph.outFile('', 'expected'))
# We run the following for all read lengths we have reads for.
for paramLine in paramsFile.readlines():
params = paramLine.split();
# Run with options parsed from params file.
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile(params[0]),
args=[ph.outFile(params[1], 'datasets'),
ph.outFile(params[2], 'datasets')] + params[3:],
to_diff=[(ph.outFile(params[0], 'expected'),
ph.outFile(params[0]))])
conf_list.append(conf)
# Execute the tests.
failures = 0
for conf in conf_list:
res = app_tests.runTest(conf)
# Output to the user.
print ' '.join(['dfi'] + conf.args),
if res:
print 'OK'
else:
failures += 1
print 'FAILED'
# Cleanup.
ph.deleteTempDir()
print '=============================='
print ' total tests: %d' % len(conf_list)
print ' failed tests: %d' % failures
print 'successful tests: %d' % (len(conf_list) - failures)
print '=============================='
# Compute and return return code.
return failures != 0
def main(source_base, binary_base):
"""Main entry point of the script."""
print 'Executing test for sam2matrix'
print '============================='
print
ph = app_tests.TestPathHelper(
source_base, binary_base,
'apps/sam2matrix/tests') # tests dir
# ============================================================
# Auto-detect the binary path.
# ============================================================
path_to_program = app_tests.autolocateBinary(
binary_base, 'apps/sam2matrix', 'sam2matrix')
# ============================================================
# Built TestConf list.
# ============================================================
# Build list with TestConf objects, analoguely to how the output
# was generated in generate_outputs.sh.
conf_list = []
# ============================================================
# First Section.
# ============================================================
# App TestConf objects to conf_list, just like this for each
# test you want to run.
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('out.stdout'),
args=['-m', ph.inFile('ecoli.sam'), '-m', ph.inFile('ehec.sam'), '-r',
ph.inFile('ecoli_0.50_ehec_0.50.fq'), '-rf', 'ecoli.fa', '-rf',
'ehec.fa', '-o', ph.outFile('test_sam2matrix.tsv')],
to_diff=[(ph.inFile('out.stdout'),
ph.outFile('out.stdout')),
(ph.inFile('gold.tsv'),
ph.outFile('test_sam2matrix.tsv'))])
conf_list.append(conf)
# ============================================================
# Execute the tests.
# ============================================================
failures = 0
for conf in conf_list:
res = app_tests.runTest(conf)
# Output to the user.
print ' '.join(['sam2matrix'] + conf.args),
if res:
print 'OK'
else:
failures += 1
print 'FAILED'
# Cleanup.
ph.deleteTempDir()
print '=============================='
print ' total tests: %d' % len(conf_list)
print ' failed tests: %d' % failures
print 'successful tests: %d' % (len(conf_list) - failures)
print '=============================='
# Compute and return return code.
return failures != 0
def main(source_base, binary_base):
"""Main entry point of the script."""
print 'Executing test for bs_tools'
print '========================='
print
##############################################################
### Casbar
##############################################################
ph = app_tests.TestPathHelper(
source_base, binary_base,
'apps/bs_tools/tests') # tests dir
# ============================================================
# Auto-detect the binary path.
# ============================================================
path_to_bisar = app_tests.autolocateBinary(
binary_base, 'apps/bs_tools', 'bisar')
path_to_casbar = app_tests.autolocateBinary(
binary_base, 'apps/bs_tools', 'casbar')
# ============================================================
# Built TestConf list.
# ============================================================
# Build list with TestConf objects, analoguely to how the output
# was generated in generate_outputs.sh.
conf_list = []
ph.outFile('-') # To ensure that the out path is set.
transforms = [
app_tests.ReplaceTransform(os.path.join(ph.source_base_path, 'apps/bs_tools/tests') + os.sep, '', right=True),
app_tests.ReplaceTransform(ph.temp_dir + os.sep, '', right=True),
app_tests.RegexpReplaceTransform(r'\tVN:[^\t]*', r'\tVN:VERSION', right=True, left=True)
]
# We prepare a list of transforms to apply to the output files. This is
# used to strip the input/output paths from the programs' output to
# make it more canonical and host independent.
# Transforms for SAM output format only. Make VN field of @PG header canonical.
#sam_transforms = [app_tests.RegexpReplaceTransform(r'\tVN:[^\t]*', r'\tVN:VERSION', right=True, left=True)]
# ============================================================
# se
# ============================================================
# App TestConf objects to conf_list, just like this for each
# test you want to run.
# 0
conf = app_tests.TestConf(
program=path_to_bisar,
redir_stdout=ph.outFile('other.stdout'),
args=['-e3', str(4), '-e4', str(5),
#-e3 4 -e4 5
'-o', ph.outFile('reads_se_N6000_0.CT_GA.verified.sam'),
ph.inFile('reads_se_N6000.CT_GA.sam'),
ph.inFile('hg18_chr21_3000.fa'),
ph.inFile('reads_se_N6000.fastq')],
to_diff=[#(ph.inFile('STDOUT_FILE'),
#ph.outFile('STDOUT_FILE')),
(ph.inFile('reads_se_N6000_0.CT_GA.verified.sam'),
ph.outFile('reads_se_N6000_0.CT_GA.verified.sam'),
transforms)])
conf_list.append(conf)
# 1
conf = app_tests.TestConf(
program=path_to_bisar,
redir_stdout=ph.outFile('other.stdout'),
args=['-gas', str(-4.5), '-ges', str(-2.0), '-der', str(0.001), '-bsc', str(0.99), '-gmr', str(0.5), '-i', str(0.8), '-rn', str(0.001), '-pms', str(0.9), '-e3', str(4), '-e4', str(5),
# -gas -4.5 -ges -2.0 -der 0.001 -bsc 0.99 -gmr 0.5 -i 0.8 -rn 0.001 -pms 0.9 -mq 0 -e3 4 -e4 5
'-o', ph.outFile('reads_se_N6000_1.CT_GA.verified.sam'),
ph.inFile('reads_se_N6000.CT_GA.sam'),
ph.inFile('hg18_chr21_3000.fa'),
ph.inFile('reads_se_N6000.fastq')],
to_diff=[#(ph.inFile('STDOUT_FILE'),
#ph.outFile('STDOUT_FILE')),
(ph.inFile('reads_se_N6000_1.CT_GA.verified.sam'),
ph.outFile('reads_se_N6000_1.CT_GA.verified.sam'),
transforms)])
conf_list.append(conf)
# 2
conf = app_tests.TestConf(
program=path_to_bisar,
redir_stdout=ph.outFile('other.stdout'),
args=['-nse', '-nsi', '-nsd', '-gas', str(-4.5), '-ges', str(-2.0), '-der', str(0.001), '-bsc', str(0.99), '-gmr', str(0.5), '-i', str(0.8), '-rn', str(0.001), '-pms', str(0.9), '-e3', str(4), '-e4', str(5),
# -nse -nsi -nsd -gas -4.5 -ges -2.0 -der 0.001 -bsc 0.99 -gmr 0.5 -i 0.8 -rn 0.001 -pms 0.9 -mq 0 -e3 4 -e4 5
'-o', ph.outFile('reads_se_N6000_2.CT_GA.verified.sam'),
ph.inFile('reads_se_N6000.CT_GA.sam'),
ph.inFile('hg18_chr21_3000.fa'),
ph.inFile('reads_se_N6000.fastq')],
to_diff=[(ph.inFile('reads_se_N6000_2.CT_GA.verified.sam'),
ph.outFile('reads_se_N6000_2.CT_GA.verified.sam'),
transforms)])
conf_list.append(conf)
# 3
conf = app_tests.TestConf(
program=path_to_bisar,
redir_stdout=ph.outFile('other.stdout'),
args=['-nse', '-nsi', '-nsd', '-gas', str(-4.5), '-ges', str(-2.0), '-der', str(0.001), '-bsc', str(0.99), '-gmr', str(0.2), '-i', str(0.8), '-rn', str(0.001), '-pms', str(0.9), '-e3', str(4), '-e4', str(5),
# -nse -nsi -nsd -gas -4.5 -ges -2.0 -der 0.001 -bsc 0.99 -gmr 0.2 -i 0.8 -rn 0.001 -pms 0.9 -mq 0 -e3 4 -e4 5
'-o', ph.outFile('reads_se_N6000_3.CT_GA.verified.sam'),
ph.inFile('reads_se_N6000.CT_GA.sam'),
ph.inFile('hg18_chr21_3000.fa'),
ph.inFile('reads_se_N6000.fastq')],
to_diff=[(ph.inFile('reads_se_N6000_3.CT_GA.verified.sam'),
ph.outFile('reads_se_N6000_3.CT_GA.verified.sam'),
transforms)])
conf_list.append(conf)
# 4
conf = app_tests.TestConf(
program=path_to_bisar,
redir_stdout=ph.outFile('other.stdout'),
args=['-nse', '-nsi', '-nsd', '-gas', str(-4.5), '-ges', str(-2.0), '-der', str(0.001), '-bsc', str(0.99), '-gmr', str(0.8), '-i', str(0.8), '-rn', str(0.001), '-pms', str(0.9), '-e3', str(4), '-e4', str(5),
# -nse -nsi -nsd -gas -4.5 -ges -2.0 -der 0.001 -bsc 0.99 -gmr 0.8 -i 0.8 -rn 0.001 -pms 0.9 -mq 0 -e3 4 -e4 5
'-o', ph.outFile('reads_se_N6000_4.CT_GA.verified.sam'),
ph.inFile('reads_se_N6000.CT_GA.sam'),
ph.inFile('hg18_chr21_3000.fa'),
ph.inFile('reads_se_N6000.fastq')],
to_diff=[(ph.inFile('reads_se_N6000_4.CT_GA.verified.sam'),
ph.outFile('reads_se_N6000_4.CT_GA.verified.sam'),
transforms)])
conf_list.append(conf)
# ============================================================
# pe
# ============================================================
# 0
conf = app_tests.TestConf(
program=path_to_bisar,
redir_stdout=ph.outFile('other.stdout'),
args=['-e3', str(4), '-e4', str(5),
#-e3 4 -e4 5
'-o', ph.outFile('reads_pe_N6000_0.CT_GA.verified.sam'),
ph.inFile('reads_pe_N6000.CT_GA.sam'),
ph.inFile('hg18_chr21_3000.fa'),
ph.inFile('reads_pe_N6000.L.fastq'),
ph.inFile('reads_pe_N6000.R.fastq')],
to_diff=[(ph.inFile('reads_pe_N6000_0.CT_GA.verified.sam'),
ph.outFile('reads_pe_N6000_0.CT_GA.verified.sam'),
transforms)])
conf_list.append(conf)
##############################################################
### Casbar
##############################################################
# 0
conf = app_tests.TestConf(
program=path_to_casbar,
redir_stdout=ph.outFile('other.stdout'),
args=['-nec', '-mc', str(6), '-msc', str(5), '-mpc', str(0.5), '-hes', str(0.005),
'-o', ph.outFile('snps_se_0.vcf'),
'-b', ph.outFile('meths_se_0.bed'),
ph.inFile('hg18_chr21_3000.fa'),
ph.inFile('reads_se_N6000_2.CT_GA.verified.pos_so.sam')],
to_diff=[(ph.inFile('snps_se_0.vcf'),
ph.outFile('snps_se_0.vcf')),
(ph.inFile('meths_se_0.bed'),
ph.outFile('meths_se_0.bed'))])
conf_list.append(conf)
# 1
conf = app_tests.TestConf(
program=path_to_casbar,
redir_stdout=ph.outFile('other.stdout'),
args=['-nec', '-mc', str(2), '-msc', str(3), '-mpc', str(0.5), '-hes', str(0.005),
'-o', ph.outFile('snps_se_1.vcf'),
'-b', ph.outFile('meths_se_1.bed'),
ph.inFile('hg18_chr21_3000.fa'),
ph.inFile('reads_se_N6000_2.CT_GA.verified.pos_so.sam')],
to_diff=[(ph.inFile('snps_se_1.vcf'),
ph.outFile('snps_se_1.vcf')),
(ph.inFile('meths_se_1.bed'),
ph.outFile('meths_se_1.bed'))])
conf_list.append(conf)
# ============================================================
# pe
# ============================================================
# 0
if not (sys.platform.startswith('freebsd') or sys.platform.startswith('win')):
conf = app_tests.TestConf(
program=path_to_casbar,
redir_stdout=ph.outFile('other.stdout'),
args=['-nec', '-mc', str(6), '-msc', str(5), '-mpc', str(0.5), '-hes', str(0.005),
'-o', ph.outFile('snps_pe_0.vcf'),
'-b', ph.outFile('meths_pe_0.bed'),
ph.inFile('hg18_chr21_3000.fa'),
ph.inFile('reads_pe_N6000_0.CT_GA.verified.pos_so.sam')],
to_diff=[(ph.inFile('snps_pe_0.vcf'),
ph.outFile('snps_pe_0.vcf')),
(ph.inFile('meths_pe_0.bed'),
ph.outFile('meths_pe_0.bed'))])
conf_list.append(conf)
else:
print "One test not executed on FreeBSD, because of lower math precision."
# ============================================================
# Execute the tests.
# ============================================================
failures = 0
for conf in conf_list:
# Output to the user.
print ' '.join([os.path.basename(conf.program)] + conf.args)
res = app_tests.runTest(conf)
if res:
print 'OK'
else:
failures += 1
print 'FAILED'
# Cleanup.
ph.deleteTempDir()
print '=============================='
print ' total tests: %d' % len(conf_list)
print ' failed tests: %d' % failures
print 'successful tests: %d' % (len(conf_list) - failures)
print '=============================='
# Compute and return return code.
return failures != 0
def main(source_base, binary_base):
"""Main entry point of the script."""
print 'Executing test for roi_intersect'
print '================================'
print
ph = app_tests.TestPathHelper(source_base, binary_base,
'apps/ngs_roi/tests') # tests dir
# ============================================================
# Auto-detect the binary path.
# ============================================================
path_to_project = app_tests.autolocateBinary(binary_base, 'apps/ngs_roi',
'roi_feature_projection')
path_to_bam2roi = app_tests.autolocateBinary(binary_base, 'apps/ngs_roi',
'bam2roi')
# ============================================================
# Built TestConf list.
# ============================================================
# Build list with TestConf objects, analoguely to how the output
# was generated in generate_outputs.sh.
conf_list = []
# We prepare a list of transforms to apply to the output files. This is
# used to strip the input/output paths from the programs' output to
# make it more canonical and host independent.
ph.outFile('-') # To ensure that the out path is set.
transforms = [
app_tests.ReplaceTransform(
os.path.join(ph.source_base_path, 'apps/ngs_roi/tests') + os.sep,
'',
right=True),
app_tests.ReplaceTransform(ph.temp_dir + os.sep, '', right=True),
]
# ------------------------------------------------------------
# Projection: Intersect with BED or GFF/GTF in BED style.
# ------------------------------------------------------------
for mode in ['projection', 'union', 'difference', 'intersection']:
for fmt in ['bed', 'gff', 'gtf']:
for ss_flag, ss_name in [('-ss', '_ss'), ('', '')]:
conf = app_tests.TestConf(
program=path_to_project,
redir_stderr=ph.outFile('out_small_%s_m%s%s.stderr' %
(fmt, mode, ss_name)),
redir_stdout=ph.outFile('out_small_%s_m%s%s.stdout' %
(fmt, mode, ss_name)),
args=[
'-m', mode, ss_flag, '-ir',
ph.inFile('small.roi'), '-if',
ph.inFile('small.%s' % fmt), '-or',
ph.outFile('out_small_%s_m%s%s.roi' %
(fmt, mode, ss_name))
],
to_diff=[
(ph.inFile('out_small_%s_m%s%s.stderr' %
(fmt, mode, ss_name)),
ph.outFile('out_small_%s_m%s%s.stderr' %
(fmt, mode, ss_name)), transforms),
(ph.inFile('out_small_%s_m%s%s.stdout' %
(fmt, mode, ss_name)),
ph.outFile('out_small_%s_m%s%s.stdout' %
(fmt, mode, ss_name)), transforms),
(ph.inFile('out_small_%s_m%s%s.roi' %
(fmt, mode, ss_name)),
ph.outFile('out_small_%s_m%s%s.roi' %
(fmt, mode, ss_name)), transforms),
])
conf_list.append(conf)
# TODO(holtgrew): Test with projection to transcripts.
# ------------------------------------------------------------
# BAM to ROI Conversion
# ------------------------------------------------------------
conf = app_tests.TestConf(
program=path_to_bam2roi,
redir_stderr=ph.outFile('out_mrna_2l_ss.roi.stderr'),
redir_stdout=ph.outFile('out_mrna_2l_ss.roi.stdout'),
args=[
'--strand-specific', '-if',
ph.inFile('micro_rna_sorted_2l.bam'), '-of',
ph.outFile('out_mrna_2l_ss.roi')
],
to_diff=[(ph.inFile('out_mrna_2l_ss.roi.stderr'),
ph.outFile('out_mrna_2l_ss.roi.stderr'), transforms),
(ph.inFile('out_mrna_2l_ss.roi.stdout'),
ph.outFile('out_mrna_2l_ss.roi.stdout'), transforms),
(ph.inFile('out_mrna_2l_ss.roi'),
ph.outFile('out_mrna_2l_ss.roi'))])
conf_list.append(conf)
conf = app_tests.TestConf(
program=path_to_bam2roi,
redir_stderr=ph.outFile('out_mrna_2l.roi.stderr'),
redir_stdout=ph.outFile('out_mrna_2l.roi.stdout'),
args=[
'-if',
ph.inFile('micro_rna_sorted_2l.bam'), '-of',
ph.outFile('out_mrna_2l.roi')
],
to_diff=[(ph.inFile('out_mrna_2l.roi.stderr'),
ph.outFile('out_mrna_2l.roi.stderr'), transforms),
(ph.inFile('out_mrna_2l.roi.stdout'),
ph.outFile('out_mrna_2l.roi.stdout'), transforms),
(ph.inFile('out_mrna_2l.roi'), ph.outFile('out_mrna_2l.roi'))
])
conf_list.append(conf)
# TODO(holtgrew): Test with paired-end data with/without ignoring pairing.
# Execute the tests.
failures = 0
for conf in conf_list:
res = app_tests.runTest(conf)
# Output to the user.
print ' '.join([os.path.basename(conf.program)] + conf.args),
if res:
print 'OK'
else:
failures += 1
print 'FAILED'
# Cleanup.
ph.deleteTempDir()
print '=============================='
print ' total tests: %d' % len(conf_list)
print ' failed tests: %d' % failures
print 'successful tests: %d' % (len(conf_list) - failures)
print '=============================='
# Compute and return return code.
return failures != 0
def main(source_base, binary_base):
"""Main entry point of the script."""
print 'Executing test for bs_tools'
print '========================='
print
##############################################################
### Casbar
##############################################################
ph = app_tests.TestPathHelper(source_base, binary_base,
'extras/apps/bs_tools/tests') # tests dir
# ============================================================
# Auto-detect the binary path.
# ============================================================
path_to_bisar = app_tests.autolocateBinary(binary_base,
'extras/apps/bs_tools', 'bisar')
path_to_casbar = app_tests.autolocateBinary(binary_base,
'extras/apps/bs_tools',
'casbar')
# ============================================================
# Built TestConf list.
# ============================================================
# Build list with TestConf objects, analoguely to how the output
# was generated in generate_outputs.sh.
conf_list = []
ph.outFile('-') # To ensure that the out path is set.
transforms = [
app_tests.ReplaceTransform(
os.path.join(ph.source_base_path, 'extras/apps/bs_tools/tests') +
os.sep,
'',
right=True),
app_tests.ReplaceTransform(ph.temp_dir + os.sep, '', right=True),
app_tests.RegexpReplaceTransform(r'\tVN:[^\t]*',
r'\tVN:VERSION',
right=True,
left=True)
]
# We prepare a list of transforms to apply to the output files. This is
# used to strip the input/output paths from the programs' output to
# make it more canonical and host independent.
# Transforms for SAM output format only. Make VN field of @PG header canonical.
#sam_transforms = [app_tests.RegexpReplaceTransform(r'\tVN:[^\t]*', r'\tVN:VERSION', right=True, left=True)]
# ============================================================
# se
# ============================================================
# App TestConf objects to conf_list, just like this for each
# test you want to run.
# 0
conf = app_tests.TestConf(
program=path_to_bisar,
redir_stdout=ph.outFile('other.stdout'),
args=[
'-e3',
str(4),
'-e4',
str(5),
#-e3 4 -e4 5
'-o',
ph.outFile('reads_se_N6000_0.CT_GA.verified.sam'),
ph.inFile('reads_se_N6000.CT_GA.sam'),
ph.inFile('hg18_chr21_3000.fa'),
ph.inFile('reads_se_N6000.fastq')
],
to_diff=[ #(ph.inFile('STDOUT_FILE'),
#ph.outFile('STDOUT_FILE')),
(ph.inFile('reads_se_N6000_0.CT_GA.verified.sam'),
ph.outFile('reads_se_N6000_0.CT_GA.verified.sam'), transforms)
])
conf_list.append(conf)
# 1
conf = app_tests.TestConf(
program=path_to_bisar,
redir_stdout=ph.outFile('other.stdout'),
args=[
'-gas',
str(-4.5),
'-ges',
str(-2.0),
'-der',
str(0.001),
'-bsc',
str(0.99),
'-gmr',
str(0.5),
'-i',
str(0.8),
'-rn',
str(0.001),
'-pms',
str(0.9),
'-e3',
str(4),
'-e4',
str(5),
# -gas -4.5 -ges -2.0 -der 0.001 -bsc 0.99 -gmr 0.5 -i 0.8 -rn 0.001 -pms 0.9 -mq 0 -e3 4 -e4 5
'-o',
ph.outFile('reads_se_N6000_1.CT_GA.verified.sam'),
ph.inFile('reads_se_N6000.CT_GA.sam'),
ph.inFile('hg18_chr21_3000.fa'),
ph.inFile('reads_se_N6000.fastq')
],
to_diff=[ #(ph.inFile('STDOUT_FILE'),
#ph.outFile('STDOUT_FILE')),
(ph.inFile('reads_se_N6000_1.CT_GA.verified.sam'),
ph.outFile('reads_se_N6000_1.CT_GA.verified.sam'), transforms)
])
conf_list.append(conf)
# 2
conf = app_tests.TestConf(
program=path_to_bisar,
redir_stdout=ph.outFile('other.stdout'),
args=[
'-nse',
'-nsi',
'-nsd',
'-gas',
str(-4.5),
'-ges',
str(-2.0),
'-der',
str(0.001),
'-bsc',
str(0.99),
'-gmr',
str(0.5),
'-i',
str(0.8),
'-rn',
str(0.001),
'-pms',
str(0.9),
'-e3',
str(4),
'-e4',
str(5),
# -nse -nsi -nsd -gas -4.5 -ges -2.0 -der 0.001 -bsc 0.99 -gmr 0.5 -i 0.8 -rn 0.001 -pms 0.9 -mq 0 -e3 4 -e4 5
'-o',
ph.outFile('reads_se_N6000_2.CT_GA.verified.sam'),
ph.inFile('reads_se_N6000.CT_GA.sam'),
ph.inFile('hg18_chr21_3000.fa'),
ph.inFile('reads_se_N6000.fastq')
],
to_diff=[(ph.inFile('reads_se_N6000_2.CT_GA.verified.sam'),
ph.outFile('reads_se_N6000_2.CT_GA.verified.sam'),
transforms)])
conf_list.append(conf)
# 3
conf = app_tests.TestConf(
program=path_to_bisar,
redir_stdout=ph.outFile('other.stdout'),
args=[
'-nse',
'-nsi',
'-nsd',
'-gas',
str(-4.5),
'-ges',
str(-2.0),
'-der',
str(0.001),
'-bsc',
str(0.99),
'-gmr',
str(0.2),
'-i',
str(0.8),
'-rn',
str(0.001),
'-pms',
str(0.9),
'-e3',
str(4),
'-e4',
str(5),
# -nse -nsi -nsd -gas -4.5 -ges -2.0 -der 0.001 -bsc 0.99 -gmr 0.2 -i 0.8 -rn 0.001 -pms 0.9 -mq 0 -e3 4 -e4 5
'-o',
ph.outFile('reads_se_N6000_3.CT_GA.verified.sam'),
ph.inFile('reads_se_N6000.CT_GA.sam'),
ph.inFile('hg18_chr21_3000.fa'),
ph.inFile('reads_se_N6000.fastq')
],
to_diff=[(ph.inFile('reads_se_N6000_3.CT_GA.verified.sam'),
ph.outFile('reads_se_N6000_3.CT_GA.verified.sam'),
transforms)])
conf_list.append(conf)
# 4
conf = app_tests.TestConf(
program=path_to_bisar,
redir_stdout=ph.outFile('other.stdout'),
args=[
'-nse',
'-nsi',
'-nsd',
'-gas',
str(-4.5),
'-ges',
str(-2.0),
'-der',
str(0.001),
'-bsc',
str(0.99),
'-gmr',
str(0.8),
'-i',
str(0.8),
'-rn',
str(0.001),
'-pms',
str(0.9),
'-e3',
str(4),
'-e4',
str(5),
# -nse -nsi -nsd -gas -4.5 -ges -2.0 -der 0.001 -bsc 0.99 -gmr 0.8 -i 0.8 -rn 0.001 -pms 0.9 -mq 0 -e3 4 -e4 5
'-o',
ph.outFile('reads_se_N6000_4.CT_GA.verified.sam'),
ph.inFile('reads_se_N6000.CT_GA.sam'),
ph.inFile('hg18_chr21_3000.fa'),
ph.inFile('reads_se_N6000.fastq')
],
to_diff=[(ph.inFile('reads_se_N6000_4.CT_GA.verified.sam'),
ph.outFile('reads_se_N6000_4.CT_GA.verified.sam'),
transforms)])
conf_list.append(conf)
# ============================================================
# pe
# ============================================================
# 0
conf = app_tests.TestConf(
program=path_to_bisar,
redir_stdout=ph.outFile('other.stdout'),
args=[
'-e3',
str(4),
'-e4',
str(5),
#-e3 4 -e4 5
'-o',
ph.outFile('reads_pe_N6000_0.CT_GA.verified.sam'),
ph.inFile('reads_pe_N6000.CT_GA.sam'),
ph.inFile('hg18_chr21_3000.fa'),
ph.inFile('reads_pe_N6000.L.fastq'),
ph.inFile('reads_pe_N6000.R.fastq')
],
to_diff=[(ph.inFile('reads_pe_N6000_0.CT_GA.verified.sam'),
ph.outFile('reads_pe_N6000_0.CT_GA.verified.sam'),
transforms)])
conf_list.append(conf)
##############################################################
### Casbar
##############################################################
# 0
conf = app_tests.TestConf(
program=path_to_casbar,
redir_stdout=ph.outFile('other.stdout'),
args=[
'-nec', '-mc',
str(6), '-msc',
str(5), '-mpc',
str(0.5), '-hes',
str(0.005), '-o',
ph.outFile('snps_se_0.vcf'), '-b',
ph.outFile('meths_se_0.bed'),
ph.inFile('hg18_chr21_3000.fa'),
ph.inFile('reads_se_N6000_2.CT_GA.verified.pos_so.sam')
],
to_diff=[(ph.inFile('snps_se_0.vcf'), ph.outFile('snps_se_0.vcf')),
(ph.inFile('meths_se_0.bed'), ph.outFile('meths_se_0.bed'))])
conf_list.append(conf)
# 1
conf = app_tests.TestConf(
program=path_to_casbar,
redir_stdout=ph.outFile('other.stdout'),
args=[
'-nec', '-mc',
str(2), '-msc',
str(3), '-mpc',
str(0.5), '-hes',
str(0.005), '-o',
ph.outFile('snps_se_1.vcf'), '-b',
ph.outFile('meths_se_1.bed'),
ph.inFile('hg18_chr21_3000.fa'),
ph.inFile('reads_se_N6000_2.CT_GA.verified.pos_so.sam')
],
to_diff=[(ph.inFile('snps_se_1.vcf'), ph.outFile('snps_se_1.vcf')),
(ph.inFile('meths_se_1.bed'), ph.outFile('meths_se_1.bed'))])
conf_list.append(conf)
# ============================================================
# pe
# ============================================================
# 0
conf = app_tests.TestConf(
program=path_to_casbar,
redir_stdout=ph.outFile('other.stdout'),
args=[
'-nec', '-mc',
str(6), '-msc',
str(5), '-mpc',
str(0.5), '-hes',
str(0.005), '-o',
ph.outFile('snps_pe_0.vcf'), '-b',
ph.outFile('meths_pe_0.bed'),
ph.inFile('hg18_chr21_3000.fa'),
ph.inFile('reads_pe_N6000_0.CT_GA.verified.pos_so.sam')
],
to_diff=[(ph.inFile('snps_pe_0.vcf'), ph.outFile('snps_pe_0.vcf')),
(ph.inFile('meths_pe_0.bed'), ph.outFile('meths_pe_0.bed'))])
conf_list.append(conf)
# ============================================================
# Execute the tests.
# ============================================================
failures = 0
for conf in conf_list:
res = app_tests.runTest(conf)
# Output to the user.
print ' '.join([os.path.basename(conf.program)] + conf.args),
if res:
print 'OK'
else:
failures += 1
print 'FAILED'
# Cleanup.
ph.deleteTempDir()
print '=============================='
print ' total tests: %d' % len(conf_list)
print ' failed tests: %d' % failures
print 'successful tests: %d' % (len(conf_list) - failures)
print '=============================='
# Compute and return return code.
return failures != 0
def main(source_base, binary_base):
"""Main entry point of the script."""
print 'Executing test for splazers'
print '========================='
print
ph = app_tests.TestPathHelper(
source_base, binary_base,
'apps/splazers/tests') # tests dir
# ============================================================
# Auto-detect the binary path.
# ============================================================
path_to_program = app_tests.autolocateBinary(
binary_base, 'apps/splazers', 'splazers')
# ============================================================
# Built TestConf list.
# ============================================================
# Build list with TestConf objects, analoguely to how the output
# was generated in generate_outputs.sh.
conf_list = []
# ============================================================
# First Section.
# ============================================================
# We run the following for all read lengths we have reads for.
for rl in [100]:
# Run with default options.
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('se-adeno-reads%d_1_default.stdout' % rl),
args=[ph.inFile('adeno-genome.fa'),
ph.inFile('adeno-reads%d_1.fa' % rl),
'-o', ph.outFile('se-adeno-reads%d_1_default.out' % rl)],
to_diff=[(ph.inFile('se-adeno-reads%d_1_default.out' % rl),
ph.outFile('se-adeno-reads%d_1_default.out' % rl)),
(ph.inFile('se-adeno-reads%d_1_default.stdout' % rl),
ph.outFile('se-adeno-reads%d_1_default.stdout' % rl))])
conf_list.append(conf)
# test different min. match lengths
for mml in range(16,26):
# test different numbers of prefix errors
for ep in range(0,2):
# test different numbers of suffix errors
for es in range(0,3):
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('se-adeno-reads%d_1_mml%d_ep%d_es%d.stdout' % (rl, mml, ep, es)),
args=['-sm', str(mml), '-ep', str(ep), '-es', str(es),
ph.inFile('adeno-genome.fa'),
ph.inFile('adeno-reads%d_1.fa' % rl),
'-o', ph.outFile('se-adeno-reads%d_1_mml%d_ep%d_es%d.out' % (rl, mml, ep, es))],
to_diff=[(ph.inFile('se-adeno-reads%d_1_mml%d_ep%d_es%d.out' % (rl, mml, ep, es)),
ph.outFile('se-adeno-reads%d_1_mml%d_ep%d_es%d.out' % (rl, mml, ep, es))),
(ph.inFile('se-adeno-reads%d_1_mml%d_ep%d_es%d.stdout' % (rl, mml, ep, es)),
ph.outFile('se-adeno-reads%d_1_mml%d_ep%d_es%d.stdout' % (rl, mml, ep, es)))])
conf_list.append(conf)
# # Allow indels.
# conf = app_tests.TestConf(
# program=path_to_program,
# redir_stdout=ph.outFile('se-adeno-reads%d_1_mml%d-id_ep%d_es%d.stdout' % (rl, mml, ep, es)),
# args=['-id', '-sm', str(mml), '-ep', str(ep), '-es', str(es),
# ph.inFile('adeno-genome.fa'),
# ph.inFile('adeno-reads%d_1.fa' % rl),
# '-o', ph.outFile('se-adeno-reads%d_1_mml%d-id_ep%d_es%d.out' % (rl, mml, ep, es))],
# to_diff=[(ph.inFile('se-adeno-reads%d_1_mml%d-id_ep%d_es%d.out' % (rl, mml, ep, es)),
# ph.outFile('se-adeno-reads%d_1_mml%d-id_ep%d_es%d.out' % (rl, mml, ep, es))),
# (ph.inFile('se-adeno-reads%d_1_mml%d-id_ep%d_es%d.stdout' % (rl, mml, ep, es)),
# ph.outFile('se-adeno-reads%d_1_mml%d-id_ep%d_es%d.stdout' % (rl, mml, ep, es)))])
# conf_list.append(conf)
# Compute forward/reverse matches only.
for o in ['-r', '-f']:
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('se-adeno-reads%d_1_mml20%s_ep1_es1.stdout' % (rl, o)),
args=[ o, '-id', '-sm', str(20), '-ep', str(1), '-es', str(1),
ph.inFile('adeno-genome.fa'),
ph.inFile('adeno-reads%d_1.fa' % rl),
'-o', ph.outFile('se-adeno-reads%d_1_mml20%s_ep1_es1.out' % (rl, o))],
to_diff=[(ph.inFile('se-adeno-reads%d_1_mml20%s_ep1_es1.out' % (rl, o)),
ph.outFile('se-adeno-reads%d_1_mml20%s_ep1_es1.out' % (rl, o))),
(ph.inFile('se-adeno-reads%d_1_mml20%s_ep1_es1.stdout' % (rl, o)),
ph.outFile('se-adeno-reads%d_1_mml20%s_ep1_es1.stdout' % (rl, o)))])
conf_list.append(conf)
# Compute with different identity rates.
for i in range(90, 100):
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('se-adeno-reads%d_1_mml20-i%d_ep1_es1.stdout' % (rl, i)),
args=['-i', str(i), '-sm', str(20), '-ep', str(1), '-es', str(1),
ph.inFile('adeno-genome.fa'),
ph.inFile('adeno-reads%d_1.fa' % rl),
'-o', ph.outFile('se-adeno-reads%d_1_mml20-i%d_ep1_es1.out' % (rl, i))],
to_diff=[(ph.inFile('se-adeno-reads%d_1_mml20-i%d_ep1_es1.out' % (rl, i)),
ph.outFile('se-adeno-reads%d_1_mml20-i%d_ep1_es1.out' % (rl, i))),
(ph.inFile('se-adeno-reads%d_1_mml20-i%d_ep1_es1.stdout' % (rl, i)),
ph.outFile('se-adeno-reads%d_1_mml20-i%d_ep1_es1.stdout' % (rl, i)))])
conf_list.append(conf)
# Compute with different output formats.
for of in [3, 4]:
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('se-adeno-reads%d_1_mml20-of%d_ep1_es1.stdout' % (rl, of)),
args=['-of', str(of), '-sm', str(20), '-ep', str(1), '-es', str(1),
ph.inFile('adeno-genome.fa'),
ph.inFile('adeno-reads%d_1.fa' % rl),
'-o', ph.outFile('se-adeno-reads%d_1_mml20-of%d_ep1_es1.out' % (rl, of))],
to_diff=[(ph.inFile('se-adeno-reads%d_1_mml20-of%d_ep1_es1.out' % (rl, of)),
ph.outFile('se-adeno-reads%d_1_mml20-of%d_ep1_es1.out' % (rl, of))),
(ph.inFile('se-adeno-reads%d_1_mml20-of%d_ep1_es1.stdout' % (rl, of)),
ph.outFile('se-adeno-reads%d_1_mml20-of%d_ep1_es1.stdout' % (rl, of)))])
conf_list.append(conf)
# Compute with different sort orders.
for so in [0, 1]:
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('se-adeno-reads%d_1_mml20-so%d_ep1_es1.stdout' % (rl, so)),
args=[ '-so', str(so), '-sm', str(20), '-ep', str(1), '-es', str(1),
ph.inFile('adeno-genome.fa'),
ph.inFile('adeno-reads%d_1.fa' % rl),
'-o', ph.outFile('se-adeno-reads%d_1_mml20-so%d_ep1_es1.out' % (rl, so))],
to_diff=[(ph.inFile('se-adeno-reads%d_1_mml20-so%d_ep1_es1.out' % (rl, so)),
ph.outFile('se-adeno-reads%d_1_mml20-so%d_ep1_es1.out' % (rl, so))),
(ph.inFile('se-adeno-reads%d_1_mml20-so%d_ep1_es1.stdout' % (rl, so)),
ph.outFile('se-adeno-reads%d_1_mml20-so%d_ep1_es1.stdout' % (rl, so)))])
conf_list.append(conf)
# Run in default anchored mode
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('anchored_adeno_example%d.stdout' % rl),
args=['-an',
ph.inFile('adeno-genome.fa'),
ph.inFile('adeno-reads-pe.sam'), # % rl),
'-o', ph.outFile('anchored_adeno_example%d.out' % rl),
'-ll', '300', '-le', '90'],
to_diff=[(ph.inFile('anchored_adeno_example%d.out' % rl),
ph.outFile('anchored_adeno_example%d.out' % rl)),
(ph.inFile('anchored_adeno_example%d.stdout' % rl),
ph.outFile('anchored_adeno_example%d.stdout' % rl))])
conf_list.append(conf)
# ============================================================
# Execute the tests.
# ============================================================
failures = 0
for conf in conf_list:
res = app_tests.runTest(conf)
# Output to the user.
print ' '.join(['splazers'] + conf.args),
if res:
print 'OK'
else:
failures += 1
print 'FAILED'
# Cleanup.
ph.deleteTempDir()
print '=============================='
print ' total tests: %d' % len(conf_list)
print ' failed tests: %d' % failures
print 'successful tests: %d' % (len(conf_list) - failures)
print '=============================='
# Compute and return return code.
return failures != 0
def main(source_base, binary_base):
"""Main entry point of the script."""
print 'Executing test for insegt'
print '========================='
print
ph = app_tests.TestPathHelper(source_base, binary_base,
'apps/insegt/tests') # tests dir
# ============================================================
# Auto-detect the binary path.
# ============================================================
path_to_program = app_tests.autolocateBinary(binary_base, 'bin', 'insegt')
# ============================================================
# Built TestConf list.
# ============================================================
# Build list with TestConf objects, analoguely to how the output
# was generated in generate_outputs.sh.
conf_list = []
# ============================================================
# First Section.
# ============================================================
# App TestConf objects to conf_list, just like this for each
# test you want to run.
conf = app_tests.TestConf(program=path_to_program,
args=[
'-ro',
ph.outFile('default_readOutput.gff'), '-ao',
ph.outFile('default_annoOutput.gff'), '-to',
ph.outFile('default_tupleOutput.gff'),
ph.inFile('alignments.sam'),
ph.inFile('annotations.gff')
],
to_diff=[(ph.inFile('default_annoOutput.gff'),
ph.outFile('default_annoOutput.gff')),
(ph.inFile('default_readOutput.gff'),
ph.outFile('default_readOutput.gff')),
(ph.inFile('default_tupleOutput.gff'),
ph.outFile('default_tupleOutput.gff'))
])
conf_list.append(conf)
conf = app_tests.TestConf(
program=path_to_program,
args=[
'-c',
str(2), '-ro',
ph.outFile('threshold-count2_readOutput.gff'), '-ao',
ph.outFile('threshold-count2_annoOutput.gff'), '-to',
ph.outFile('threshold-count2_tupleOutput.gff'),
ph.inFile('alignments.sam'),
ph.inFile('annotations.gff')
],
to_diff=[(ph.inFile('threshold-count2_annoOutput.gff'),
ph.outFile('threshold-count2_annoOutput.gff')),
(ph.inFile('threshold-count2_readOutput.gff'),
ph.outFile('threshold-count2_readOutput.gff')),
(ph.inFile('threshold-count2_tupleOutput.gff'),
ph.outFile('threshold-count2_tupleOutput.gff'))])
conf_list.append(conf)
conf = app_tests.TestConf(program=path_to_program,
args=[
'-n',
str(3), '-ro',
ph.outFile('ntuple3_readOutput.gff'), '-ao',
ph.outFile('ntuple3_annoOutput.gff'), '-to',
ph.outFile('ntuple3_tupleOutput.gff'),
ph.inFile('alignments.sam'),
ph.inFile('annotations.gff')
],
to_diff=[(ph.inFile('ntuple3_annoOutput.gff'),
ph.outFile('ntuple3_annoOutput.gff')),
(ph.inFile('ntuple3_readOutput.gff'),
ph.outFile('ntuple3_readOutput.gff')),
(ph.inFile('ntuple3_tupleOutput.gff'),
ph.outFile('ntuple3_tupleOutput.gff'))
])
conf_list.append(conf)
conf = app_tests.TestConf(program=path_to_program,
args=[
'-m', '-ro',
ph.outFile('max-tuple_readOutput.gff'),
'-ao',
ph.outFile('max-tuple_annoOutput.gff'),
'-to',
ph.outFile('max-tuple_tupleOutput.gff'),
ph.inFile('alignments.sam'),
ph.inFile('annotations.gff')
],
to_diff=[
(ph.inFile('max-tuple_annoOutput.gff'),
ph.outFile('max-tuple_annoOutput.gff')),
(ph.inFile('max-tuple_readOutput.gff'),
ph.outFile('max-tuple_readOutput.gff')),
(ph.inFile('max-tuple_tupleOutput.gff'),
ph.outFile('max-tuple_tupleOutput.gff'))
])
conf_list.append(conf)
conf = app_tests.TestConf(program=path_to_program,
args=[
'-e', '-ro',
ph.outFile('exact-ntuple_readOutput.gff'),
'-ao',
ph.outFile('exact-ntuple_annoOutput.gff'),
'-to',
ph.outFile('exact-ntuple_tupleOutput.gff'),
ph.inFile('alignments.sam'),
ph.inFile('annotations.gff')
],
to_diff=[
(ph.inFile('exact-ntuple_annoOutput.gff'),
ph.outFile('exact-ntuple_annoOutput.gff')),
(ph.inFile('exact-ntuple_readOutput.gff'),
ph.outFile('exact-ntuple_readOutput.gff')),
(ph.inFile('exact-ntuple_tupleOutput.gff'),
ph.outFile('exact-ntuple_tupleOutput.gff'))
])
conf_list.append(conf)
# ============================================================
# Execute the tests.
# ============================================================
failures = 0
for conf in conf_list:
res = app_tests.runTest(conf)
# Output to the user.
print ' '.join(['insegt'] + conf.args),
if res:
print 'OK'
else:
failures += 1
print 'FAILED'
# Cleanup.
ph.deleteTempDir()
print '=============================='
print ' total tests: %d' % len(conf_list)
print ' failed tests: %d' % failures
print 'successful tests: %d' % (len(conf_list) - failures)
print '=============================='
# Compute and return return code.
return failures != 0
def main(source_base, binary_base):
"""Main entry point of the script."""
print 'Executing test for fiona'
print '========================'
print
ph = app_tests.TestPathHelper(
source_base, binary_base,
'apps/fiona/tests') # tests dir
# ============================================================
# Auto-detect the binary path.
# ============================================================
path_to_fiona = app_tests.autolocateBinary(
binary_base, 'apps/fiona', 'fiona')
path_to_fiona_illumina = app_tests.autolocateBinary(
binary_base, 'apps/fiona', 'fiona_illumina')
path_to_compute_gain = app_tests.autolocateBinary(
binary_base, 'apps/fiona', 'compute_gain')
# ============================================================
# Built TestConf list.
# ============================================================
# Build list with TestConf objects, analoguely to how the output
# was generated in generate_outputs.sh.
conf_list = []
# We prepare a list of transforms to apply to the output files. This is
# used to strip the input/output paths from the programs' output to
# make it more canonical and host independent.
ph.outFile('-') # To ensure that the out path is set.
transforms = [
app_tests.ReplaceTransform(
os.path.join(ph.source_base_path,
'apps/fiona/tests') + os.sep,
'', right=True),
app_tests.ReplaceTransform(ph.temp_dir + os.sep, '', right=True),
app_tests.NormalizeScientificExponentsTransform(),
]
# ============================================================
# Run on uniformly random DNA.
# ============================================================
# Note that instead of comparing the results with expected results, we
# use a checker that computes the gain and compares it with a threshold.
# Illumina Mode
for i in [1, 2]:
min_gain = {1: 40.0, 2: 50.0}
conf = app_tests.TestConf(
program=path_to_fiona_illumina,
args=['-nt', '1',
'-i', str(i),
'-g', '10000',
ph.inFile('reads.illumina.fq'),
ph.outFile('reads.illumina.corrected.i%d.fa' % i)],
redir_stdout=ph.outFile('reads.illumina.fq.i%d.stdout' % i),
redir_stderr=ph.outFile('reads.illumina.fq.i%d.stderr' % i),
check_callback=ResultChecker(
path_to_compute_gain, ph.inFile('genome.10k.fa'),
ph.inFile('reads.illumina.sam'),
ph.outFile('reads.illumina.corrected.i%d.fa' % i),
min_gain.get(i, 100.0)),
to_diff=[(ph.inFile('reads.illumina.fq.i%d.stdout' % i),
ph.outFile('reads.illumina.fq.i%d.stdout' % i),
transforms),
(ph.inFile('reads.illumina.fq.i%d.stderr' % i),
ph.outFile('reads.illumina.fq.i%d.stderr' % i),
transforms),
])
conf_list.append(conf)
# Indel Mode
for i in [1, 2]:
min_gain = {1: 70.0, 2: 85.0}
conf = app_tests.TestConf(
program=path_to_fiona,
args=['-nt', '1',
'-i', str(i),
'-g', '10000',
ph.inFile('reads.454.fq'),
ph.outFile('reads.454.corrected.i%d.fa' % i)],
redir_stdout=ph.outFile('reads.454.fq.i%d.stdout' % i),
redir_stderr=ph.outFile('reads.454.fq.i%d.stderr' % i),
check_callback=ResultChecker(
path_to_compute_gain, ph.inFile('genome.10k.fa'),
ph.inFile('reads.454.sam'),
ph.outFile('reads.454.corrected.i%d.fa' % i),
min_gain.get(i, 100.0)),
to_diff=[(ph.inFile('reads.454.fq.i%d.stdout' % i),
ph.outFile('reads.454.fq.i%d.stdout' % i),
transforms),
(ph.inFile('reads.454.fq.i%d.stderr' % i),
ph.outFile('reads.454.fq.i%d.stderr' % i),
transforms),
])
conf_list.append(conf)
# Execute the tests.
failures = 0
for conf in conf_list:
res = app_tests.runTest(conf)
# Output to the user.
print ' '.join(conf.commandLineArgs())
if res:
print 'OK'
else:
failures += 1
print 'FAILED'
# Cleanup.
ph.deleteTempDir()
print '=============================='
print ' total tests: %d' % len(conf_list)
print ' failed tests: %d' % failures
print 'successful tests: %d' % (len(conf_list) - failures)
print '=============================='
# Compute and return return code.
return failures != 0
def main(source_base, binary_base):
"""Main entry point of the script."""
print 'Executing test for mason_variator'
print '======================'
print
ph = app_tests.TestPathHelper(
source_base, binary_base,
'apps/mason2/tests') # tests dir
# ============================================================
# Auto-detect the binary path.
# ============================================================
path_to_genome = app_tests.autolocateBinary(
binary_base, 'bin', 'mason_genome')
path_to_methylation = app_tests.autolocateBinary(
binary_base, 'bin', 'mason_methylation')
path_to_variator = app_tests.autolocateBinary(
binary_base, 'bin', 'mason_variator')
path_to_materializer = app_tests.autolocateBinary(
binary_base, 'bin', 'mason_materializer')
path_to_simulator = app_tests.autolocateBinary(
binary_base, 'bin', 'mason_simulator')
libcpp = (os.environ.has_key('CC') and 'gcc' in os.environ["CC"]) or sys.platform == "linux" or sys.platform == "linux2"
# ============================================================
# Built TestConf list.
# ============================================================
# Build list with TestConf objects, analoguely to how the output
# was generated in generate_outputs.sh.
conf_list = []
# We prepare a list of transforms to apply to the output files. This is
# used to strip the input/output paths from the programs' output to
# make it more canonical and host independent.
ph.outFile('-') # To ensure that the out path is set.
transforms = [
app_tests.ReplaceTransform(
os.path.join(ph.source_base_path,
'apps/mason2/tests') + os.sep,
'', right=True),
app_tests.ReplaceTransform(ph.temp_dir + os.sep, '', right=True),
app_tests.NormalizeScientificExponentsTransform(),
]
# ============================================================
# Test mason_genome
# ============================================================
conf = app_tests.TestConf(
program=path_to_genome,
args=['-l', '1000',
'-o', ph.outFile('genome.test1.fasta'),
],
redir_stdout=ph.outFile('genome.test1.stdout'),
redir_stderr=ph.outFile('genome.test1.stderr'),
to_diff=[(ph.inFile('genome.test1.fasta'),
ph.outFile('genome.test1.fasta')),
(ph.inFile('genome.test1.stdout'),
ph.outFile('genome.test1.stdout'),
transforms),
(ph.inFile('genome.test1.stderr'),
ph.outFile('genome.test1.stderr'),
transforms),
])
conf_list.append(conf)
conf = app_tests.TestConf(
program=path_to_genome,
args=['-s', '1',
'-l', '1000',
'-l', '100',
'-o', ph.outFile('genome.test2.fasta'),
],
redir_stdout=ph.outFile('genome.test2.stdout'),
redir_stderr=ph.outFile('genome.test2.stderr'),
to_diff=[(ph.inFile('genome.test2.fasta'),
ph.outFile('genome.test2.fasta')),
(ph.inFile('genome.test2.stdout'),
ph.outFile('genome.test2.stdout'),
transforms),
(ph.inFile('genome.test2.stderr'),
ph.outFile('genome.test2.stderr'),
transforms),
])
conf_list.append(conf)
# ============================================================
# Test mason_methylation
# ============================================================
conf = app_tests.TestConf(
program=path_to_methylation,
args=['--seed', '33',
'-i', ph.inFile('random.fasta'),
'-o', ph.outFile('random_meth1.fasta'),
],
redir_stdout=ph.outFile('methylation.test1.stdout'),
redir_stderr=ph.outFile('methylation.test1.stderr'),
to_diff=[(ph.inFile('methylation.test1.fasta'),
ph.outFile('methylation.test1.fasta')),
(ph.inFile('methylation.test1.stdout'),
ph.outFile('methylation.test1.stdout'),
transforms),
(ph.inFile('methylation.test1.stderr'),
ph.outFile('methylation.test1.stderr'),
transforms),
])
# ============================================================
# Test mason_variator
# ============================================================
# Generation methylation in variator.
conf = app_tests.TestConf(
program=path_to_variator,
args=['-ir', ph.inFile('random.fasta'),
'-n', '2',
'-ov', ph.outFile('random_var1.vcf'),
'-of', ph.outFile('random_var1.fasta'),
'--snp-rate', '0.001',
'--small-indel-rate', '0.001',
'--sv-indel-rate', '0.001',
'--sv-inversion-rate', '0.001',
'--sv-translocation-rate', '0.001',
'--sv-duplication-rate', '0.001',
'--min-sv-size', '50',
'--max-sv-size', '100',
'--methylation-levels',
'--meth-fasta-out', ph.outFile('random_var1_meth.fasta'),
'--out-breakpoints', ph.outFile('random_var1_bp.txt'),
],
redir_stdout=ph.outFile('random_var1.vcf.stdout'),
redir_stderr=ph.outFile('random_var1.vcf.stderr'),
to_diff=[(ph.inFile('random_var1.vcf'),
ph.outFile('random_var1.vcf'),
transforms),
(ph.inFile('random_var1.fasta'),
ph.outFile('random_var1.fasta')),
(ph.inFile('random_var1_bp.txt'),
ph.outFile('random_var1_bp.txt')),
(ph.inFile('random_var1_meth.fasta'),
ph.outFile('random_var1_meth.fasta')),
(ph.inFile('random_var1.vcf.stderr'),
ph.outFile('random_var1.vcf.stderr'),
transforms),
(ph.inFile('random_var1.vcf.stdout'),
ph.outFile('random_var1.vcf.stdout'),
transforms),
])
if libcpp:
conf_list.append(conf)
# Generation methylation in variator.
conf = app_tests.TestConf(
program=path_to_variator,
args=['-ir', ph.inFile('random.fasta'),
'-n', '2',
'-ov', ph.outFile('random_var2.vcf'),
'-of', ph.outFile('random_var2.fasta'),
'--snp-rate', '0.001',
'--small-indel-rate', '0.001',
'--sv-indel-rate', '0.001',
'--sv-inversion-rate', '0.001',
'--sv-translocation-rate', '0.001',
'--sv-duplication-rate', '0.001',
'--min-sv-size', '50',
'--max-sv-size', '100',
'--methylation-levels',
'--meth-fasta-in', ph.inFile('random_meth1.fasta'),
'--meth-fasta-out', ph.outFile('random_var2_meth.fasta'),
'--out-breakpoints', ph.outFile('random_var2_bp.txt'),
],
redir_stdout=ph.outFile('random_var2.vcf.stdout'),
redir_stderr=ph.outFile('random_var2.vcf.stderr'),
to_diff=[(ph.inFile('random_var2.vcf'),
ph.outFile('random_var2.vcf'),
transforms),
(ph.inFile('random_var2.fasta'),
ph.outFile('random_var2.fasta')),
(ph.inFile('random_var2_bp.txt'),
ph.outFile('random_var2_bp.txt')),
(ph.inFile('random_var2_meth.fasta'),
ph.outFile('random_var2_meth.fasta')),
(ph.inFile('random_var2.vcf.stderr'),
ph.outFile('random_var2.vcf.stderr'),
transforms),
(ph.inFile('random_var2.vcf.stdout'),
ph.outFile('random_var2.vcf.stdout'),
transforms),
])
if libcpp:
conf_list.append(conf)
# Variation without methylation levels.
conf = app_tests.TestConf(
program=path_to_variator,
args=['-ir', ph.inFile('random.fasta'),
'-n', '2',
'-ov', ph.outFile('random_var3.vcf'),
'-of', ph.outFile('random_var3.fasta'),
'--snp-rate', '0.001',
'--small-indel-rate', '0.001',
'--sv-indel-rate', '0.001',
'--sv-inversion-rate', '0.001',
'--sv-translocation-rate', '0.001',
'--sv-duplication-rate', '0.001',
'--min-sv-size', '50',
'--max-sv-size', '100',
'--out-breakpoints', ph.outFile('random_var3_bp.txt'),
],
redir_stdout=ph.outFile('random_var3.vcf.stdout'),
redir_stderr=ph.outFile('random_var3.vcf.stderr'),
to_diff=[(ph.inFile('random_var3.vcf'),
ph.outFile('random_var3.vcf'),
transforms),
(ph.inFile('random_var3.fasta'),
ph.outFile('random_var3.fasta')),
(ph.inFile('random_var3_bp.txt'),
ph.outFile('random_var3_bp.txt')),
(ph.inFile('random_var3.vcf.stderr'),
ph.outFile('random_var3.vcf.stderr'),
transforms),
(ph.inFile('random_var3.vcf.stdout'),
ph.outFile('random_var3.vcf.stdout'),
transforms),
])
if libcpp:
conf_list.append(conf)
# Previously crashing test
conf = app_tests.TestConf(
program=path_to_variator,
args=['-ir', ph.inFile('adeno_virus.fa'),
'-ov', ph.outFile('random_var9.vcf'),
'-of', ph.outFile('random_var9.fasta'),
'--sv-indel-rate', '0.01',
'--sv-duplication-rate', '0.01',
'--sv-inversion-rate', '0.01',
'--min-sv-size', '20',
'--max-sv-size', '300',
],
redir_stdout=ph.outFile('random_var9.vcf.stdout'),
redir_stderr=ph.outFile('random_var9.vcf.stderr'),
to_diff=[(ph.inFile('random_var9.vcf'),
ph.outFile('random_var9.vcf'),
transforms),
(ph.inFile('random_var9.vcf.stderr'),
ph.outFile('random_var9.vcf.stderr'),
transforms),
(ph.inFile('random_var9.vcf.stdout'),
ph.outFile('random_var9.vcf.stdout'),
transforms),
])
if libcpp:
conf_list.append(conf)
# ============================================================
# Test mason_materializer
# ============================================================
# Without methylation levels.
conf = app_tests.TestConf(
program=path_to_materializer,
args=['-ir', ph.inFile('random.fasta'),
'-iv', ph.inFile('random_var1.vcf'),
'-o', ph.outFile('materializer.random_var1.fasta'),
],
redir_stdout=ph.outFile('materializer.random_var1.stdout'),
redir_stderr=ph.outFile('materializer.random_var1.stderr'),
to_diff=[(ph.inFile('random_var1.fasta'),
ph.outFile('materializer.random_var1.fasta')),
(ph.inFile('materializer.random_var1.stdout'),
ph.outFile('materializer.random_var1.stdout'),
transforms),
(ph.inFile('materializer.random_var1.stderr'),
ph.outFile('materializer.random_var1.stderr'),
transforms),
])
conf_list.append(conf)
# With methylation levels.
conf = app_tests.TestConf(
program=path_to_materializer,
args=['-ir', ph.inFile('random.fasta'),
'-iv', ph.inFile('random_var2.vcf'),
'-o', ph.outFile('materializer.random_var2.fasta'),
'--meth-fasta-in', ph.inFile('random_meth1.fasta'),
'--meth-fasta-out', ph.outFile('materializer.random_meth2.fasta'),
],
redir_stdout=ph.outFile('materializer.random_var2.stdout'),
redir_stderr=ph.outFile('materializer.random_var2.stderr'),
to_diff=[(ph.inFile('random_var1.fasta'),
ph.outFile('materializer.random_var1.fasta')),
(ph.inFile('random_var2_meth.fasta'),
ph.outFile('materializer.random_meth2.fasta'),
transforms),
(ph.inFile('materializer.random_var2.stdout'),
ph.outFile('materializer.random_var2.stdout'),
transforms),
(ph.inFile('materializer.random_var2.stderr'),
ph.outFile('materializer.random_var2.stderr'),
transforms),
])
if libcpp:
conf_list.append(conf)
# ============================================================
# Test mason_simulator
# ============================================================
# Illumina Model
conf = app_tests.TestConf(
program=path_to_simulator,
args=['-n', '1000',
'-ir', ph.inFile('random.fasta'),
'-o', ph.outFile('simulator.left1.fq'),
'-or', ph.outFile('simulator.right1.fq'),
'-oa', ph.outFile('simulator.out1.sam'),
],
redir_stdout=ph.outFile('simulator.out1.stdout'),
redir_stderr=ph.outFile('simulator.out1.stderr'),
to_diff=[(ph.inFile('simulator.left1.fq'),
ph.outFile('simulator.left1.fq')),
(ph.inFile('simulator.right1.fq'),
ph.outFile('simulator.right1.fq')),
(ph.inFile('simulator.out1.sam'),
ph.outFile('simulator.out1.sam')),
(ph.inFile('simulator.out1.stdout'),
ph.outFile('simulator.out1.stdout'),
transforms),
(ph.inFile('simulator.out1.stderr'),
ph.outFile('simulator.out1.stderr'),
transforms),
])
if libcpp:
conf_list.append(conf)
conf = app_tests.TestConf(
program=path_to_simulator,
args=['-n', '1000',
'-ir', ph.inFile('random.fasta'),
'-iv', ph.inFile('random_var1.vcf'),
'-o', ph.outFile('simulator.left2.fq'),
'-or', ph.outFile('simulator.right2.fq'),
'-oa', ph.outFile('simulator.out2.sam'),
],
redir_stdout=ph.outFile('simulator.out2.stdout'),
redir_stderr=ph.outFile('simulator.out2.stderr'),
to_diff=[(ph.inFile('simulator.left2.fq'),
ph.outFile('simulator.left2.fq')),
(ph.inFile('simulator.right2.fq'),
ph.outFile('simulator.right2.fq')),
(ph.inFile('simulator.out2.sam'),
ph.outFile('simulator.out2.sam')),
(ph.inFile('simulator.out2.stdout'),
ph.outFile('simulator.out2.stdout'),
transforms),
(ph.inFile('simulator.out2.stderr'),
ph.outFile('simulator.out2.stderr'),
transforms),
])
if libcpp:
conf_list.append(conf)
conf = app_tests.TestConf(
program=path_to_simulator,
args=['-n', '1000',
'-ir', ph.inFile('random.fasta'),
'-o', ph.outFile('simulator.left3.fa'),
'-or', ph.outFile('simulator.right3.fa'),
],
redir_stdout=ph.outFile('simulator.out3.stdout'),
redir_stderr=ph.outFile('simulator.out3.stderr'),
to_diff=[(ph.inFile('simulator.left3.fa'),
ph.outFile('simulator.left3.fa')),
(ph.inFile('simulator.right3.fa'),
ph.outFile('simulator.right3.fa')),
(ph.inFile('simulator.out3.stdout'),
ph.outFile('simulator.out3.stdout'),
transforms),
(ph.inFile('simulator.out3.stderr'),
ph.outFile('simulator.out3.stderr'),
transforms),
])
if libcpp:
conf_list.append(conf)
conf = app_tests.TestConf(
program=path_to_simulator,
args=['-n', '1000',
'-ir', ph.inFile('random.fasta'),
'-iv', ph.inFile('random_var1.vcf'),
'-o', ph.outFile('simulator.left7.fa'),
'-oa', ph.outFile('simulator.out7.sam'),
],
redir_stdout=ph.outFile('simulator.out7.stdout'),
redir_stderr=ph.outFile('simulator.out7.stderr'),
to_diff=[(ph.inFile('simulator.left7.fa'),
ph.outFile('simulator.left7.fa')),
(ph.inFile('simulator.out7.sam'),
ph.outFile('simulator.out7.sam')),
(ph.inFile('simulator.out7.stdout'),
ph.outFile('simulator.out7.stdout'),
transforms),
(ph.inFile('simulator.out7.stderr'),
ph.outFile('simulator.out7.stderr'),
transforms),
])
if libcpp:
conf_list.append(conf)
conf = app_tests.TestConf(
program=path_to_simulator,
args=['-n', '1000',
'-ir', ph.inFile('random.fasta'),
'-o', ph.outFile('simulator.left4.fa'),
'-oa', ph.outFile('simulator.out4.sam'),
],
redir_stdout=ph.outFile('simulator.out4.stdout'),
redir_stderr=ph.outFile('simulator.out4.stderr'),
to_diff=[(ph.inFile('simulator.left4.fa'),
ph.outFile('simulator.left4.fa')),
(ph.inFile('simulator.out4.sam'),
ph.outFile('simulator.out4.sam')),
(ph.inFile('simulator.out4.stdout'),
ph.outFile('simulator.out4.stdout'),
transforms),
(ph.inFile('simulator.out4.stderr'),
ph.outFile('simulator.out4.stderr'),
transforms),
])
if libcpp:
conf_list.append(conf)
conf = app_tests.TestConf(
program=path_to_simulator,
args=['-n', '1000',
'-ir', ph.inFile('random.fasta'),
'--meth-fasta-in', ph.inFile('random_meth1.fasta'),
'--methylation-levels',
'--enable-bs-seq',
'-o', ph.outFile('simulator.left5.fq'),
'-or', ph.outFile('simulator.right5.fq'),
],
redir_stdout=ph.outFile('simulator.out5.stdout'),
redir_stderr=ph.outFile('simulator.out5.stderr'),
to_diff=[(ph.inFile('simulator.left5.fq'),
ph.outFile('simulator.left5.fq')),
(ph.inFile('simulator.right5.fq'),
ph.outFile('simulator.right5.fq')),
(ph.inFile('simulator.out5.stdout'),
ph.outFile('simulator.out5.stdout'),
transforms),
(ph.inFile('simulator.out5.stderr'),
ph.outFile('simulator.out5.stderr'),
transforms),
])
if libcpp:
conf_list.append(conf)
conf = app_tests.TestConf(
program=path_to_simulator,
args=['-n', '1000',
'-ir', ph.inFile('random.fasta'),
'-iv', ph.inFile('random_var1.vcf'),
'--meth-fasta-in', ph.inFile('random_meth1.fasta'),
'--methylation-levels',
'--enable-bs-seq',
'-o', ph.outFile('simulator.left6.fq'),
'-or', ph.outFile('simulator.right6.fq'),
],
redir_stdout=ph.outFile('simulator.out6.stdout'),
redir_stderr=ph.outFile('simulator.out6.stderr'),
to_diff=[(ph.inFile('simulator.left6.fq'),
ph.outFile('simulator.left6.fq')),
(ph.inFile('simulator.right6.fq'),
ph.outFile('simulator.right6.fq')),
(ph.inFile('simulator.out6.stdout'),
ph.outFile('simulator.out6.stdout'),
transforms),
(ph.inFile('simulator.out6.stderr'),
ph.outFile('simulator.out6.stderr'),
transforms),
])
if libcpp:
conf_list.append(conf)
# 454 Model
conf = app_tests.TestConf(
program=path_to_simulator,
args=['--seq-technology', '454',
'--fragment-mean-size', '800',
'--454-read-length-mean', '200',
'--454-read-length-stddev', '20',
'-n', '1000', '-v',
'-ir', ph.inFile('random.fasta'),
'-o', ph.outFile('simulator.left8.fq'),
'-oa', ph.outFile('simulator.out8.sam'),
],
redir_stdout=ph.outFile('simulator.out8.stdout'),
redir_stderr=ph.outFile('simulator.out8.stderr'),
to_diff=[(ph.inFile('simulator.left8.fq'),
ph.outFile('simulator.left8.fq')),
(ph.inFile('simulator.out8.sam'),
ph.outFile('simulator.out8.sam')),
(ph.inFile('simulator.out8.stdout'),
ph.outFile('simulator.out8.stdout'),
transforms),
(ph.inFile('simulator.out8.stderr'),
ph.outFile('simulator.out8.stderr'),
transforms),
])
if libcpp:
conf_list.append(conf)
# Execute the tests.
failures = 0
for conf in conf_list:
res = app_tests.runTest(conf)
# Output to the user.
print ' '.join([os.path.basename(conf.program)] + conf.args),
if res:
print 'OK'
else:
failures += 1
print 'FAILED'
# Cleanup.
ph.deleteTempDir()
print '=============================='
print ' total tests: %d' % len(conf_list)
print ' failed tests: %d' % failures
print 'successful tests: %d' % (len(conf_list) - failures)
print '=============================='
# Compute and return return code.
return failures != 0
def main(source_base, binary_base):
"""Main entry point of the script."""
print 'Executing test for samcat'
print '========================='
print
ph = app_tests.TestPathHelper(
source_base, binary_base,
'apps/samcat/tests') # tests dir
# ============================================================
# Auto-detect the binary path.
# ============================================================
path_to_program = app_tests.autolocateBinary(
binary_base, 'apps/samcat', 'samcat')
# ============================================================
# Built TestConf list.
# ============================================================
# Build list with TestConf objects, analoguely to how the output
# was generated in generate_outputs.sh.
conf_list = []
# ============================================================
# Run on DNA (Adenoviruses).
# ============================================================
conf = app_tests.TestConf(
program=path_to_program,
args=[ph.inFile('ex1_a1.sam'),
ph.inFile('ex1_a2.sam'),
ph.inFile('ex1_a3.sam'),
'-o', ph.outFile('ex1_merged.sam')],
to_diff=[(ph.inFile('ex1_merged.sam'),
ph.outFile('ex1_merged.sam'))])
conf_list.append(conf)
conf = app_tests.TestConf(
program=path_to_program,
args=[ph.inFile('ex1_a1.sam'),
ph.inFile('ex1_a2.sam'),
ph.inFile('ex1_a3.sam'),
'-o', ph.outFile('ex1_merged.bam')],
to_diff=[(ph.inFile('ex1_merged.bam'),
ph.outFile('ex1_merged.bam'), "gunzip")])
conf_list.append(conf)
# Execute the tests.
failures = 0
for conf in conf_list:
res = app_tests.runTest(conf)
# Output to the user.
print ' '.join(conf.commandLineArgs())
if res:
print 'OK'
else:
failures += 1
print 'FAILED'
# Cleanup.
ph.deleteTempDir()
print '=============================='
print ' total tests: %d' % len(conf_list)
print ' failed tests: %d' % failures
print 'successful tests: %d' % (len(conf_list) - failures)
print '=============================='
# Compute and return return code.
return failures != 0
def main(source_base, binary_base):
"""Main entry point of the script."""
print 'Executing test for pair_align'
print '============================='
print
ph = app_tests.TestPathHelper(
source_base, binary_base,
'apps/pair_align/tests') # tests dir
# ============================================================
# Auto-detect the binary path.
# ============================================================
path_to_program = app_tests.autolocateBinary(
binary_base, 'apps/pair_align', 'pair_align')
# ============================================================
# Built TestConf list.
# ============================================================
# Build list with TestConf objects, analoguely to how the output
# was generated in generate_outputs.sh.
conf_list = []
# ============================================================
# Run on Proteins (Balibase).
# ============================================================
# Run with defaults for all non-mandatory options.
for fname in ['1aab', '1ad2', '2trx']:
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('%s.stdout' % fname),
args=['-s', ph.inFile('%s.fa' % fname),
'-o', ph.outFile('%s.fa' % fname)],
to_diff=[(ph.inFile('%s_out.fa' % fname),
ph.outFile('%s.fa' % fname)),
(ph.inFile('%s.stdout' % fname),
ph.outFile('%s.stdout' % fname))])
conf_list.append(conf)
# Run with explicit alphabet.
for fname in ['1aab', '1ad2', '2trx']:
conf = app_tests.TestConf(
program=path_to_program,
args=['-a', 'protein',
'-s', ph.inFile('%s.fa' % fname),
'-o', ph.outFile('%s.protein.fa' % fname)],
redir_stdout=ph.outFile('%s.protein.stdout' % fname),
to_diff=[(ph.inFile('%s.protein_out.fa' % fname),
ph.outFile('%s.protein.fa' % fname)),
(ph.inFile('%s.protein.stdout' % fname),
ph.outFile('%s.protein.stdout' % fname))])
conf_list.append(conf)
# Run with different alignment methods.
for fname in ['1aab', '1ad2', '2trx']:
for m in ['nw', 'gotoh', 'sw', 'lcs']:
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('%s.m%s.stdout' % (fname, m)),
args=['-m', m,
'-s', ph.inFile('%s.fa' % fname),
'-o', ph.outFile('%s.m%s.fa' % (fname, m))],
to_diff=[(ph.inFile('%s.m%s_out.fa' % (fname, m)),
ph.outFile('%s.m%s.fa' % (fname, m))),
(ph.inFile('%s.m%s.stdout' % (fname, m)),
ph.outFile('%s.m%s.stdout' % (fname, m)))])
conf_list.append(conf)
# Run with different scoring options.
for fname in ['1aab', '1ad2', '2trx']:
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('%s.g-20.stdout' % fname),
args=['-g', '-20',
'-s', ph.inFile('%s.fa' % fname),
'-o', ph.outFile('%s.g-20.fa' % fname)],
to_diff=[(ph.inFile('%s.g-20_out.fa' % fname),
ph.outFile('%s.g-20.fa' % fname)),
(ph.inFile('%s.g-20.stdout' % fname),
ph.outFile('%s.g-20.stdout' % fname))])
conf_list.append(conf)
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('%s.e-5.stdout' % fname),
args=['-e', '-5',
'-s', ph.inFile('%s.fa' % fname),
'-o', ph.outFile('%s.e-5.fa' % fname)],
to_diff=[(ph.inFile('%s.e-5_out.fa' % fname),
ph.outFile('%s.e-5.fa' % fname)),
(ph.inFile('%s.e-5.stdout' % fname),
ph.outFile('%s.e-5.stdout' % fname))])
conf_list.append(conf)
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('%s.ms10.stdout' % fname),
args=['-ms', '10',
'-s', ph.inFile('%s.fa' % fname),
'-o', ph.outFile('%s.ms10.fa' % fname)],
to_diff=[(ph.inFile('%s.ms10_out.fa' % fname),
ph.outFile('%s.ms10.fa' % fname)),
(ph.inFile('%s.ms10.stdout' % fname),
ph.outFile('%s.ms10.stdout' % fname))])
conf_list.append(conf)
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('%s.mm-8.stdout' % fname),
args=['-mm', '-8',
'-s', ph.inFile('%s.fa' % fname),
'-o', ph.outFile('%s.mm-8.fa' % fname)],
to_diff=[(ph.inFile('%s.mm-8_out.fa' % fname),
ph.outFile('%s.mm-8.fa' % fname)),
(ph.inFile('%s.mm-8.stdout' % fname),
ph.outFile('%s.mm-8.stdout' % fname))])
conf_list.append(conf)
# Run with matrix file.
for fname in ['1aab', '1ad2', '2trx']:
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('%s.maVTML200.stdout' % fname),
args=['-ma', ph.inFile('VTML200I'),
'-s', ph.inFile('%s.fa' % fname),
'-o', ph.outFile('%s.maVTML200.fa' % fname)],
to_diff=[(ph.inFile('%s.maVTML200_out.fa' % fname),
ph.outFile('%s.maVTML200.fa' % fname)),
(ph.inFile('%s.maVTML200.stdout' % fname),
ph.outFile('%s.maVTML200.stdout' % fname))])
conf_list.append(conf)
# Run with different banded alignment options.
for fname in ['1aab', '1ad2', '2trx']:
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('%s.lo5.stdout' % fname),
args=['-lo', '5',
'-s', ph.inFile('%s.fa' % fname),
'-o', ph.outFile('%s.lo5.fa' % fname)],
to_diff=[(ph.inFile('%s.lo5_out.fa' % fname),
ph.outFile('%s.lo5.fa' % fname)),
(ph.inFile('%s.lo5.stdout' % fname),
ph.outFile('%s.lo5.stdout' % fname))])
conf_list.append(conf)
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('%s.hi5.stdout' % fname),
args=['-hi', '5',
'-s', ph.inFile('%s.fa' % fname),
'-o', ph.outFile('%s.hi5.fa' % fname)],
to_diff=[(ph.inFile('%s.hi5_out.fa' % fname),
ph.outFile('%s.hi5.fa' % fname)),
(ph.inFile('%s.hi5.stdout' % fname),
ph.outFile('%s.hi5.stdout' % fname))])
conf_list.append(conf)
# Run with different matrix configuraiton options.
for fname in ['1aab', '1ad2', '2trx']:
for c in ['ffff', 'tttt', 'ffft', 'fftf', 'ftff', 'tfff', 'fftt',
'fttf', 'ttff', 'tfft']:
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('%s.c%s.stdout' % (fname, c)),
args=['-c', c,
'-s', ph.inFile('%s.fa' % fname),
'-o', ph.outFile('%s.c%s.fa' % (fname, c))],
to_diff=[(ph.inFile('%s.c%s_out.fa' % (fname, c)),
ph.outFile('%s.c%s.fa' % (fname, c))),
(ph.inFile('%s.c%s.stdout' % (fname, c)),
ph.outFile('%s.c%s.stdout' % (fname, c)))])
conf_list.append(conf)
# ============================================================
# Run on DNA (Adenoviruses).
# ============================================================
# Run with defaults for all non-mandatory options.
for i in [1, 2, 3]:
conf = app_tests.TestConf(
program=path_to_program,
args=['-a', 'dna',
'-s', ph.inFile('adeno%d.fa' % i),
'-o', ph.outFile('adeno%d.fa' % i)],
to_diff=[(ph.inFile('adeno%d_out.fa' % i),
ph.outFile('adeno%d.fa' % i))])
conf_list.append(conf)
# ============================================================
# Run on RNA.
# ============================================================
# Run with defaults for all non-mandatory options.
for i in [1, 2, 3]:
conf = app_tests.TestConf(
program=path_to_program,
args=['-a', 'rna',
'-s', ph.inFile('adeno%d-rna.fa' % i),
'-o', ph.outFile('adeno%d-rna.fa' % i)],
to_diff=[(ph.inFile('adeno%d-rna_out.fa' % i),
ph.outFile('adeno%d-rna.fa' % i))])
conf_list.append(conf)
# Execute the tests.
failures = 0
for conf in conf_list:
res = app_tests.runTest(conf)
# Output to the user.
print ' '.join(['pair_align'] + conf.args),
if res:
print 'OK'
else:
failures += 1
print 'FAILED'
# Cleanup.
ph.deleteTempDir()
print '=============================='
print ' total tests: %d' % len(conf_list)
print ' failed tests: %d' % failures
print 'successful tests: %d' % (len(conf_list) - failures)
print '=============================='
# Compute and return return code.
return failures != 0
def main(source_base, binary_base):
"""Main entry point of the script."""
if platform.machine().startswith('mips') or platform.machine().startswith('s390'):
print 'Skipping tests for seqan_tcoffee on mips* and s390*'
print '==================================================='
return 0
print 'Executing test for seqan_tcoffee'
print '================================'
print
ph = app_tests.TestPathHelper(
source_base, binary_base,
'apps/seqan_tcoffee/tests') # tests dir
# ============================================================
# Auto-detect the binary path.
# ============================================================
path_to_program = app_tests.autolocateBinary(
binary_base, 'apps/seqan_tcoffee', 'seqan_tcoffee')
# ============================================================
# Built TestConf list.
# ============================================================
# Build list with TestConf objects, analoguely to how the output
# was generated in generate_outputs.sh.
conf_list = []
# ============================================================
# Run on Proteins (Balibase).
# ============================================================
# Run with defaults for all non-mandatory options.
for fname in ['1aab', '1ad2', '2trx']:
conf = app_tests.TestConf(
program=path_to_program,
args=['-s', ph.inFile('%s.fa' % fname),
'-o', ph.outFile('%s.fasta' % fname)],
to_diff=[(ph.inFile('%s.fasta' % fname),
ph.outFile('%s.fasta' % fname))])
conf_list.append(conf)
# Run with explicit alphabet.
for fname in ['1aab', '1ad2', '2trx']:
conf = app_tests.TestConf(
program=path_to_program,
args=['-a', 'protein',
'-s', ph.inFile('%s.fa' % fname),
'-o', ph.outFile('%s.protein.fasta' % fname)],
to_diff=[(ph.inFile('%s.protein.fasta' % fname),
ph.outFile('%s.protein.fasta' % fname))])
conf_list.append(conf)
# Run with different segment match generation options. We run
# with with single values and combinations of neighbours
for fname in ['1aab', '1ad2', '2trx']:
for m in ['global', 'local', 'overlap', 'lcs']:
conf = app_tests.TestConf(
program=path_to_program,
args=['-m', m,
'-s', ph.inFile('%s.fa' % fname),
'-o', ph.outFile('%s.m%s.fasta' % (fname, m))],
to_diff=[(ph.inFile('%s.m%s.fasta' % (fname, m)),
ph.outFile('%s.m%s.fasta' % (fname, m)))])
conf_list.append(conf)
m1 = 'global'
m2 = 'local'
conf = app_tests.TestConf(
program=path_to_program,
args=['-m', m1,
'-m', m2,
'-s', ph.inFile('%s.fa' % fname),
'-o', ph.outFile('%s.m%s.m%s.fasta' % (fname, m1, m2))],
to_diff=[(ph.inFile('%s.m%s.m%s.fasta' % (fname, m1, m2)),
ph.outFile('%s.m%s.m%s.fasta' % (fname, m1, m2)))])
conf_list.append(conf)
m1 = 'local'
m2 = 'overlap'
conf = app_tests.TestConf(
program=path_to_program,
args=['-m', m1,
'-m', m2,
'-s', ph.inFile('%s.fa' % fname),
'-o', ph.outFile('%s.m%s.m%s.fasta' % (fname, m1, m2))],
to_diff=[(ph.inFile('%s.m%s.m%s.fasta' % (fname, m1, m2)),
ph.outFile('%s.m%s.m%s.fasta' % (fname, m1, m2)))])
conf_list.append(conf)
m1 = 'overlap'
m2 = 'lcs'
conf = app_tests.TestConf(
program=path_to_program,
args=['-m', m1,
'-m', m2,
'-s', ph.inFile('%s.fa' % fname),
'-o', ph.outFile('%s.m%s.m%s.fasta' % (fname, m1, m2))],
to_diff=[(ph.inFile('%s.m%s.m%s.fasta' % (fname, m1, m2)),
ph.outFile('%s.m%s.m%s.fasta' % (fname, m1, m2)))])
m1 = 'global'
m2 = 'lcs'
conf = app_tests.TestConf(
program=path_to_program,
args=['-m', m1,
'-m', m2,
'-s', ph.inFile('%s.fa' % fname),
'-o', ph.outFile('%s.m%s.m%s.fasta' % (fname, m1, m2))],
to_diff=[(ph.inFile('%s.m%s.m%s.fasta' % (fname, m1, m2)),
ph.outFile('%s.m%s.m%s.fasta' % (fname, m1, m2)))])
# Run with different match files variations.
# TODO
# Run with different scoring options.
for fname in ['1aab', '1ad2', '2trx']:
conf = app_tests.TestConf(
program=path_to_program,
args=['-g', '-20',
'-s', ph.inFile('%s.fa' % fname),
'-o', ph.outFile('%s.g-20.fasta' % fname)],
to_diff=[(ph.inFile('%s.g-20.fasta' % fname),
ph.outFile('%s.g-20.fasta' % fname))])
conf_list.append(conf)
conf = app_tests.TestConf(
program=path_to_program,
args=['-e', '-5',
'-s', ph.inFile('%s.fa' % fname),
'-o', ph.outFile('%s.e-5.fasta' % fname)],
to_diff=[(ph.inFile('%s.e-5.fasta' % fname),
ph.outFile('%s.e-5.fasta' % fname))])
conf_list.append(conf)
conf = app_tests.TestConf(
program=path_to_program,
args=['-ms', '10',
'-s', ph.inFile('%s.fa' % fname),
'-o', ph.outFile('%s.ms10.fasta' % fname)],
to_diff=[(ph.inFile('%s.ms10.fasta' % fname),
ph.outFile('%s.ms10.fasta' % fname))])
conf_list.append(conf)
conf = app_tests.TestConf(
program=path_to_program,
args=['-mm', '-8',
'-s', ph.inFile('%s.fa' % fname),
'-o', ph.outFile('%s.mm-8.fasta' % fname)],
to_diff=[(ph.inFile('%s.mm-8.fasta' % fname),
ph.outFile('%s.mm-8.fasta' % fname))])
conf_list.append(conf)
# Run with matrix file.
for fname in ['1aab', '1ad2', '2trx']:
conf = app_tests.TestConf(
program=path_to_program,
args=['-ma', ph.inFile('VTML200I'),
'-s', ph.inFile('%s.fa' % fname),
'-o', ph.outFile('%s.maVTML200.fasta' % fname)],
to_diff=[(ph.inFile('%s.maVTML200.fasta' % fname),
ph.outFile('%s.maVTML200.fasta' % fname))])
conf_list.append(conf)
# Run with manual guide tree.
for fname in ['1aab', '1ad2', '2trx']:
conf = app_tests.TestConf(
program=path_to_program,
args=['-u', ph.inFile('%s.newick' % fname),
'-s', ph.inFile('%s.fa' % fname),
'-o', ph.outFile('%s.u.fasta' % fname)],
to_diff=[(ph.inFile('%s.u.fasta' % fname),
ph.outFile('%s.u.fasta' % fname))])
conf_list.append(conf)
# Run with different guide tree building options.
for fname in ['1aab', '1ad2', '2trx']:
for b in ['nj', 'min', 'max', 'avg', 'wavg']:
conf = app_tests.TestConf(
program=path_to_program,
args=['-b', b,
'-s', ph.inFile('%s.fa' % fname),
'-o', ph.outFile('%s.b%s.fasta' % (fname, b))],
to_diff=[(ph.inFile('%s.b%s.fasta' % (fname, b)),
ph.outFile('%s.b%s.fasta' % (fname, b)))])
conf_list.append(conf)
# Run alignment evaluation.
for fname in ['1aab', '1ad2', '2trx']:
conf = app_tests.TestConf(
program=path_to_program,
args=['-i', ph.inFile('%s.fasta' % fname)],
redir_stdout=ph.outFile('%s.i.fasta' % fname),
to_diff=[(ph.inFile('%s.i.fasta' % fname),
ph.outFile('%s.i.fasta' % fname))])
conf_list.append(conf)
# ============================================================
# Run on DNA (Adenoviruses).
# ============================================================
# Run with defaults for all non-mandatory options.
for i in [2, 3, 4]:
conf = app_tests.TestConf(
program=path_to_program,
args=['-a', 'dna',
'-s', ph.inFile('adeno%d.fa' % i),
'-o', ph.outFile('adeno%d.fasta' % i)],
to_diff=[(ph.inFile('adeno%d.fasta' % i),
ph.outFile('adeno%d.fasta' % i))])
conf_list.append(conf)
# ============================================================
# Run on RNA.
# ============================================================
# Run with defaults for all non-mandatory options.
for i in [2, 3, 4]:
conf = app_tests.TestConf(
program=path_to_program,
args=['-a', 'rna',
'-s', ph.inFile('adeno%d-rna.fa' % i),
'-o', ph.outFile('adeno%d-rna.fasta' % i)],
to_diff=[(ph.inFile('adeno%d-rna.fasta' % i),
ph.outFile('adeno%d-rna.fasta' % i))])
conf_list.append(conf)
# Execute the tests.
failures = 0
for conf in conf_list:
res = app_tests.runTest(conf)
# Output to the user.
print ' '.join(['seqan_tcoffee'] + conf.args),
if res:
print 'OK'
else:
failures += 1
print 'FAILED'
# Cleanup.
ph.deleteTempDir()
print '=============================='
print ' total tests: %d' % len(conf_list)
print ' failed tests: %d' % failures
print 'successful tests: %d' % (len(conf_list) - failures)
print '=============================='
# Compute and return return code.
return failures != 0
def main(source_base, binary_base):
"""Main entry point of the script."""
print('Executing test for pair_align')
print('=============================')
print()
ph = app_tests.TestPathHelper(source_base, binary_base,
'apps/pair_align/tests') # tests dir
# ============================================================
# Auto-detect the binary path.
# ============================================================
path_to_program = app_tests.autolocateBinary(binary_base,
'apps/pair_align',
'pair_align')
# ============================================================
# Built TestConf list.
# ============================================================
# Build list with TestConf objects, analoguely to how the output
# was generated in generate_outputs.sh.
conf_list = []
# ============================================================
# Run on Proteins (Balibase).
# ============================================================
# Run with defaults for all non-mandatory options.
for fname in ['1aab', '1ad2', '2trx']:
conf = app_tests.TestConf(program=path_to_program,
redir_stdout=ph.outFile('%s.stdout' % fname),
args=[
'-s',
ph.inFile('%s.fa' % fname), '-o',
ph.outFile('%s.fa' % fname)
],
to_diff=[(ph.inFile('%s_out.fa' % fname),
ph.outFile('%s.fa' % fname)),
(ph.inFile('%s.stdout' % fname),
ph.outFile('%s.stdout' % fname))])
conf_list.append(conf)
# Run with explicit alphabet.
for fname in ['1aab', '1ad2', '2trx']:
conf = app_tests.TestConf(
program=path_to_program,
args=[
'-a', 'protein', '-s',
ph.inFile('%s.fa' % fname), '-o',
ph.outFile('%s.protein.fa' % fname)
],
redir_stdout=ph.outFile('%s.protein.stdout' % fname),
to_diff=[(ph.inFile('%s.protein_out.fa' % fname),
ph.outFile('%s.protein.fa' % fname)),
(ph.inFile('%s.protein.stdout' % fname),
ph.outFile('%s.protein.stdout' % fname))])
conf_list.append(conf)
# Run with different alignment methods.
for fname in ['1aab', '1ad2', '2trx']:
for m in ['nw', 'gotoh', 'sw', 'lcs']:
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('%s.m%s.stdout' % (fname, m)),
args=[
'-m', m, '-s',
ph.inFile('%s.fa' % fname), '-o',
ph.outFile('%s.m%s.fa' % (fname, m))
],
to_diff=[(ph.inFile('%s.m%s_out.fa' % (fname, m)),
ph.outFile('%s.m%s.fa' % (fname, m))),
(ph.inFile('%s.m%s.stdout' % (fname, m)),
ph.outFile('%s.m%s.stdout' % (fname, m)))])
conf_list.append(conf)
# Run with different scoring options.
for fname in ['1aab', '1ad2', '2trx']:
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('%s.g-20.stdout' % fname),
args=[
'-g', '-20', '-s',
ph.inFile('%s.fa' % fname), '-o',
ph.outFile('%s.g-20.fa' % fname)
],
to_diff=[(ph.inFile('%s.g-20_out.fa' % fname),
ph.outFile('%s.g-20.fa' % fname)),
(ph.inFile('%s.g-20.stdout' % fname),
ph.outFile('%s.g-20.stdout' % fname))])
conf_list.append(conf)
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('%s.e-5.stdout' % fname),
args=[
'-e', '-5', '-s',
ph.inFile('%s.fa' % fname), '-o',
ph.outFile('%s.e-5.fa' % fname)
],
to_diff=[(ph.inFile('%s.e-5_out.fa' % fname),
ph.outFile('%s.e-5.fa' % fname)),
(ph.inFile('%s.e-5.stdout' % fname),
ph.outFile('%s.e-5.stdout' % fname))])
conf_list.append(conf)
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('%s.ms10.stdout' % fname),
args=[
'-ms', '10', '-s',
ph.inFile('%s.fa' % fname), '-o',
ph.outFile('%s.ms10.fa' % fname)
],
to_diff=[(ph.inFile('%s.ms10_out.fa' % fname),
ph.outFile('%s.ms10.fa' % fname)),
(ph.inFile('%s.ms10.stdout' % fname),
ph.outFile('%s.ms10.stdout' % fname))])
conf_list.append(conf)
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('%s.mm-8.stdout' % fname),
args=[
'-mm', '-8', '-s',
ph.inFile('%s.fa' % fname), '-o',
ph.outFile('%s.mm-8.fa' % fname)
],
to_diff=[(ph.inFile('%s.mm-8_out.fa' % fname),
ph.outFile('%s.mm-8.fa' % fname)),
(ph.inFile('%s.mm-8.stdout' % fname),
ph.outFile('%s.mm-8.stdout' % fname))])
conf_list.append(conf)
# Run with matrix file.
for fname in ['1aab', '1ad2', '2trx']:
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('%s.maVTML200.stdout' % fname),
args=[
'-ma',
ph.inFile('VTML200I'), '-s',
ph.inFile('%s.fa' % fname), '-o',
ph.outFile('%s.maVTML200.fa' % fname)
],
to_diff=[(ph.inFile('%s.maVTML200_out.fa' % fname),
ph.outFile('%s.maVTML200.fa' % fname)),
(ph.inFile('%s.maVTML200.stdout' % fname),
ph.outFile('%s.maVTML200.stdout' % fname))])
conf_list.append(conf)
# Run with different banded alignment options.
for fname in ['1aab', '1ad2', '2trx']:
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('%s.lo5.stdout' % fname),
args=[
'-lo', '5', '-s',
ph.inFile('%s.fa' % fname), '-o',
ph.outFile('%s.lo5.fa' % fname)
],
to_diff=[(ph.inFile('%s.lo5_out.fa' % fname),
ph.outFile('%s.lo5.fa' % fname)),
(ph.inFile('%s.lo5.stdout' % fname),
ph.outFile('%s.lo5.stdout' % fname))])
conf_list.append(conf)
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('%s.hi5.stdout' % fname),
args=[
'-hi', '5', '-s',
ph.inFile('%s.fa' % fname), '-o',
ph.outFile('%s.hi5.fa' % fname)
],
to_diff=[(ph.inFile('%s.hi5_out.fa' % fname),
ph.outFile('%s.hi5.fa' % fname)),
(ph.inFile('%s.hi5.stdout' % fname),
ph.outFile('%s.hi5.stdout' % fname))])
conf_list.append(conf)
# Run with different matrix configuraiton options.
for fname in ['1aab', '1ad2', '2trx']:
for c in [
'ffff', 'tttt', 'ffft', 'fftf', 'ftff', 'tfff', 'fftt', 'fttf',
'ttff', 'tfft'
]:
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('%s.c%s.stdout' % (fname, c)),
args=[
'-c', c, '-s',
ph.inFile('%s.fa' % fname), '-o',
ph.outFile('%s.c%s.fa' % (fname, c))
],
to_diff=[(ph.inFile('%s.c%s_out.fa' % (fname, c)),
ph.outFile('%s.c%s.fa' % (fname, c))),
(ph.inFile('%s.c%s.stdout' % (fname, c)),
ph.outFile('%s.c%s.stdout' % (fname, c)))])
conf_list.append(conf)
# ============================================================
# Run on DNA (Adenoviruses).
# ============================================================
# Run with defaults for all non-mandatory options.
for i in [1, 2, 3]:
conf = app_tests.TestConf(program=path_to_program,
args=[
'-a', 'dna', '-s',
ph.inFile('adeno%d.fa' % i), '-o',
ph.outFile('adeno%d.fa' % i)
],
to_diff=[(ph.inFile('adeno%d_out.fa' % i),
ph.outFile('adeno%d.fa' % i))])
conf_list.append(conf)
# ============================================================
# Run on RNA.
# ============================================================
# Run with defaults for all non-mandatory options.
for i in [1, 2, 3]:
conf = app_tests.TestConf(program=path_to_program,
args=[
'-a', 'rna', '-s',
ph.inFile('adeno%d-rna.fa' % i), '-o',
ph.outFile('adeno%d-rna.fa' % i)
],
to_diff=[
(ph.inFile('adeno%d-rna_out.fa' % i),
ph.outFile('adeno%d-rna.fa' % i))
])
conf_list.append(conf)
# Execute the tests.
failures = 0
for conf in conf_list:
res = app_tests.runTest(conf)
# Output to the user.
print(' '.join(['pair_align'] + conf.args), end=' ')
if res:
print('OK')
else:
failures += 1
print('FAILED')
# Cleanup.
ph.deleteTempDir()
print('==============================')
print(' total tests: %d' % len(conf_list))
print(' failed tests: %d' % failures)
print('successful tests: %d' % (len(conf_list) - failures))
print('==============================')
# Compute and return return code.
return failures != 0
def main(source_base, binary_base):
"""Main entry point of the script."""
print 'Executing test for breakpoint_calculator'
print '========================='
print
ph = app_tests.TestPathHelper(
source_base, binary_base,
'extras/apps/breakpoint_calculator/tests') # tests dir
# ============================================================
# Auto-detect the binary path.
# ============================================================
path_to_program = app_tests.autolocateBinary(
binary_base, 'extras/apps/breakpoint_calculator',
'breakpoint_calculator')
# ============================================================
# Built TestConf list.
# ============================================================
# Build list with TestConf objects, analoguely to how the output
# was generated in generate_outputs.sh.
conf_list = []
# ============================================================
# Run breakpoint_calculator
# ============================================================
# pairwise counts, xmfa format
conf = app_tests.TestConf(program=path_to_program,
redir_stdout=ph.outFile('d2_xmfa.stdout'),
args=['-d2', ph.inFile('alignment.xmfa')],
to_diff=[(ph.inFile('d2_xmfa.stdout'),
ph.outFile('d2_xmfa.stdout'))])
conf_list.append(conf)
# pairwise counts, maf format, detailed list of all pairs
conf = app_tests.TestConf(program=path_to_program,
redir_stdout=ph.outFile('d2_maf.stdout'),
args=['-d2', '-d',
ph.inFile('alignment.maf')],
to_diff=[(ph.inFile('d2_maf.stdout'),
ph.outFile('d2_maf.stdout'))])
conf_list.append(conf)
# threeway counts, xmfa format, format directly specified
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('d3_xmfa.stdout'),
args=['-d3', '-f', 'xmfa',
ph.inFile('alignment.xmfa')],
to_diff=[(ph.inFile('d3_xmfa.stdout'), ph.outFile('d3_xmfa.stdout'))])
conf_list.append(conf)
# threeway counts, maf format, detailed list of all triplets
conf = app_tests.TestConf(program=path_to_program,
redir_stdout=ph.outFile('d3_maf.stdout'),
args=['-d3', '-d',
ph.inFile('alignment.maf')],
to_diff=[(ph.inFile('d3_maf.stdout'),
ph.outFile('d3_maf.stdout'))])
conf_list.append(conf)
# ============================================================
# Execute the tests.
# ============================================================
failures = 0
for conf in conf_list:
res = app_tests.runTest(conf)
# Output to the user.
print ' '.join(['breakpoint_calculator'] + conf.args),
if res:
print 'OK'
else:
failures += 1
print 'FAILED'
# Cleanup.
ph.deleteTempDir()
print '=============================='
print ' total tests: %d' % len(conf_list)
print ' failed tests: %d' % failures
print 'successful tests: %d' % (len(conf_list) - failures)
print '=============================='
# Compute and return return code.
return failures != 0
def main(source_base, binary_base):
"""Main entry point of the script."""
print 'Executing test for rabema'
print '========================='
print
ph = app_tests.TestPathHelper(source_base, binary_base,
'apps/rabema/tests') # tests dir
# ============================================================
# Auto-detect the binary path.
# ============================================================
path_to_prepare = app_tests.autolocateBinary(binary_base, 'apps/rabema',
'rabema_prepare_sam')
path_to_build = app_tests.autolocateBinary(binary_base, 'apps/rabema',
'rabema_build_gold_standard')
path_to_evaluate = app_tests.autolocateBinary(binary_base, 'apps/rabema',
'rabema_evaluate')
# ============================================================
# Copy Files To Temp Dir.
# ============================================================
# We copy over the genome because an FAI file will be created.
shutil.copyfile(ph.inFile('adeno-genome.fa'),
ph.outFile('adeno-genome.fa'))
# ============================================================
# Build TestConf list.
# ============================================================
# Build list with TestConf objects, analoguely to how the output
# was generated in generate_outputs.sh.
conf_list = []
# ============================================================
# Prepare SAM
# ============================================================
conf = app_tests.TestConf(
program=path_to_prepare,
args=[
'-i',
ph.inFile('gold-adeno-hamming-08.sam'), '-o',
ph.outFile('gold-adeno-hamming-08.by_qname.sam')
],
to_diff=[(ph.inFile('gold-adeno-hamming-08.by_qname.sam'),
ph.outFile('gold-adeno-hamming-08.by_qname.sam'))])
conf_list.append(conf)
conf = app_tests.TestConf(
program=path_to_prepare,
args=[
'-i',
ph.inFile('gold-adeno-edit-08.sam'), '-o',
ph.outFile('gold-adeno-edit-08.by_qname.sam')
],
to_diff=[(ph.inFile('gold-adeno-edit-08.by_qname.sam'),
ph.outFile('gold-adeno-edit-08.by_qname.sam'))])
conf_list.append(conf)
# ============================================================
# Build Gold Standard
# ============================================================
conf = app_tests.TestConf(
program=path_to_build,
redir_stdout=ph.outFile('gold-adeno-hamming-08.stdout'),
args=[
'--distance-metric', 'hamming', '-e', '8', '-o',
ph.outFile('gold-adeno-hamming-08.gsi'), '--reference',
ph.outFile('adeno-genome.fa'), '--in-bam',
ph.inFile('gold-adeno-hamming-08.by_coordinate.sam')
],
to_diff=[(ph.inFile('gold-adeno-hamming-08.stdout'),
ph.outFile('gold-adeno-hamming-08.stdout')),
(ph.inFile('gold-adeno-hamming-08.gsi'),
ph.outFile('gold-adeno-hamming-08.gsi'))])
conf_list.append(conf)
conf = app_tests.TestConf(
program=path_to_build,
redir_stdout=ph.outFile('gold-adeno-edit-08.stdout'),
args=[
'--distance-metric', 'edit', '-e', '8', '-o',
ph.outFile('gold-adeno-edit-08.gsi'), '--reference',
ph.outFile('adeno-genome.fa'), '--in-bam',
ph.inFile('gold-adeno-edit-08.by_coordinate.sam')
],
to_diff=[(ph.inFile('gold-adeno-edit-08.stdout'),
ph.outFile('gold-adeno-edit-08.stdout')),
(ph.inFile('gold-adeno-edit-08.gsi'),
ph.outFile('gold-adeno-edit-08.gsi'))])
conf_list.append(conf)
# ============================================================
# Compare.
# ============================================================
conf = app_tests.TestConf(
program=path_to_evaluate,
redir_stdout=ph.outFile('razers2-adeno-hamming-08.stdout'),
args=[
'--distance-metric', 'hamming', '-e', '8', '--reference',
ph.outFile('adeno-genome.fa'), '--in-bam',
ph.inFile('razers2-adeno-hamming-08.sam'), '--in-gsi',
ph.inFile('gold-adeno-hamming-08.gsi')
],
to_diff=[(ph.inFile('razers2-adeno-hamming-08.stdout'),
ph.outFile('razers2-adeno-hamming-08.stdout'))])
conf_list.append(conf)
conf = app_tests.TestConf(
program=path_to_evaluate,
redir_stdout=ph.outFile('razers2-adeno-hamming-04.stdout'),
args=[
'--distance-metric', 'hamming', '-e', '8', '--reference',
ph.outFile('adeno-genome.fa'), '--in-bam',
ph.inFile('razers2-adeno-hamming-04.sam'), '--in-gsi',
ph.inFile('gold-adeno-hamming-08.gsi')
],
to_diff=[(ph.inFile('razers2-adeno-hamming-04.stdout'),
ph.outFile('razers2-adeno-hamming-04.stdout'))])
conf_list.append(conf)
conf = app_tests.TestConf(
program=path_to_evaluate,
redir_stdout=ph.outFile('razers2-adeno-edit-08.stdout'),
args=[
'--distance-metric', 'edit', '-e', '8', '--reference',
ph.outFile('adeno-genome.fa'), '--in-bam',
ph.inFile('razers2-adeno-edit-08.sam'), '--in-gsi',
ph.inFile('gold-adeno-edit-08.gsi')
],
to_diff=[(ph.inFile('razers2-adeno-edit-08.stdout'),
ph.outFile('razers2-adeno-edit-08.stdout'))])
conf_list.append(conf)
conf = app_tests.TestConf(
program=path_to_evaluate,
redir_stdout=ph.outFile('razers2-adeno-edit-04.stdout'),
args=[
'--distance-metric', 'edit', '-e', '8', '--reference',
ph.outFile('adeno-genome.fa'), '--in-bam',
ph.inFile('razers2-adeno-edit-04.sam'), '--in-gsi',
ph.inFile('gold-adeno-edit-08.gsi')
],
to_diff=[(ph.inFile('razers2-adeno-edit-04.stdout'),
ph.outFile('razers2-adeno-edit-04.stdout'))])
conf_list.append(conf)
# Execute the tests.
failures = 0
for conf in conf_list:
res = app_tests.runTest(conf)
# Output to the user.
print ' '.join([os.path.basename(conf.program)] + conf.args),
if res:
print 'OK'
else:
failures += 1
print 'FAILED'
# Cleanup.
ph.deleteTempDir()
print '=============================='
print ' total tests: %d' % len(conf_list)
print ' failed tests: %d' % failures
print 'successful tests: %d' % (len(conf_list) - failures)
print '=============================='
# Compute and return return code.
return failures != 0
def main(source_base, binary_base):
"""Main entry point of the script."""
print 'Executing test for seqan_flexbar'
print '================================'
print
ph = app_tests.TestPathHelper(
source_base, binary_base,
'extras/apps/seqan_flexbar/tests') # tests dir
# ============================================================
# Auto-detect the binary path.
# ============================================================
path_to_program = []
path_to_program.append(app_tests.autolocateBinary(
binary_base, 'extras/apps/seqan_flexbar', 'sflexQC'))
path_to_program.append(app_tests.autolocateBinary(
binary_base, 'extras/apps/seqan_flexbar', 'sflexFilter'))
path_to_program.append(app_tests.autolocateBinary(
binary_base, 'extras/apps/seqan_flexbar', 'sflexAR'))
# ============================================================
# Built TestConf list.
# ============================================================
# Build list with TestConf objects, analoguely to how the output
# was generated in generate_outputs.sh.
conf_list = []
# ============================================================
# First Section.
# ============================================================
# App TestConf objects to conf_list, just like this for each
# test you want to run.
conf = app_tests.TestConf(
program=path_to_program[0],
redir_stdout=ph.outFile('out.stdout'),
args=[ph.inFile('testsample.fq'), '-q', '20', '-o',
ph.outFile('qc_test.fa'), '-t', '-ni'],
to_diff=[(ph.inFile('qc_test.stdout'),
ph.outFile('out.stdout')),
(ph.inFile('gold_qc_test.fa'),
ph.outFile('qc_test.fa'))])
conf_list.append(conf)
conf = app_tests.TestConf(
program=path_to_program[1],
redir_stdout=ph.outFile('out.stdout'),
args=[ph.inFile('testsample.fq'), '-tl', '3', '-tr', '4', '-ml',
'70', '-u', '1', '-s', 'A', '-fl', '70', '-ni', '-o',
ph.outFile('filter_test.fq')],
to_diff=[(ph.inFile('filter_test.stdout'),
ph.outFile('out.stdout')),
(ph.inFile('gold_filter_test.fq'),
ph.outFile('filter_test.fq'))])
conf_list.append(conf)
conf = app_tests.TestConf(
program=path_to_program[2],
redir_stdout=ph.outFile('out.stdout'),
args=[ph.inFile('testsample.fq'), '-a',
ph.inFile('adapter.fasta'),
'-o', ph.outFile('ar_test.fq'), '-ni'],
to_diff=[(ph.inFile('ar_test.stdout'),
ph.outFile('out.stdout')),
(ph.inFile('gold_ar_test.fq'),
ph.outFile('ar_test.fq'))])
conf_list.append(conf)
# ============================================================
# Execute the tests.
# ============================================================
failures = 0
counter = 0
for conf in conf_list:
res = app_tests.runTest(conf)
# Output to the user.
print ' '.join([path_to_program[counter]] + conf.args),
if res:
print 'OK'
else:
failures += 1
print 'FAILED'
counter += 1
# Cleanup.
ph.deleteTempDir()
print '=============================='
print ' total tests: %d' % len(conf_list)
print ' failed tests: %d' % failures
print 'successful tests: %d' % (len(conf_list) - failures)
print '=============================='
# Compute and return return code.
return failures != 0
def main(source_base, binary_base, num_threads=1):
"""Main entry point of the script."""
print('Executing test for razers3')
print('===========================')
print()
ph = app_tests.TestPathHelper(source_base, binary_base,
'apps/razers3/tests') # tests dir
# ============================================================
# Auto-detect the binary path.
# ============================================================
path_to_program = app_tests.autolocateBinary(binary_base, 'bin', 'razers3')
# ============================================================
# Built TestConf list.
# ============================================================
# Build list with TestConf objects, analoguely to how the output
# was generated in generate_outputs.sh.
conf_list = []
# We prepare a list of transforms to apply to the output files. This is
# used to strip the input/output paths from the programs' output to
# make it more canonical and host independent.
ph.outFile('-') # To ensure that the out path is set.
transforms = [
app_tests.ReplaceTransform(
os.path.join(ph.source_base_path, 'apps/razers3/tests') + os.sep,
'',
right=True),
app_tests.ReplaceTransform(ph.temp_dir + os.sep, '', right=True),
]
# Transforms for SAM output format only. Make VN field of @PG header canonical.
sam_transforms = [
app_tests.RegexpReplaceTransform(r'\tVN:[^\t]*',
r'\tVN:VERSION',
right=True,
left=True)
]
# Transforms for RazerS output format only. Remove pair id column.
razers_transforms = [RemovePairIdColumn()]
# ============================================================
# Run Adeno Single-End Tests
# ============================================================
# We run the following for all read lengths we have reads for.
for rl in [36, 100]:
# Run with default options.
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('se-adeno-reads%d_1-tc%d.stdout' %
(rl, num_threads)),
args=[
'-tc',
str(num_threads),
ph.inFile('adeno-genome.fa'),
ph.inFile('adeno-reads%d_1.fa' % rl), '-o',
ph.outFile('se-adeno-reads%d_1-tc%d.razers' %
(rl, num_threads))
],
to_diff=[(ph.inFile('se-adeno-reads%d_1-tc%d.razers' %
(rl, num_threads)),
ph.outFile('se-adeno-reads%d_1-tc%d.razers' %
(rl, num_threads))),
(ph.inFile('se-adeno-reads%d_1-tc%d.stdout' %
(rl, num_threads)),
ph.outFile('se-adeno-reads%d_1-tc%d.stdout' %
(rl, num_threads)))])
conf_list.append(conf)
# Allow indels.
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('se-adeno-reads%d_1-ng-tc%d.stdout' %
(rl, num_threads)),
args=[
'-tc',
str(num_threads), '-ng',
ph.inFile('adeno-genome.fa'),
ph.inFile('adeno-reads%d_1.fa' % rl), '-o',
ph.outFile('se-adeno-reads%d_1-ng-tc%d.razers' %
(rl, num_threads))
],
to_diff=[(ph.inFile('se-adeno-reads%d_1-ng-tc%d.razers' %
(rl, num_threads)),
ph.outFile('se-adeno-reads%d_1-ng-tc%d.razers' %
(rl, num_threads))),
(ph.inFile('se-adeno-reads%d_1-ng-tc%d.stdout' %
(rl, num_threads)),
ph.outFile('se-adeno-reads%d_1-ng-tc%d.stdout' %
(rl, num_threads)))])
conf_list.append(conf)
# Compute forward/reverse matches only.
for o in ['-r', '-f']:
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('se-adeno-reads%d_1%s-tc%d.stdout' %
(rl, o, num_threads)),
args=[
'-tc',
str(num_threads), o,
ph.inFile('adeno-genome.fa'),
ph.inFile('adeno-reads%d_1.fa' % rl), '-o',
ph.outFile('se-adeno-reads%d_1%s-tc%d.razers' %
(rl, o, num_threads))
],
to_diff=[(ph.inFile('se-adeno-reads%d_1%s-tc%d.razers' %
(rl, o, num_threads)),
ph.outFile('se-adeno-reads%d_1%s-tc%d.razers' %
(rl, o, num_threads))),
(ph.inFile('se-adeno-reads%d_1%s-tc%d.stdout' %
(rl, o, num_threads)),
ph.outFile('se-adeno-reads%d_1%s-tc%d.stdout' %
(rl, o, num_threads)))])
conf_list.append(conf)
# Compute with different identity rates.
for i in range(90, 101):
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('se-adeno-reads%d_1-i%d-tc%d.stdout' %
(rl, i, num_threads)),
args=[
'-tc',
str(num_threads), '-i',
str(i),
ph.inFile('adeno-genome.fa'),
ph.inFile('adeno-reads%d_1.fa' % rl), '-o',
ph.outFile('se-adeno-reads%d_1-i%d-tc%d.razers' %
(rl, i, num_threads))
],
to_diff=[(ph.inFile('se-adeno-reads%d_1-i%d-tc%d.razers' %
(rl, i, num_threads)),
ph.outFile('se-adeno-reads%d_1-i%d-tc%d.razers' %
(rl, i, num_threads))),
(ph.inFile('se-adeno-reads%d_1-i%d-tc%d.stdout' %
(rl, i, num_threads)),
ph.outFile('se-adeno-reads%d_1-i%d-tc%d.stdout' %
(rl, i, num_threads)))])
conf_list.append(conf)
# Compute with different output formats.
for of, suffix in enumerate(
['razers', 'fa', 'eland', 'gff', 'sam', 'afg']):
this_transforms = list(transforms)
if suffix == 'razers':
this_transforms += razers_transforms
elif suffix == 'sam':
this_transforms += sam_transforms
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('se-adeno-reads%d_1-of%d-tc%d.stdout' %
(rl, of, num_threads)),
args=[
'-tc',
str(num_threads),
ph.inFile('adeno-genome.fa'),
ph.inFile('adeno-reads%d_1.fa' % rl), '-o',
ph.outFile('se-adeno-reads%d_1-of%d-tc%d.%s' %
(rl, of, num_threads, suffix))
],
to_diff=[(ph.inFile('se-adeno-reads%d_1-of%d-tc%d.%s' %
(rl, of, num_threads, suffix)),
ph.outFile('se-adeno-reads%d_1-of%d-tc%d.%s' %
(rl, of, num_threads, suffix)),
this_transforms),
(ph.inFile('se-adeno-reads%d_1-of%d-tc%d.stdout' %
(rl, of, num_threads)),
ph.outFile('se-adeno-reads%d_1-of%d-tc%d.stdout' %
(rl, of, num_threads)), transforms)])
conf_list.append(conf)
# Compute with different sort orders.
for so in [0, 1]:
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('se-adeno-reads%d_1-so%d-tc%d.stdout' %
(rl, so, num_threads)),
args=[
'-tc',
str(num_threads), '-so',
str(so),
ph.inFile('adeno-genome.fa'),
ph.inFile('adeno-reads%d_1.fa' % rl), '-o',
ph.outFile('se-adeno-reads%d_1-so%d-tc%d.razers' %
(rl, so, num_threads))
],
to_diff=[(ph.inFile('se-adeno-reads%d_1-so%d-tc%d.razers' %
(rl, so, num_threads)),
ph.outFile('se-adeno-reads%d_1-so%d-tc%d.razers' %
(rl, so, num_threads))),
(ph.inFile('se-adeno-reads%d_1-so%d-tc%d.stdout' %
(rl, so, num_threads)),
ph.outFile('se-adeno-reads%d_1-so%d-tc%d.stdout' %
(rl, so, num_threads)))])
conf_list.append(conf)
# ============================================================
# Run Adeno Paired-End Tests
# ============================================================
# We run the following for all read lengths we have reads for.
for rl in [36, 100]:
# Run with default options.
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('pe-adeno-reads%d_2-tc%d.stdout' %
(rl, num_threads)),
args=[
'-tc',
str(num_threads),
ph.inFile('adeno-genome.fa'),
ph.inFile('adeno-reads%d_1.fa' % rl),
ph.inFile('adeno-reads%d_2.fa' % rl), '-o',
ph.outFile('pe-adeno-reads%d_2-tc%d.razers' %
(rl, num_threads))
],
to_diff=[(ph.inFile('pe-adeno-reads%d_2-tc%d.razers' %
(rl, num_threads)),
ph.outFile('pe-adeno-reads%d_2-tc%d.razers' %
(rl, num_threads)), razers_transforms),
(ph.inFile('pe-adeno-reads%d_2-tc%d.stdout' %
(rl, num_threads)),
ph.outFile('pe-adeno-reads%d_2-tc%d.stdout' %
(rl, num_threads)))])
conf_list.append(conf)
# Allow indels.
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('pe-adeno-reads%d_2-tc%d.stdout' %
(rl, num_threads)),
args=[
'-tc',
str(num_threads),
ph.inFile('adeno-genome.fa'),
ph.inFile('adeno-reads%d_1.fa' % rl),
ph.inFile('adeno-reads%d_2.fa' % rl), '-o',
ph.outFile('pe-adeno-reads%d_2-tc%d.razers' %
(rl, num_threads))
],
to_diff=[(ph.inFile('pe-adeno-reads%d_2-tc%d.razers' %
(rl, num_threads)),
ph.outFile('pe-adeno-reads%d_2-tc%d.razers' %
(rl, num_threads)), razers_transforms),
(ph.inFile('pe-adeno-reads%d_2-tc%d.stdout' %
(rl, num_threads)),
ph.outFile('pe-adeno-reads%d_2-tc%d.stdout' %
(rl, num_threads)))])
conf_list.append(conf)
# Compute forward/reverse matches only.
for o in ['-r', '-f']:
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('pe-adeno-reads%d_2%s-tc%d.stdout' %
(rl, o, num_threads)),
args=[
'-tc',
str(num_threads), o,
ph.inFile('adeno-genome.fa'),
ph.inFile('adeno-reads%d_1.fa' % rl),
ph.inFile('adeno-reads%d_2.fa' % rl), '-o',
ph.outFile('pe-adeno-reads%d_2%s-tc%d.razers' %
(rl, o, num_threads))
],
to_diff=[(ph.inFile('pe-adeno-reads%d_2%s-tc%d.razers' %
(rl, o, num_threads)),
ph.outFile('pe-adeno-reads%d_2%s-tc%d.razers' %
(rl, o, num_threads)), razers_transforms),
(ph.inFile('pe-adeno-reads%d_2%s-tc%d.stdout' %
(rl, o, num_threads)),
ph.outFile('pe-adeno-reads%d_2%s-tc%d.stdout' %
(rl, o, num_threads)))])
conf_list.append(conf)
# Compute with different identity rates.
for i in range(90, 101):
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('pe-adeno-reads%d_2-i%d-tc%d.stdout' %
(rl, i, num_threads)),
args=[
'-tc',
str(num_threads), '-i',
str(i),
ph.inFile('adeno-genome.fa'),
ph.inFile('adeno-reads%d_1.fa' % rl),
ph.inFile('adeno-reads%d_2.fa' % rl), '-o',
ph.outFile('pe-adeno-reads%d_2-i%d-tc%d.razers' %
(rl, i, num_threads))
],
to_diff=[(ph.inFile('pe-adeno-reads%d_2-i%d-tc%d.razers' %
(rl, i, num_threads)),
ph.outFile('pe-adeno-reads%d_2-i%d-tc%d.razers' %
(rl, i, num_threads)), razers_transforms),
(ph.inFile('pe-adeno-reads%d_2-i%d-tc%d.stdout' %
(rl, i, num_threads)),
ph.outFile('pe-adeno-reads%d_2-i%d-tc%d.stdout' %
(rl, i, num_threads)))])
conf_list.append(conf)
# Compute with different output formats.
for of, suffix in enumerate(
['razers', 'fa', 'eland', 'gff', 'sam', 'afg']):
this_transforms = list(transforms)
if suffix == 'razers':
this_transforms += razers_transforms
elif suffix == 'sam':
this_transforms += sam_transforms
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('pe-adeno-reads%d_2-of%d-tc%d.stdout' %
(rl, of, num_threads)),
args=[
'-tc',
str(num_threads),
ph.inFile('adeno-genome.fa'),
ph.inFile('adeno-reads%d_1.fa' % rl),
ph.inFile('adeno-reads%d_2.fa' % rl), '-o',
ph.outFile('pe-adeno-reads%d_2-of%d-tc%d.%s' %
(rl, of, num_threads, suffix))
],
to_diff=[(ph.inFile('pe-adeno-reads%d_2-of%d-tc%d.%s' %
(rl, of, num_threads, suffix)),
ph.outFile('pe-adeno-reads%d_2-of%d-tc%d.%s' %
(rl, of, num_threads, suffix)),
this_transforms),
(ph.inFile('pe-adeno-reads%d_2-of%d-tc%d.stdout' %
(rl, of, num_threads)),
ph.outFile('pe-adeno-reads%d_2-of%d-tc%d.stdout' %
(rl, of, num_threads)), this_transforms)])
conf_list.append(conf)
# Compute with different sort orders.
for so in [0, 1]:
conf = app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('pe-adeno-reads%d_2-so%d-tc%d.stdout' %
(rl, so, num_threads)),
args=[
'-tc',
str(num_threads), '-so',
str(so),
ph.inFile('adeno-genome.fa'),
ph.inFile('adeno-reads%d_1.fa' % rl),
ph.inFile('adeno-reads%d_2.fa' % rl), '-o',
ph.outFile('pe-adeno-reads%d_2-so%d-tc%d.razers' %
(rl, so, num_threads))
],
to_diff=[(ph.inFile('pe-adeno-reads%d_2-so%d-tc%d.razers' %
(rl, so, num_threads)),
ph.outFile('pe-adeno-reads%d_2-so%d-tc%d.razers' %
(rl, so, num_threads)),
razers_transforms),
(ph.inFile('pe-adeno-reads%d_2-so%d-tc%d.stdout' %
(rl, so, num_threads)),
ph.outFile('pe-adeno-reads%d_2-so%d-tc%d.stdout' %
(rl, so, num_threads)))])
conf_list.append(conf)
# Execute the tests.
failures = 0
for conf in conf_list:
res = app_tests.runTest(conf)
# Output to the user.
print(' '.join(['razers3'] + conf.args), end=' ')
if res:
print('OK')
else:
failures += 1
print('FAILED')
# Cleanup.
ph.deleteTempDir()
print('==============================')
print(' total tests: %d' % len(conf_list))
print(' failed tests: %d' % failures)
print('successful tests: %d' % (len(conf_list) - failures))
print('==============================')
# Compute and return return code.
return failures != 0
