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 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 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 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 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 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 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 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 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, 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
