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 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 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
"""
import logging
import os.path
import sys
import glob
# Automagically add util/py_lib to PYTHONPATH environment variable.
path = os.path.abspath(
os.path.join(os.path.dirname(__file__), '..', '..', '..', '..', 'util',
'py_lib'))
sys.path.insert(0, path)
import seqan.app_tests as app_tests
transforms = [
app_tests.RegexpReplaceTransform("[0-9\.\-e]+ sec", "0.0 sec"),
app_tests.RegexpReplaceTransform("Free [0-9]+ of [0-9]+ MB",
"Free 0 of 0 MB")
]
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
"""
import logging
import os.path
import sys
import glob
# Automagically add util/py_lib to PYTHONPATH environment variable.
path = os.path.abspath(
os.path.join(os.path.dirname(__file__), '..', '..', '..', 'util',
'py_lib'))
sys.path.insert(0, path)
import seqan.app_tests as app_tests
log_transforms = [
app_tests.RegexpReplaceTransform("[0-9\.\-e]+ sec", "0.0 sec"),
app_tests.RegexpReplaceTransform("Free [0-9]+ of [0-9]+ MB",
"Free 0 of 0 MB")
]
sam_transforms = [app_tests.RegexpReplaceTransform("@PG.*", "@PG")]
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
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
Usage: run_tests.py SOURCE_ROOT_PATH BINARY_ROOT_PATH
"""
import logging
import os.path
import sys
import glob
# Automagically add util/py_lib to PYTHONPATH environment variable.
path = os.path.abspath(os.path.join(os.path.dirname(__file__), '..', '..',
'..', '..', 'util', 'py_lib'))
sys.path.insert(0, path)
import seqan.app_tests as app_tests
transforms = [
app_tests.RegexpReplaceTransform("[0-9\.\-e]+ sec", "0.0 sec")
]
defaultFormat = 'raw'
samFormat = 'sam'
def getMapperConf(ph, path_to_program, rl, optionName, optionValue):
return app_tests.TestConf(
program=path_to_program,
redir_stdout=ph.outFile('se-adeno-reads%d_1-%s%s.stdout' % (rl, optionName, optionValue)),
args=['-'+optionName, str(optionValue),
ph.inFile('adeno-genome.fa'),
ph.inFile('adeno-reads%d_1.fa' % rl),
'-o', ph.outFile('se-adeno-reads%d_1-%s%s.out.%s' % (rl, optionName, optionValue, defaultFormat))],
to_diff=[(ph.inFile('se-adeno-reads%d_1-%s%s.out.%s' % (rl, optionName, optionValue, defaultFormat)),
ph.outFile('se-adeno-reads%d_1-%s%s.out.%s' % (rl, optionName, optionValue, defaultFormat)), 'md5'),