def test_CAP_CNA_dry_run(self):
out_dir = os.path.join(self.tmp.name, 'CAP_CNA_dry_run')
os.mkdir(out_dir)
self.args.config = os.path.join(self.dataDir, 'CAP_CNA', 'study.txt')
self.args.out = out_dir
main(self.args)
self.verify_checksums(self.base_checksums, out_dir)
def verify_legacy_mutation(self, name, additional_checksums={}):
"""test the legacy mutation scripts for real"""
out_dir = os.path.join(self.tmp.name, name)
os.mkdir(out_dir)
self.args.config = os.path.join(self.dataDir, name, 'study.txt')
self.args.out = out_dir
self.args.dry_run = False
main(self.args)
checksums = self.base_checksums.copy()
checksums.update(additional_checksums)
self.verify_checksums(checksums, out_dir)
def test_sequenza(self):
out_dir = os.path.join(self.tmp.name, 'sequenza')
os.mkdir(out_dir)
self.args.dry_run = False
self.args.config = os.path.join(self.dataDir, 'Sequenza', 'study.txt')
self.args.out = out_dir
main(self.args)
checksums = self.base_checksums.copy()
sequenza_checksums = {
'data_segments_concat.txt': 'ea71ab46e72eafaaec415f3ed1520c68',
'meta_segments.txt': '056bc1c506c856f52197389676d9a4d3'
}
checksums.update(sequenza_checksums)
self.verify_checksums(checksums, out_dir)
def test_legacy_mutation_dry_run(self):
"""test the legacy mutation scripts in dry-run mode"""
names = [
'CAP_mutation',
#'GATK_haplotype_caller', # no config in /.mounts/labs/gsiprojects/gsi/cBioGSI/
'Mutect',
'Mutect2',
'MutectStrelka',
'Strelka'
]
for name in names:
out_dir = os.path.join(self.tmp.name, name)
os.mkdir(out_dir)
self.args.config = os.path.join(self.dataDir, name, 'study.txt')
self.args.out = out_dir
main(self.args)
self.verify_checksums(self.base_checksums, out_dir)
def test_cufflinks(self):
out_dir = os.path.join(self.tmp.name, 'Cufflinks')
os.mkdir(out_dir)
self.args.config = os.path.join(self.dataDir, 'Cufflinks', 'study.txt')
self.args.out = out_dir
self.args.dry_run = False
main(self.args)
checksums = self.base_checksums.copy()
cufflinks_checksums = {
'data_expression_continous.txt':
'0b5d72e82f10637dd791a35a85f08349',
'data_expression_zscores.txt': '2944c5b792e697eb37976de9225f21fe',
'meta_expression_continous.txt':
'5db83d4ca1925117abc8837b2eebeb46',
'meta_expression_zscores.txt': '4c807196b4d1e1e47710bd96343b3ccc',
'case_lists/cases_rna_seq_mrna.txt':
'412bd0b09e0a788dd03d7eb9841d271c'
}
self.verify_checksums(cufflinks_checksums, out_dir)
def test_CAP_expression(self):
out_dir = os.path.join(self.tmp.name, 'CAP_expression')
os.mkdir(out_dir)
self.args.config = os.path.join(self.dataDir, 'CAP_expression',
'study.txt')
self.args.out = out_dir
self.args.dry_run = False
main(self.args)
checksums = self.base_checksums.copy()
CAP_expression_checksums = {
'data_expression_continous.txt':
'e2b50dc44307e0b9bee27d253b02c6d9',
'data_expression_zscores.txt': '0a04f5f68265ca9a1aded16dd013738c',
'meta_expression_continous.txt':
'5db83d4ca1925117abc8837b2eebeb46',
'meta_expression_zscores.txt': '4c807196b4d1e1e47710bd96343b3ccc',
'case_lists/cases_rna_seq_mrna.txt':
'1497b32c3999df39b04333da92be5018'
}
checksums.update(CAP_expression_checksums)
self.verify_checksums(checksums, out_dir)
"--out",
help="Path to output file, or - for STDOUT",
metavar='PATH',
required=True)
parser.add_argument("-s",
"--schema",
help="Path to Janus schema file",
metavar='PATH',
required=True)
def add_validation_arguments(parser):
parser.add_argument("-c",
"--config",
help="Path to Janus config file",
metavar='PATH',
required=True)
parser.add_argument("-s",
"--schema",
help="Path to Janus schema file",
metavar='PATH',
required=True)
if __name__ == '__main__':
parser = super_parser()
if len(sys.argv) == 1:
parser.print_help(sys.stderr)
sys.exit(1)
main(parser.parse_args())