def check_and_run_validate(self, lib):
# run validation
self.assertTrue(glob_exists(self.temp_output, lib,
SUBCOMMAND.VALIDATE))
qsub = unique_exists(
os.path.join(self.temp_output, lib, SUBCOMMAND.VALIDATE,
'*-1/submit.sh'))
args = convert_qsub_to_args(qsub) # read the arguments from the file
print(args)
with patch.object(sys, 'argv', args):
self.assertEqual(0, main())
for suffix in [
'contigs.bam', 'contigs.fa', 'contigs.sorted.bam',
'contigs.sorted.bam.bai', 'evidence.bed', 'igv.batch',
'raw_evidence.bam', 'raw_evidence.sorted.bam',
'raw_evidence.sorted.bam.bai', 'validation-failed.tab',
'validation-passed.tab'
]:
self.assertTrue(
glob_exists(self.temp_output, lib,
SUBCOMMAND.VALIDATE + '/*-1', '*.' + suffix))
self.assertTrue(
glob_exists(self.temp_output, lib, SUBCOMMAND.VALIDATE + '/*-1',
'*.COMPLETE'))
def test_clean_files(self):
args = [
'mavis', SUBCOMMAND.PIPELINE, CLEAN_CONFIG, '-o', self.temp_output
]
with patch.object(sys, 'argv', args):
self.assertEqual(0, main())
# check that the subdirectories were built
for lib in [MOCK_GENOME + '_*', MOCK_TRANS + '_*']:
self.check_cluster(lib)
# run validation
self.assertTrue(
glob_exists(self.temp_output, lib, SUBCOMMAND.VALIDATE))
qsub = unique_exists(
os.path.join(self.temp_output, lib, SUBCOMMAND.VALIDATE,
'*-1/submit.sh'))
args = convert_qsub_to_args(
qsub) # read the arguments from the file
print(args)
with patch.object(sys, 'argv', args):
self.assertEqual(0, main())
for suffix in [
'evidence.bed', 'validation-failed.tab',
'validation-passed.tab'
]:
self.assertTrue(
glob_exists(self.temp_output, lib,
SUBCOMMAND.VALIDATE + '/*-1', '*.' + suffix))
for suffix in [
'contigs.bam',
'contigs.blat_out.pslx',
'contigs.fa',
'contigs.sorted.bam',
'contigs.sorted.bam.bai',
'igv.batch',
'raw_evidence.bam',
'raw_evidence.sorted.bam',
'raw_evidence.sorted.bam.bai',
]:
self.assertFalse(
glob_exists(self.temp_output, lib,
SUBCOMMAND.VALIDATE + '/*-1', '*.' + suffix))
self.assertTrue(
glob_exists(self.temp_output, lib,
SUBCOMMAND.VALIDATE + '/*-1', '*.COMPLETE'))
self.check_and_run_annotate(lib)
# now run the pairing
self.check_and_run_pairing()
# now run the summary
self.check_and_run_summary()
with patch.object(
sys, 'argv',
['mavis', SUBCOMMAND.CHECKER, '-o', self.temp_output]):
self.assertEqual(0, main())
self.assertTrue(glob_exists(self.temp_output, 'submit_pipeline*.sh'))
def check_and_run_pairing(self):
# now run the pairing
self.assertTrue(glob_exists(self.temp_output, SUBCOMMAND.PAIR))
qsub = unique_exists(
os.path.join(self.temp_output, SUBCOMMAND.PAIR, 'submit.sh'))
args = convert_qsub_to_args(qsub)
with patch.object(sys, 'argv', args):
self.assertEqual(0, main())
self.assertTrue(
glob_exists(self.temp_output, SUBCOMMAND.PAIR,
'mavis_paired*.tab'))
self.assertTrue(
glob_exists(self.temp_output, SUBCOMMAND.PAIR, '*.COMPLETE'))
def run_main(self, inputfile, file_type, strand_specific=False):
outputfile = os.path.join(TEMP_OUTPUT, file_type + '.tab')
args = [
'mavis', SUBCOMMAND.CONVERT, '-o', outputfile, '-n', inputfile,
'--file_type', file_type, '--strand_specific', strand_specific
]
with patch.object(sys, 'argv', args):
self.assertEqual(0, main())
print('output', outputfile)
self.assertTrue(unique_exists(outputfile))
result = {}
for pair in read_bpp_from_input_file(outputfile):
result.setdefault(pair.tracking_id, []).append(pair)
return result
def check_and_run_summary(self, count=3):
# now run the summary
self.assertTrue(glob_exists(self.temp_output, SUBCOMMAND.SUMMARY))
qsub = unique_exists(
os.path.join(self.temp_output, SUBCOMMAND.SUMMARY, 'submit.sh'))
args = convert_qsub_to_args(qsub)
with patch.object(sys, 'argv', args):
self.assertEqual(0, main())
self.assertTrue(
glob_exists(self.temp_output,
SUBCOMMAND.SUMMARY,
'mavis_summary*.tab',
n=count))
self.assertTrue(
glob_exists(self.temp_output, SUBCOMMAND.SUMMARY, '*.COMPLETE'))
def check_and_run_annotate(self, lib):
# run annotation
self.assertTrue(glob_exists(self.temp_output, lib,
SUBCOMMAND.ANNOTATE))
qsub = unique_exists(
os.path.join(self.temp_output, lib, SUBCOMMAND.ANNOTATE,
'*-1/submit.sh'))
args = convert_qsub_to_args(qsub)
with patch.object(sys, 'argv', args):
self.assertEqual(0, main())
# check the generated files
self.assertTrue(
glob_exists(self.temp_output, lib, SUBCOMMAND.ANNOTATE + '/*-1',
'annotations.tab'))
self.assertTrue(
glob_exists(self.temp_output, lib, SUBCOMMAND.ANNOTATE + '/*-1',
'annotations.fusion-cdna.fa'))
self.assertTrue(
glob_exists(self.temp_output, lib, SUBCOMMAND.ANNOTATE + '/*-1',
'drawings'))
self.assertTrue(
glob_exists(self.temp_output,
lib,
SUBCOMMAND.ANNOTATE + '/*-1',
'drawings',
'*svg',
strict=False))
self.assertTrue(
glob_exists(self.temp_output,
lib,
SUBCOMMAND.ANNOTATE + '/*-1',
'drawings',
'*json',
strict=False))
self.assertTrue(
glob_exists(self.temp_output, lib, SUBCOMMAND.ANNOTATE + '/*-1',
'*.COMPLETE'))