def test_check_input_bam_barcoded_warnIfForced(self):
sam_contents = \
'''@HD|VN:1.4|GO:none|SO:coordinate
@SQ|SN:chr10|LN:135534747
readNameA1|99|chr10|100|20|8M|=|300|200|NNNAAAAA|>>>>>>>>
readNameA1|147|chr10|100|20|8M|=|300|200|AAAAANNN|>>>>>>>>
readNameA2|99|chr10|100|20|8M|=|300|200|NNNAAAAA|>>>>>>>>
readNameA2|147|chr10|100|20|8M|=|300|200|AAAAANNN|>>>>>>>>
readNameA3|99|chr10|100|20|3S5M|=|300|200|NNNAAAAA|>>>>>>>>
readNameA3|147|chr10|100|20|5M3S|=|300|200|AAAAANNN|>>>>>>>>
readNameA4|99|chr10|100|20|3S5M|=|300|200|NNNAAAAA|>>>>>>>>
readNameA4|147|chr10|100|20|5M3S|=|300|200|AAAAANNN|>>>>>>>>
readNameA5|99|chr10|100|20|3S5M|=|300|200|NNNAAAAA|>>>>>>>>
readNameA5|147|chr10|100|20|5M3S|=|300|200|AAAAANNN|>>>>>>>>
'''
sam_contents = sam_contents.replace("|", "\t")
with TempDirectory() as tmp_dir:
input_bam_path = samtools_test.create_bam(tmp_dir.path,
"input.sam",
sam_contents,
index=True)
args = Namespace(input_bam=input_bam_path, force=True)
validator._check_input_bam_barcoded(args, self.mock_logger)
warnings = self.mock_logger._log_calls['WARNING']
self.assertEqual(1, len(warnings))
regex = r'\[.*input.bam\] reads do not appear to have barcodes.*forcing'
self.assertRegexpMatches(warnings[0], regex)
def test_check_input_bam_barcoded_okAtThreshold(self):
sam_contents = \
'''@HD|VN:1.4|GO:none|SO:coordinate
@SQ|SN:chr10|LN:135534747
readNameA1|99|chr10|100|20|8M|=|300|200|NNNAAAAA|>>>>>>>>
readNameA1|147|chr10|100|20|8M|=|300|200|AAAAANNN|>>>>>>>>
readNameA2|99|chr10|100|20|3S5M|=|300|200|NNNAAAAA|>>>>>>>>
readNameA2|147|chr10|100|20|5M3S|=|300|200|AAAAANNN|>>>>>>>>
readNameA3|99|chr10|100|20|3S5M|=|300|200|NNNAAAAA|>>>>>>>>
readNameA3|147|chr10|100|20|5M3S|=|300|200|AAAAANNN|>>>>>>>>
readNameA4|99|chr10|100|20|3S5M|=|300|200|NNNAAAAA|>>>>>>>>
readNameA4|147|chr10|100|20|5M3S|=|300|200|AAAAANNN|>>>>>>>>
readNameA5|99|chr10|100|20|3S5M|=|300|200|NNNAAAAA|>>>>>>>>
readNameA5|147|chr10|100|20|5M3S|=|300|200|AAAAANNN|>>>>>>>>
'''
sam_contents = sam_contents.replace("|", "\t")
with TempDirectory() as tmp_dir:
input_bam_path = samtools_test.create_bam(tmp_dir.path,
"input.sam",
sam_contents,
index=True)
args = Namespace(input_bam=input_bam_path, force=False)
validator._check_input_bam_barcoded(args, self.mock_logger)
self.ok()
self.assertEquals(0, len(self.mock_logger._log_calls))
def test_check_input_bam_barcoded_rightUnbarcodedRaisesUsageError(self):
sam_contents = \
'''@HD|VN:1.4|GO:none|SO:coordinate
@SQ|SN:chr10|LN:135534747
readNameA1|99|chr10|100|20|8M|=|300|200|NNNAAAAA|>>>>>>>>
readNameA1|147|chr10|100|20|8M|=|300|200|AAAAANNN|>>>>>>>>
readNameA2|99|chr10|100|20|3S5M|=|300|200|NNNAAAAA|>>>>>>>>
readNameA2|147|chr10|100|20|8M|=|300|200|AAAAANNN|>>>>>>>>
readNameA3|99|chr10|100|20|3S5M|=|300|200|NNNAAAAA|>>>>>>>>
readNameA3|147|chr10|100|20|5M3S|=|300|200|AAAAANNN|>>>>>>>>
readNameA4|99|chr10|100|20|3S5M|=|300|200|NNNAAAAA|>>>>>>>>
readNameA4|147|chr10|100|20|5M3S|=|300|200|AAAAANNN|>>>>>>>>
readNameA5|99|chr10|100|20|3S5M|=|300|200|NNNAAAAA|>>>>>>>>
readNameA5|147|chr10|100|20|5M3S|=|300|200|AAAAANNN|>>>>>>>>
'''
sam_contents = sam_contents.replace("|", "\t")
with TempDirectory() as tmp_dir:
input_bam_path = samtools_test.create_bam(tmp_dir.path,
"input.sam",
sam_contents,
index=True)
args = Namespace(input_bam=input_bam_path, force=False)
regex = r'\[.*input.bam\] reads do not appear to have barcodes'
self.assertRaisesRegexp(utils.UsageError, regex,
validator._check_input_bam_barcoded, args)
def test_check_input_bam_indexed_ok(self):
sam_contents = \
'''@HD|VN:1.4|GO:none|SO:coordinate
@SQ|SN:chr10|LN:135534747
readNameA1|99|chr10|100|20|5M|=|300|200|AAAAA|>>>>>'''.replace("|", "\t")
with TempDirectory() as tmp_dir:
input_bam_path = samtools_test.create_bam(tmp_dir.path,
"input.sam",
sam_contents,
index=True)
args = Namespace(input_bam=input_bam_path)
validator._check_input_bam_indexed(args)
self.ok()
def test_check_input_bam_indexed_raisesUsageError(self):
sam_contents = \
'''@HD|VN:1.4|GO:none|SO:coordinate
@SQ|SN:chr10|LN:135534747
readNameA1|99|chr10|100|20|5M|=|300|200|AAAAA|>>>>>'''.replace("|", "\t")
with TempDirectory() as tmp_dir:
input_bam_path = samtools_test.create_bam(tmp_dir.path,
"input.sam",
sam_contents,
index=False)
args = Namespace(input_bam=input_bam_path)
self.assertRaisesRegexp(utils.UsageError,
r'\[.*input.bam\] is not indexed',
validator._check_input_bam_indexed, args)
def test_check_input_bam_not_empty_raiseUsageError(self):
sam_contents = \
'''@HD|VN:1.4|GO:none|SO:coordinate
@SQ|SN:chr10|LN:135534747
'''.replace("|", "\t")
with TempDirectory() as tmp_dir:
input_bam_path = samtools_test.create_bam(tmp_dir.path,
"input.sam",
sam_contents,
index=True)
args = Namespace(input_bam=input_bam_path, force=False)
self.assertRaisesRegexp(utils.UsageError,
r'\[.*input.bam\] is empty',
validator._check_input_bam_not_empty, args)
def test_check_input_bam_paired_raisesUsageError(self):
sam_contents = \
'''@HD|VN:1.4|GO:none|SO:coordinate
@SQ|SN:chr10|LN:135534747
readNameA1|{flag}|chr10|100|20|5M|=|300|200|AAAAA|>>>>>'''
sam_contents = sam_contents.format(flag='16').replace("|", "\t")
with TempDirectory() as tmp_dir:
input_bam_path = samtools_test.create_bam(tmp_dir.path,
"input.sam",
sam_contents,
index=True)
args = Namespace(input_bam=input_bam_path, force=False)
regex = r'\[.*input.bam\] does not appear to contain paired reads'
self.assertRaisesRegexp(utils.UsageError, regex,
validator._check_input_bam_paired, args)
def test_check_input_bam_not_deduped_ok(self):
sam_contents = \
'''@HD|VN:1.4|GO:none|SO:coordinate
@SQ|SN:chr10|LN:135534747
@PG|ID:foo|PN:bwa
readNameA1|99|chr10|100|20|5M|=|300|200|AAAAA|>>>>>'''.replace("|", "\t")
with TempDirectory() as tmp_dir:
input_bam_path = samtools_test.create_bam(tmp_dir.path,
"input.sam",
sam_contents,
index=True)
args = Namespace(input_bam=input_bam_path, force=True)
validator._check_input_bam_not_deduped(args, self.mock_logger)
self.ok()
self.assertEqual(0, len(self.mock_logger._log_calls))
def test_check_input_bam_not_deduped_raisesUsageError(self):
sam_contents = \
'''@HD|VN:1.4|GO:none|SO:coordinate
@SQ|SN:chr10|LN:135534747
@PG|ID:foo|PN:connor
readNameA1|99|chr10|100|20|5M|=|300|200|AAAAA|>>>>>'''.replace("|", "\t")
with TempDirectory() as tmp_dir:
input_bam_path = samtools_test.create_bam(tmp_dir.path,
"input.sam",
sam_contents,
index=True)
args = Namespace(input_bam=input_bam_path, force=False)
regex = (r'\[.*input.bam\] has already been processed with Connor'
r'.*Are you sure.*force')
self.assertRaisesRegexp(utils.UsageError, regex,
validator._check_input_bam_not_deduped,
args)
def test_check_input_bam_paired_ok(self):
sam_contents = \
'''@HD|VN:1.4|GO:none|SO:coordinate
@SQ|SN:chr10|LN:135534747
readNameA1|{unpaired_flag}|chr10|100|20|5M|=|300|200|AAAAA|>>>>>
readNameA1|{paired_flag}|chr10|100|20|5M|=|300|200|AAAAA|>>>>>'''
sam_contents = sam_contents.format(unpaired_flag='16', paired_flag='99')
sam_contents = sam_contents.replace("|", "\t")
with TempDirectory() as tmp_dir:
input_bam_path = samtools_test.create_bam(tmp_dir.path,
"input.sam",
sam_contents,
index=True)
args = Namespace(input_bam=input_bam_path, force=True)
validator._check_input_bam_paired(args, self.mock_logger)
self.ok()
self.assertEqual(0, len(self.mock_logger._log_calls))
def test_check_input_bam_paired_warnIfForced(self):
sam_contents = \
'''@HD|VN:1.4|GO:none|SO:coordinate
@SQ|SN:chr10|LN:135534747
readNameA1|{flag}|chr10|100|20|5M|=|300|200|AAAAA|>>>>>'''
sam_contents = sam_contents.format(flag='16').replace("|", "\t")
with TempDirectory() as tmp_dir:
input_bam_path = samtools_test.create_bam(tmp_dir.path,
"input.sam",
sam_contents,
index=True)
args = Namespace(input_bam=input_bam_path, force=True)
validator._check_input_bam_paired(args, self.mock_logger)
warnings = self.mock_logger._log_calls['WARNING']
self.assertEqual(1, len(warnings))
regex = (r'\[.*input.bam\] does not appear to contain paired '
r'reads.*forcing')
self.assertRegexpMatches(warnings[0], regex)
def test_check_input_bam_not_deduped_warnIfForced(self):
sam_contents = \
'''@HD|VN:1.4|GO:none|SO:coordinate
@SQ|SN:chr10|LN:135534747
@PG|ID:foo|PN:connor
readNameA1|99|chr10|100|20|5M|=|300|200|AAAAA|>>>>>'''.replace("|", "\t")
with TempDirectory() as tmp_dir:
input_bam_path = samtools_test.create_bam(tmp_dir.path,
"input.sam",
sam_contents,
index=True)
args = Namespace(input_bam=input_bam_path, force=True)
validator._check_input_bam_not_deduped(args, log=self.mock_logger)
warnings = self.mock_logger._log_calls['WARNING']
self.assertEqual(1, len(warnings))
regex = (r'\[.*input.bam\] has already been processed with Connor'
r'.*forcing')
self.assertRegexpMatches(warnings[0], regex)
def test_check_input_bam_consistent_length_warnIfForced(self):
sam_contents = \
'''@HD|VN:1.4|GO:none|SO:coordinate
@SQ|SN:chr10|LN:135534747
readNameA1|99|chr10|100|20|10M|=|300|200|AAAAANNNNN|>>>>>!!!!!
readNameA2|99|chr10|100|20|8M|=|300|200|AAAAANNN|>>>>>!!!
readNameA3|99|chr10|100|20|5M|=|300|200|AAAAA|>>>>>
readNameA4|99|chr10|100|20|5M|=|300|200|AAAAA|>>>>>
readNameA5|99|chr10|100|20|5M|=|300|200|AAAAA|>>>>>
readNameA6|99|chr10|100|20|5M|=|300|200|AAAAA|>>>>>
readNameA7|99|chr10|100|20|5M|=|300|200|AAAAA|>>>>>
readNameA8|99|chr10|100|20|5M|=|300|200|AAAAA|>>>>>
readNameA9|99|chr10|100|20|5M|=|300|200|AAAAA|>>>>>
readNameA0|99|chr10|100|20|5M|=|300|200|AAAAA|>>>>>
readNameA1|147|chr10|100|20|10M|=|300|200|AAAAANNNNN|>>>>>!!!!!
readNameA2|147|chr10|100|20|5M|=|300|200|AAANN|>>>!!
readNameA3|147|chr10|100|20|3M|=|300|200|AAA|>>>
readNameA4|147|chr10|100|20|3M|=|300|200|AAA|>>>
readNameA5|147|chr10|100|20|3M|=|300|200|AAA|>>>
readNameA6|147|chr10|100|20|3M|=|300|200|AAA|>>>
readNameA7|147|chr10|100|20|3M|=|300|200|AAA|>>>
readNameA8|147|chr10|100|20|3M|=|300|200|AAA|>>>
readNameA9|147|chr10|100|20|3M|=|300|200|AAA|>>>
readNameA0|147|chr10|100|20|3M|=|300|200|AAA|>>>
'''
sam_contents = sam_contents.replace("|", "\t")
with TempDirectory() as tmp_dir:
input_bam_path = samtools_test.create_bam(tmp_dir.path,
"input.sam",
sam_contents,
index=True)
args = Namespace(input_bam=input_bam_path, force=True)
validator._check_input_bam_consistent_length(
args, self.mock_logger)
self.ok()
warnings = self.mock_logger._log_calls['WARNING']
self.assertEqual(1, len(warnings))
regex = (r'\[.*input.bam\] reads appear to have inconsistent '
r'sequence lengths\..*forcing')
self.assertRegexpMatches(warnings[0], regex)
def test_check_input_bam_consistent_length_negRaisesUsageError(self):
sam_contents = \
'''@HD|VN:1.4|GO:none|SO:coordinate
@SQ|SN:chr10|LN:135534747
readNameA1|99|chr10|100|20|10M|=|300|200|AAAAANNNNN|>>>>>!!!!!
readNameA2|99|chr10|100|20|5M|=|300|200|AAAAA|>>>>>
readNameA3|99|chr10|100|20|5M|=|300|200|AAAAA|>>>>>
readNameA4|99|chr10|100|20|5M|=|300|200|AAAAA|>>>>>
readNameA5|99|chr10|100|20|5M|=|300|200|AAAAA|>>>>>
readNameA6|99|chr10|100|20|5M|=|300|200|AAAAA|>>>>>
readNameA7|99|chr10|100|20|5M|=|300|200|AAAAA|>>>>>
readNameA8|99|chr10|100|20|5M|=|300|200|AAAAA|>>>>>
readNameA9|99|chr10|100|20|5M|=|300|200|AAAAA|>>>>>
readNameA0|99|chr10|100|20|5M|=|300|200|AAAAA|>>>>>
readNameA1|147|chr10|100|20|10M|=|300|200|AAAAANNNNN|>>>>>!!!!!
readNameA2|147|chr10|100|20|5M|=|300|200|AAANN|>>>!!
readNameA3|147|chr10|100|20|3M|=|300|200|AAA|>>>
readNameA4|147|chr10|100|20|3M|=|300|200|AAA|>>>
readNameA5|147|chr10|100|20|3M|=|300|200|AAA|>>>
readNameA6|147|chr10|100|20|3M|=|300|200|AAA|>>>
readNameA7|147|chr10|100|20|3M|=|300|200|AAA|>>>
readNameA8|147|chr10|100|20|3M|=|300|200|AAA|>>>
readNameA9|147|chr10|100|20|3M|=|300|200|AAA|>>>
readNameA0|147|chr10|100|20|3M|=|300|200|AAA|>>>
'''
sam_contents = sam_contents.replace("|", "\t")
with TempDirectory() as tmp_dir:
input_bam_path = samtools_test.create_bam(tmp_dir.path,
"input.sam",
sam_contents,
index=True)
args = Namespace(input_bam=input_bam_path, force=False)
regex = (r'\[.*input.bam\] reads appear to have inconsistent '
r'sequence lengths\..*force')
self.assertRaisesRegexp(UsageError,
regex,
validator._check_input_bam_consistent_length,
args)
