def test_2(self):
# now some errors
file_name = op.join(DATA_DIR, "tst_2_subreads.bam")
e, c = bam.validate_bam(file_name, validate_index=True)
errors = sorted(list(set([type(err).__name__ for err in e])))
self.assertEqual(errors, [
'AlignmentCigarError', 'AlignmentCigarMatchError',
'AlignmentNotUniqueError', 'AlignmentUnmappedError',
'BasecallerVersionError', 'MissingCodecError', 'MissingIndexError',
'MissingPlatformError', 'QnameFormatError', 'QnameRangeError',
'ReadGroupChemistryError', 'ReadGroupIdMismatchError',
"ReadLengthError", 'TagValueError', 'UninitializedSNRError',
'UnsortedError'
])
e, c = bam.validate_bam(file_name,
validate_index=True,
permissive_headers=True)
errors2 = set([type(err).__name__ for err in e])
self.assertEqual(len(errors2), len(errors) - 2)
self.assertFalse("ReadGroupChemistryError" in errors2)
self.assertFalse("BasecallerVersionError" in errors2)
def test_2(self):
# now some errors
file_name = op.join(DATA_DIR, "tst_2_subreads.bam")
e, c = bam.validate_bam(file_name, validate_index=True)
errors = sorted(list(set([type(err).__name__ for err in e])))
self.assertEqual(errors,
['AlignmentCigarError', 'AlignmentCigarMatchError',
'AlignmentNotUniqueError',
'AlignmentUnmappedError',
'BasecallerVersionError',
'MissingCodecError', 'MissingIndexError',
'MissingPlatformError', 'QnameFormatError',
'QnameRangeError', 'ReadGroupChemistryError',
'ReadGroupIdMismatchError', "ReadLengthError",
'TagValueError',
'UninitializedSNRError', 'UnsortedError'])
e, c = bam.validate_bam(file_name, validate_index=True,
permissive_headers=True)
errors2 = set([type(err).__name__ for err in e])
self.assertEqual(len(errors2), len(errors) - 2)
self.assertFalse("ReadGroupChemistryError" in errors2)
self.assertFalse("BasecallerVersionError" in errors2)
def test_4_unmapped(self):
file_name = op.join(DATA_DIR, "tst_4_subreads.bam")
e, c = bam.validate_bam(file_name)
errors1 = sorted([type(err).__name__ for err in e])
assert errors1 == [
'BasecallerVersionError', 'MissingCodecError',
'QnameHoleNumberError', 'QnameMovieError',
'ReadGroupChemistryError', 'UninitializedSNRError',
'UnmappedPropertiesError', 'UnsortedError', 'WrongPlatformError'
]
e, c = bam.validate_bam(file_name, aligned=True)
errors2 = sorted([type(err).__name__ for err in e])
assert errors2 == [
'BasecallerVersionError', 'FileNotAlignedError',
'MissingCodecError', 'QnameHoleNumberError', 'QnameMovieError',
'ReadGroupChemistryError', 'UninitializedSNRError',
'UnsortedError', 'WrongPlatformError'
]
# this should yield the same result as the first run
e, c = bam.validate_bam(file_name, aligned=False)
errors3 = sorted([type(err).__name__ for err in e])
assert errors3 == errors1
def test_4_unmapped(self):
file_name = op.join(DATA_DIR, "tst_4_subreads.bam")
e, c = bam.validate_bam(file_name)
errors1 = sorted([type(err).__name__ for err in e])
self.assertEqual(errors1, ['BasecallerVersionError',
'MissingCodecError',
'PulseFeatureError', 'QnameHoleNumberError', 'QnameMovieError', 'ReadGroupChemistryError',
'UninitializedSNRError',
'UnmappedPropertiesError', 'UnsortedError',
'WrongPlatformError'])
e, c = bam.validate_bam(file_name, aligned=True)
errors2 = sorted([type(err).__name__ for err in e])
self.assertEqual(errors2,
['BasecallerVersionError',
'FileNotAlignedError', 'MissingCodecError',
'PulseFeatureError',
'QnameHoleNumberError', 'QnameMovieError',
'ReadGroupChemistryError',
'UninitializedSNRError', 'UnsortedError',
'WrongPlatformError'])
# this should yield the same result as the first run
e, c = bam.validate_bam(file_name, aligned=False)
errors3 = sorted([type(err).__name__ for err in e])
self.assertEqual(errors3, errors1)
def test_1c_reference_fasta(self):
file_name = op.join(DATA_DIR, "tst_1_subreads.bam")
fasta_file = op.join(DATA_DIR, "tst1.fasta")
e, c = bam.validate_bam(file_name, reference=fasta_file)
self.assertEqual(len(e), 0)
e, c = bam.validate_bam(file_name, aligned=False)
def test_1b(self):
file_name = op.join(DATA_DIR, "tst_1_subreads.bam")
e, c = bam.validate_bam(file_name, aligned=False, contents="CCS")
errors = sorted([type(err).__name__ for err in e])
self.assertEqual(errors,
['FileAlignedError', 'FileContentMismatchError'])
def test_zero_length_scrap(self):
BAM = "/pbi/dept/secondary/siv/testdata/SA3-Sequel/ecoli/EmptyRecords/m54043_180414_094215.scraps.bam"
with warnings.catch_warnings(record=True) as w:
e, c = bam.validate_bam(BAM, aligned=False)
assert len(e) == 0
assert len(w) == 7
def test_overlapping_alignments(self):
BAM = "/pbi/dept/secondary/siv/testdata/pbreports-unittest/data/mapping_stats/pbmm2/aligned.bam"
e, c = bam.validate_bam(BAM, aligned=True)
errors2 = list(set(sorted([type(err).__name__ for err in e])))
assert errors2 == ["AlignmentNotUniqueError"]
def test_transcript_bam(self):
BAM = "/pbi/dept/secondary/siv/testdata/isoseqs/TranscriptSet/unpolished.bam"
e, c = bam.validate_bam(BAM, max_records=10)
assert len(e) == 0
def test_valid_ccs_strand_suffix(self):
file_name = op.join(DATA_DIR, "tst_6.ccs.bam")
e, c = bam.validate_bam(file_name)
assert len(e) == 0
def test_bad_encoding(self):
file_name = op.join(DATA_DIR, "tst_5_subreads.bam")
e, c = bam.validate_bam(file_name)
errors1 = sorted([type(err).__name__ for err in e])
assert errors1 == ["BadEncodingError"]
def test_3_unmapped(self):
file_name = op.join(DATA_DIR, "tst_3_subreads.bam")
e, c = bam.validate_bam(file_name)
assert len(e) == 0
def test_1c_reference_fasta(self):
file_name = op.join(DATA_DIR, "tst_1_subreads.bam")
fasta_file = op.join(DATA_DIR, "tst1.fasta")
e, c = bam.validate_bam(file_name, reference=fasta_file)
assert len(e) == 0
e, c = bam.validate_bam(file_name, aligned=False)
def test_1b(self):
file_name = op.join(DATA_DIR, "tst_1_subreads.bam")
e, c = bam.validate_bam(file_name, aligned=False, contents="CCS")
errors = sorted([type(err).__name__ for err in e])
assert errors == ['FileAlignedError', 'FileContentMismatchError']
def test_3_unmapped(self):
file_name = op.join(DATA_DIR, "tst_3_subreads.bam")
e, c = bam.validate_bam(file_name)
self.assertEqual(len(e), 0)
def test_invalid_ccs_strand_suffix(self):
file_name = op.join(DATA_DIR, "tst_7.ccs.bam")
e, c = bam.validate_bam(file_name)
errors1 = sorted(list(set([type(err).__name__ for err in e])))
assert errors1 == ['QnameFormatError']
def test_1(self):
file_name = op.join(DATA_DIR, "tst_1_subreads.bam")
e, c = bam.validate_bam(file_name)
self.assertEqual(len(e), 0)
