def test_read_evidence_variant_matching_gatk_mini_bundle_extract():
handle = Samfile(data_path("gatk_mini_bundle_extract.bam"))
loci = [
Locus.from_inclusive_coordinates("20", 10008951), # 0
Locus.from_inclusive_coordinates("20", 10009053), # 1
Locus.from_inclusive_coordinates("20", 10009053, 10009054), # 2
Locus.from_inclusive_coordinates("20", 10006822), # 3
Locus.from_inclusive_coordinates("20", 10006822, 10006823), # 4
]
evidence = PileupCollection.from_bam(handle, loci)
eq_(evidence.match_summary(Variant(loci[0], "A", "C")), [('A', 1),
('C', 4)])
eq_(
evidence.filter(drop_duplicates=True).match_summary(
Variant(loci[0], "A", "C")), [('A', 0), ('C', 3)])
eq_(evidence.match_summary(Variant(loci[1], "A", "C")), [('A', 3),
('C', 0)])
eq_(evidence.match_summary(Variant(loci[1], "A", "CC")), [('A', 3),
('CC', 0)])
eq_(evidence.match_summary(Variant(loci[1], "A", "")), [('A', 3), ('', 0)])
eq_(evidence.match_summary(Variant(loci[1], "A", "")), [('A', 3), ('', 0)])
eq_(evidence.match_summary(Variant(loci[2], "AT", "")), [('AT', 3),
('', 0)])
eq_(evidence.match_summary(Variant(loci[3], "A", "")), [('A', 2), ('', 6)])
eq_(evidence.match_summary(Variant(loci[4], "AC", "")), [('AC', 2),
('', 6)])
eq_(
evidence.match_summary(
Variant(loci[4], "AC", ""),
lambda e: e.read_attributes().mapping_quality.mean()),
[('AC', 60.0), ('', 65.0)])
def test_read_evidence_variant_matching_gatk_mini_bundle_extract_warning():
filename = data_path("gatk_mini_bundle_extract.bam")
# Should log a warning but pass.
loci = [
Locus.from_inclusive_coordinates("20", 10009053, 10009054), # 0
]
evidence = PileupCollection.from_bam(filename, loci)
eq_(evidence.match_summary(Variant(loci[0], "A", "")), [('A', 0), ('', 0),
('AT', 3)])
def test_read_evidence_variant_matching_gatk_mini_bundle_extract_warning():
filename = data_path("gatk_mini_bundle_extract.bam")
# Should log a warning but pass.
loci = [
Locus.from_inclusive_coordinates("20", 10009053, 10009054), # 0
]
evidence = PileupCollection.from_bam(filename, loci)
eq_(evidence.match_summary(Variant(loci[0], "A", "")),
[('A', 0), ('', 0), ('AT', 3)])
def test_read_evidence_variant_matching_gatk_bundle_native_varcode_variant():
# Try native varcode Variant.
handle = Samfile(data_path("gatk_mini_bundle_extract.bam"))
locus = Locus.from_inclusive_coordinates("20", 10008951)
variant = VarcodeVariant(
locus.contig,
locus.position + 1, # inclusive not interbase
"A",
"C")
evidence = PileupCollection.from_bam(handle, [variant])
eq_(evidence.match_summary(variant), [('A', 1), ('C', 4)])
def test_read_evidence_variant_matching_gatk_bundle_native_varcode_variant():
# Try native varcode Variant.
handle = Samfile(data_path("gatk_mini_bundle_extract.bam"))
locus = Locus.from_inclusive_coordinates("20", 10008951)
variant = VarcodeVariant(
locus.contig,
locus.position + 1, # inclusive not interbase
"A",
"C")
evidence = PileupCollection.from_bam(handle, [variant])
eq_(evidence.match_summary(variant),
[('A', 1), ('C', 4)])
def test_read_evidence_variant_matching_gatk_mini_bundle_extract():
handle = Samfile(data_path("gatk_mini_bundle_extract.bam"))
loci = [
Locus.from_inclusive_coordinates("20", 10008951), # 0
Locus.from_inclusive_coordinates("20", 10009053), # 1
Locus.from_inclusive_coordinates("20", 10009053, 10009054), # 2
Locus.from_inclusive_coordinates("20", 10006822), # 3
Locus.from_inclusive_coordinates("20", 10006822, 10006823), # 4
]
evidence = PileupCollection.from_bam(handle, loci)
eq_(evidence.match_summary(Variant(loci[0], "A", "C")),
[('A', 1), ('C', 4)])
eq_(evidence.filter(drop_duplicates=True).match_summary(
Variant(loci[0], "A", "C")),
[('A', 0), ('C', 3)])
eq_(evidence.match_summary(Variant(loci[1], "A", "C")),
[('A', 3), ('C', 0)])
eq_(evidence.match_summary(Variant(loci[1], "A", "CC")),
[('A', 3), ('CC', 0)])
eq_(evidence.match_summary(Variant(loci[1], "A", "")),
[('A', 3), ('', 0)])
eq_(evidence.match_summary(Variant(loci[1], "A", "")),
[('A', 3), ('', 0)])
eq_(evidence.match_summary(Variant(loci[2], "AT", "")),
[('AT', 3), ('', 0)])
eq_(evidence.match_summary(Variant(loci[3], "A", "")),
[('A', 2), ('', 6)])
eq_(evidence.match_summary(Variant(loci[4], "AC", "")),
[('AC', 2), ('', 6)])
eq_(evidence.match_summary(
Variant(loci[4], "AC", ""),
lambda e: e.read_attributes().mapping_quality.mean()),
[('AC', 60.0), ('', 65.0)])
def test_read_evidence_rna1_multi_base_loci():
loci = [
Locus.from_inclusive_coordinates("17", 41244853, 41244854), # 0
Locus.from_inclusive_coordinates("17", 41244853, 41244857), # 1
Locus.from_inclusive_coordinates("17", 41244854, 41244857), # 2
Locus.from_inclusive_coordinates("17", 41244852, 41244857), # 3
Locus.from_inclusive_coordinates("17", 41244933, 41244936), # 4
Locus.from_inclusive_coordinates("17", 41244933, 41244937), # 5
Locus.from_inclusive_coordinates("17", 41244971, 41244973), # 6
Locus.from_inclusive_coordinates("17", 41265063, 41265067), # 7
]
evidence = PileupCollection.from_bam(data_path("rna_chr17_41244936.bam"),
loci)
eq_(evidence.allele_summary(loci[0]), [("CT", 1)])
eq_(evidence.allele_summary(loci[1]), [("CTTTT", 1)])
eq_(evidence.allele_summary(loci[2]), [("TTTT", 1)])
eq_(evidence.allele_summary(loci[3]), [])
eq_(evidence.allele_summary(loci[4]), [("AACA", 11), ("AACG", 6),
("GACG", 1)])
eq_(evidence.allele_summary(loci[5]), [("AACAG", 10), ("AACGG", 6),
("AACAA", 1), ("GACGG", 1)])
eq_(evidence.allele_summary(loci[6]), [("ATT", 11)])
eq_(evidence.allele_summary(loci[7]), [("ACCCG", 1)])
def test_read_evidence_rna1_multi_base_loci():
loci = [
Locus.from_inclusive_coordinates("17", 41244853, 41244854), # 0
Locus.from_inclusive_coordinates("17", 41244853, 41244857), # 1
Locus.from_inclusive_coordinates("17", 41244854, 41244857), # 2
Locus.from_inclusive_coordinates("17", 41244852, 41244857), # 3
Locus.from_inclusive_coordinates("17", 41244933, 41244936), # 4
Locus.from_inclusive_coordinates("17", 41244933, 41244937), # 5
Locus.from_inclusive_coordinates("17", 41244971, 41244973), # 6
Locus.from_inclusive_coordinates("17", 41265063, 41265067), # 7
]
evidence = PileupCollection.from_bam(
data_path("rna_chr17_41244936.bam"), loci)
eq_(evidence.allele_summary(loci[0]), [("CT", 1)])
eq_(evidence.allele_summary(loci[1]), [("CTTTT", 1)])
eq_(evidence.allele_summary(loci[2]), [("TTTT", 1)])
eq_(evidence.allele_summary(loci[3]), [])
eq_(evidence.allele_summary(loci[4]),
[("AACA", 11), ("AACG", 6), ("GACG", 1)])
eq_(evidence.allele_summary(loci[5]),
[("AACAG", 10), ("AACGG", 6), ("AACAA", 1), ("GACGG", 1)])
eq_(evidence.allele_summary(loci[6]), [("ATT", 11)])
eq_(evidence.allele_summary(loci[7]), [("ACCCG", 1)])
def test_read_evidence_rna1_single_base_loci():
loci = [
Locus.from_inclusive_coordinates("17", 41244936, 41244936), # 0
Locus.from_inclusive_coordinates("17", 41244937, 41244937), # 1
Locus.from_inclusive_coordinates("17", 41244935, 41244935), # 2
Locus.from_inclusive_coordinates("17", 41244933, 41244933), # 3
Locus.from_inclusive_coordinates("17", 41244853, 41244853), # 4
Locus.from_inclusive_coordinates("17", 41244857, 41244857), # 5
Locus.from_inclusive_coordinates("17", 41244864, 41244864), # 6
Locus.from_inclusive_coordinates("17", 41244879, 41244879), # 7
Locus.from_inclusive_coordinates("17", 41244901, 41244901), # 8
Locus.from_inclusive_coordinates("17", 41244910, 41244910), # 9
Locus.from_inclusive_coordinates("17", 41244917, 41244917), # 10
Locus.from_inclusive_coordinates("17", 41244972, 41244972), # 11
Locus.from_inclusive_coordinates("17", 41244973, 41244973), # 12
Locus.from_inclusive_coordinates("17", 41245026, 41245026), # 13
Locus.from_inclusive_coordinates("17", 41245027, 41245027), # 14
Locus.from_inclusive_coordinates("17", 41245019, 41245019), # 15
Locus.from_inclusive_coordinates("17", 41245018, 41245018), # 16
]
evidence = PileupCollection.from_bam(data_path("rna_chr17_41244936.bam"),
loci)
eq_(evidence.allele_summary(loci[0]), [("A", 11), ("G", 7)])
eq_(evidence.allele_summary(loci[1]), [("G", 17), ("A", 1)])
eq_(evidence.allele_summary(loci[2]), [("C", 18)])
eq_(evidence.allele_summary(loci[3]), [("A", 17), ("G", 1)])
eq_(evidence.allele_summary(loci[4]), [("C", 1)])
eq_(evidence.allele_summary(loci[5]), [("T", 2)])
eq_(evidence.allele_summary(loci[6]), [("T", 4)])
eq_(evidence.allele_summary(loci[7]), [("C", 8)])
eq_(evidence.allele_summary(loci[8]), [("C", 8)])
eq_(evidence.allele_summary(loci[9]), [("C", 9)])
eq_(evidence.allele_summary(loci[10]), [("A", 10)])
eq_(evidence.allele_summary(loci[11]), [("T", 11)])
eq_(evidence.allele_summary(loci[12]), [("T", 11)])
eq_(evidence.allele_summary(loci[13]), [("C", 1)])
eq_(evidence.allele_summary(loci[14]), [("G", 1)])
eq_(evidence.allele_summary(loci[15]), [("T", 8)])
eq_(evidence.allele_summary(loci[16]), [("T", 8)])
def test_read_evidence_gatk_mini_bundle_extract():
loci = [
Locus.from_inclusive_coordinates("20", 9999996, 9999996), # 0
Locus.from_inclusive_coordinates("20", 10260442), # 1
Locus.from_inclusive_coordinates("20", 10006823), # 2
Locus.from_inclusive_coordinates("20", 10006819, 10006823), # 3
Locus.from_inclusive_coordinates("20", 10006819, 10006825), # 4
Locus.from_inclusive_coordinates("20", 10006822, 10006827), # 5
Locus.from_inclusive_coordinates("20", 10007175), # 6
Locus.from_inclusive_coordinates("20", 10007174, 10007176), # 7
Locus.from_inclusive_coordinates("20", 1, 3), # 8
Locus.from_inclusive_coordinates("20", 10008796), # 9
Locus.from_inclusive_coordinates("20", 10008921), # 10
]
handle = Samfile(data_path("gatk_mini_bundle_extract.bam"))
evidence = PileupCollection.from_bam(handle, loci)
eq_(evidence.allele_summary(loci[0]), [("ACT", 9)])
eq_(
evidence.filter(drop_duplicates=True).allele_summary(loci[0]),
[("ACT", 8)])
eq_(evidence.allele_summary(loci[1]), [("T", 7)])
eq_(evidence.filter().allele_summary(loci[2]), [("", 6), ("C", 2)])
eq_(
evidence.filter(drop_duplicates=True,
min_base_quality=50).allele_summary(loci[2]), [])
eq_(
evidence.filter(drop_duplicates=True).allele_summary(loci[2]),
[("", 5), ("C", 1)])
eq_(
evidence.filter(drop_duplicates=True,
min_mapping_quality=60).allele_summary(loci[2]),
[("", 5), ("C", 1)])
eq_(
evidence.filter(drop_duplicates=True,
min_mapping_quality=61).allele_summary(loci[2]),
[("", 2)])
eq_(
evidence.filter(drop_duplicates=True,
min_mapping_quality=61).allele_summary(loci[3]),
[("A", 2)])
eq_(
evidence.filter(drop_duplicates=True,
min_mapping_quality=61).allele_summary(loci[4]),
[("AAA", 2)])
eq_(
evidence.filter(drop_duplicates=True,
min_mapping_quality=61).allele_summary(loci[5]),
[("AAAC", 2)])
eq_(evidence.filter().allele_summary(loci[6]), [("T", 5), ("C", 3)])
eq_(
evidence.filter(min_base_quality=30).allele_summary(loci[6]),
[("T", 4), ("C", 3)])
eq_(evidence.filter().allele_summary(loci[7]), [("CTT", 5), ("CCT", 3)])
eq_(
evidence.filter(min_base_quality=30).allele_summary(loci[7]),
[("CTT", 3), ("CCT", 2)])
eq_(
evidence.filter(min_base_quality=32).allele_summary(loci[2]),
[("", 6), ("C", 1)])
eq_(filtered_read_names(evidence.at(loci[2]).filter(min_base_quality=32)),
{'20GAVAAXX100126:4:3:18352:43857'})
eq_(evidence.allele_summary(loci[8]), [])
eq_(evidence.filter(drop_duplicates=True).allele_summary(loci[8]), [])
assert_raises(KeyError, evidence.allele_summary,
Locus.from_inclusive_coordinates("20", 10009174, 10009176))
eq_(
filtered_read_names(
evidence.at(loci[9]).filter(drop_improper_mate_pairs=True)),
{'20FUKAAXX100202:8:68:1530:49310'})
eq_(len(evidence.at(loci[8]).read_attribute('mapping_quality')), 0)
eq_(list(evidence.at(loci[9]).read_attribute('mapping_quality')),
list(evidence.at(loci[9]).read_attributes().mapping_quality))
eq_(
evidence.filter(drop_duplicates=True).allele_summary(loci[10]),
[('C', 2), ('CA', 1), ('CAA', 1)])
eq_(
evidence.filter(drop_duplicates=True).allele_summary(
Locus.from_interbase_coordinates(loci[10].contig, loci[10].start,
loci[10].start)), [('', 2),
('A', 1),
('AA', 1)])
def test_read_evidence_rna1_single_base_loci():
loci = [
Locus.from_inclusive_coordinates("17", 41244936, 41244936), # 0
Locus.from_inclusive_coordinates("17", 41244937, 41244937), # 1
Locus.from_inclusive_coordinates("17", 41244935, 41244935), # 2
Locus.from_inclusive_coordinates("17", 41244933, 41244933), # 3
Locus.from_inclusive_coordinates("17", 41244853, 41244853), # 4
Locus.from_inclusive_coordinates("17", 41244857, 41244857), # 5
Locus.from_inclusive_coordinates("17", 41244864, 41244864), # 6
Locus.from_inclusive_coordinates("17", 41244879, 41244879), # 7
Locus.from_inclusive_coordinates("17", 41244901, 41244901), # 8
Locus.from_inclusive_coordinates("17", 41244910, 41244910), # 9
Locus.from_inclusive_coordinates("17", 41244917, 41244917), # 10
Locus.from_inclusive_coordinates("17", 41244972, 41244972), # 11
Locus.from_inclusive_coordinates("17", 41244973, 41244973), # 12
Locus.from_inclusive_coordinates("17", 41245026, 41245026), # 13
Locus.from_inclusive_coordinates("17", 41245027, 41245027), # 14
Locus.from_inclusive_coordinates("17", 41245019, 41245019), # 15
Locus.from_inclusive_coordinates("17", 41245018, 41245018), # 16
]
evidence = PileupCollection.from_bam(
data_path("rna_chr17_41244936.bam"), loci)
eq_(evidence.allele_summary(loci[0]), [("A", 11), ("G", 7)])
eq_(evidence.allele_summary(loci[1]), [("G", 17), ("A", 1)])
eq_(evidence.allele_summary(loci[2]), [("C", 18)])
eq_(evidence.allele_summary(loci[3]), [("A", 17), ("G", 1)])
eq_(evidence.allele_summary(loci[4]), [("C", 1)])
eq_(evidence.allele_summary(loci[5]), [("T", 2)])
eq_(evidence.allele_summary(loci[6]), [("T", 4)])
eq_(evidence.allele_summary(loci[7]), [("C", 8)])
eq_(evidence.allele_summary(loci[8]), [("C", 8)])
eq_(evidence.allele_summary(loci[9]), [("C", 9)])
eq_(evidence.allele_summary(loci[10]), [("A", 10)])
eq_(evidence.allele_summary(loci[11]), [("T", 11)])
eq_(evidence.allele_summary(loci[12]), [("T", 11)])
eq_(evidence.allele_summary(loci[13]), [("C", 1)])
eq_(evidence.allele_summary(loci[14]), [("G", 1)])
eq_(evidence.allele_summary(loci[15]), [("T", 8)])
eq_(evidence.allele_summary(loci[16]), [("T", 8)])
def test_read_evidence_gatk_mini_bundle_extract():
loci = [
Locus.from_inclusive_coordinates("20", 9999996, 9999996), # 0
Locus.from_inclusive_coordinates("20", 10260442), # 1
Locus.from_inclusive_coordinates("20", 10006823), # 2
Locus.from_inclusive_coordinates("20", 10006819, 10006823), # 3
Locus.from_inclusive_coordinates("20", 10006819, 10006825), # 4
Locus.from_inclusive_coordinates("20", 10006822, 10006827), # 5
Locus.from_inclusive_coordinates("20", 10007175), # 6
Locus.from_inclusive_coordinates("20", 10007174, 10007176), # 7
Locus.from_inclusive_coordinates("20", 1, 3), # 8
Locus.from_inclusive_coordinates("20", 10008796), # 9
Locus.from_inclusive_coordinates("20", 10008921), # 10
]
handle = Samfile(data_path("gatk_mini_bundle_extract.bam"))
evidence = PileupCollection.from_bam(handle, loci)
eq_(evidence.allele_summary(loci[0]), [("ACT", 9)])
eq_(evidence.filter(drop_duplicates=True).allele_summary(loci[0]),
[("ACT", 8)])
eq_(evidence.allele_summary(loci[1]), [("T", 7)])
eq_(evidence.filter().allele_summary(loci[2]), [("", 6), ("C", 2)])
eq_(evidence.filter(
drop_duplicates=True, min_base_quality=50).allele_summary(loci[2]),
[])
eq_(evidence.filter(drop_duplicates=True).allele_summary(loci[2]),
[("", 5), ("C", 1)])
eq_(evidence.filter(
drop_duplicates=True, min_mapping_quality=60).allele_summary(
loci[2]),
[("", 5), ("C", 1)])
eq_(evidence.filter(drop_duplicates=True,
min_mapping_quality=61).allele_summary(loci[2]), [("", 2)])
eq_(evidence.filter(drop_duplicates=True,
min_mapping_quality=61).allele_summary(loci[3]), [("A", 2)])
eq_(evidence.filter(drop_duplicates=True,
min_mapping_quality=61).allele_summary(loci[4]), [("AAA", 2)])
eq_(evidence.filter(drop_duplicates=True,
min_mapping_quality=61).allele_summary(loci[5]), [("AAAC", 2)])
eq_(evidence.filter().allele_summary(loci[6]), [("T", 5), ("C", 3)])
eq_(evidence.filter(min_base_quality=30).allele_summary(loci[6]),
[("T", 4), ("C", 3)])
eq_(evidence.filter().allele_summary(loci[7]),
[("CTT", 5), ("CCT", 3)])
eq_(evidence.filter(min_base_quality=30).allele_summary(loci[7]),
[("CTT", 3), ("CCT", 2)])
eq_(evidence.filter(min_base_quality=32).allele_summary(loci[2]),
[("", 6), ("C", 1)])
eq_(filtered_read_names(evidence.at(loci[2]).filter(min_base_quality=32)),
{'20GAVAAXX100126:4:3:18352:43857'})
eq_(evidence.allele_summary(loci[8]), [])
eq_(evidence.filter(drop_duplicates=True).allele_summary(loci[8]), [])
assert_raises(KeyError,
evidence.allele_summary,
Locus.from_inclusive_coordinates("20", 10009174, 10009176))
eq_(filtered_read_names(
evidence.at(loci[9]).filter(drop_improper_mate_pairs=True)),
{'20FUKAAXX100202:8:68:1530:49310'})
eq_(len(evidence.at(loci[8]).read_attribute('mapping_quality')), 0)
eq_(list(evidence.at(loci[9]).read_attribute('mapping_quality')),
list(evidence.at(loci[9]).read_attributes().mapping_quality))
eq_(evidence.filter(drop_duplicates=True).allele_summary(loci[10]),
[('C', 2), ('CA', 1), ('CAA', 1)])
eq_(evidence.filter(drop_duplicates=True).allele_summary(
Locus.from_interbase_coordinates(
loci[10].contig, loci[10].start, loci[10].start)),
[('', 2), ('A', 1), ('AA', 1)])