def _cluster_vcf_record_list(cls, vcf_records, max_distance_between_variants=1):
new_list = [vcf_record_cluster.VcfRecordCluster(max_distance_between_variants=max_distance_between_variants)]
for vcf_record in vcf_records:
if not new_list[-1].add_vcf_record(vcf_record):
new_list.append(vcf_record_cluster.VcfRecordCluster(vcf_record=vcf_record, max_distance_between_variants=max_distance_between_variants))
return new_list
def test_add_vcf_record_and_len(self):
'''test add_vcf_record and len'''
record1 = vcf_record.VcfRecord(
'ref_42\t11\tid_1\tA\tG\t42.42\tPASS\tKMER=31;SVLEN=0;SVTYPE=SNP\tGT:COV:GT_CONF\t1/1:0,52:39.80'
)
record2 = vcf_record.VcfRecord(
'ref_42\t12\tid_2\tC\tG\t42.42\tPASS\tKMER=31;SVLEN=0;SVTYPE=SNP\tGT:COV:GT_CONF\t1/1:0,52:39.80'
)
record3 = vcf_record.VcfRecord(
'ref_42\t15\tid_2\tC\tG\t42.42\tPASS\tKMER=31;SVLEN=0;SVTYPE=SNP\tGT:COV:GT_CONF\t1/1:0,52:39.80'
)
record4 = vcf_record.VcfRecord(
'ref_42\t19\tid_2\tCCCCC\tG\t42.42\tPASS\tKMER=31;SVLEN=0;SVTYPE=SNP\tGT:COV:GT_CONF\t1/1:0,52:39.80'
)
record5 = vcf_record.VcfRecord(
'ref_42\t23\tid_2\tC\tG\t42.42\tPASS\tKMER=31;SVLEN=0;SVTYPE=SNP\tGT:COV:GT_CONF\t1/1:0,52:39.80'
)
cluster = vcf_record_cluster.VcfRecordCluster(
max_distance_between_variants=3)
self.assertEqual(0, len(cluster))
self.assertTrue(cluster.add_vcf_record(record1))
self.assertEqual(1, len(cluster))
self.assertTrue(cluster.add_vcf_record(record2))
self.assertEqual(2, len(cluster))
self.assertTrue(cluster.add_vcf_record(record3))
self.assertEqual(3, len(cluster))
self.assertFalse(cluster.add_vcf_record(record4))
self.assertEqual(3, len(cluster))
cluster.max_distance_between_variants = 5
self.assertTrue(cluster.add_vcf_record(record4))
self.assertEqual(4, len(cluster))
self.assertTrue(cluster.add_vcf_record(record5))
self.assertEqual(5, len(cluster))
def test_make_simple_merged_vcf_with_no_combinations(self):
'''test make_simple_merged_vcf_with_no_combinations'''
ref_seq = pyfastaq.sequences.Fasta('ref', 'AGCTAGGTCAG')
record1 = vcf_record.VcfRecord(
'ref\t2\t.\tG\tAA\t228\t.\tINDEL;IDV=54;IMF=0.885246;DP=61;VDB=7.33028e-19;SGB=-0.693147;MQSB=0.9725;MQ0F=0;AC=2;AN=2;DP4=0,0,23,31;MQ=57\tGT:PL\t1/1:255,163,0'
)
record2 = vcf_record.VcfRecord(
'ref\t3\t.\tC\tCAT\t21.4018\t.\tINDEL;IDV=2;IMF=0.0338983;DP=59;VDB=0.18;SGB=-0.453602;MQ0F=0;AC=2;AN=2;DP4=0,0,0,2;MQ=60\tGT:PL\t1/1:48,6,0'
)
record3 = vcf_record.VcfRecord(
'ref\t8\t.\tT\tA\t21.4018\t.\t.\tSVTYPE=MERGED\tGT\t1/1')
cluster = vcf_record_cluster.VcfRecordCluster(vcf_record=record1)
self.assertTrue(cluster.add_vcf_record(record2))
self.assertTrue(cluster.add_vcf_record(record3))
cluster.make_simple_merged_vcf_with_no_combinations(ref_seq)
self.assertEqual(1, len(cluster))
expected = vcf_record.VcfRecord(
'ref\t2\t.\tGCTAGGT\tAACATTAGGA\t.\t.\tSVTYPE=MERGED\tGT\t1/1')
self.assertEqual(expected, cluster[0])
# add in record 1 again, then try merging. The merging should not work
self.assertTrue(cluster.add_vcf_record(record1))
cluster.make_simple_merged_vcf_with_no_combinations(ref_seq)
self.assertEqual(2, len(cluster))
self.assertEqual(expected, cluster[0])
self.assertEqual(record1, cluster[1])
# Test insertion next to SNP
# (same example as in test_make_one_merged_vcf_record_for_gramtools,
# byt now we don't get combinations, just the two ALT changes from
# the VCF records)
ref_seq = pyfastaq.sequences.Fasta('ref', 'AGCTATCTGCGTATTCGATC')
record1 = vcf_record.VcfRecord(
'ref\t3\t.\tC\tCG\t42.42\tPASS\tSVTPYPE=INDEL\tGT\t1/1')
record2 = vcf_record.VcfRecord(
'ref\t4\t.\tT\tA\t42.42\tPASS\tSVTPYPE=SNP\tGT\t1/1')
cluster = vcf_record_cluster.VcfRecordCluster(
vcf_record=record1, max_distance_between_variants=1)
self.assertTrue(cluster.add_vcf_record(record2))
cluster.make_simple_merged_vcf_with_no_combinations(ref_seq)
self.assertEqual(1, len(cluster))
expected = vcf_record.VcfRecord(
'ref\t3\t.\tCT\tCGA\t.\t.\tSVTYPE=MERGED\tGT\t1/1')
self.assertEqual(expected, cluster[0])
def _cluster_vcf_record_list(cls, vcf_records, cluster_boundary_size=0):
new_cluster_list = [
vcf_record_cluster.VcfRecordCluster(
cluster_boundary_size=cluster_boundary_size
)
]
# We try adding each vcf_record to the lastmost cluster; if this fails, we put it in a new cluster of its own.
for vcf_record in vcf_records:
last_cluster = new_cluster_list[-1]
successfully_added = last_cluster.add_vcf_record(vcf_record)
if not successfully_added: # Make a new cluster
new_cluster = vcf_record_cluster.VcfRecordCluster(
vcf_record=vcf_record, cluster_boundary_size=cluster_boundary_size,
)
new_cluster_list.append(new_cluster)
return new_cluster_list
def test_record_with_zero_pos_valueerror_raised(self):
ref_seq = 'AGCTATCTGCGTATTCGATC'
record_1 = vcf_record.VcfRecord(
'ref\t0\t.\tC\tCG\t42.42\tPASS\tSVTPYPE=INDEL\tGT\t1/1')
record_2 = vcf_record.VcfRecord(
'ref\t1\t.\tT\tA\t42.42\tPASS\tSVTPYPE=SNP\tGT\t1/1')
cluster = vcf_record_cluster.VcfRecordCluster(
vcf_record=record_1, max_distance_between_variants=1)
cluster.add_vcf_record(record_2)
with self.assertRaises(ValueError):
cluster.make_one_merged_vcf_record_for_gramtools(ref_seq)
def test_cluster_vcf_record_list(self):
'''test _cluster_vcf_record_list'''
record1 = vcf_record.VcfRecord('ref_42\t11\tid_1\tA\tG\t42.42\tPASS\tKMER=31;SVLEN=0;SVTYPE=SNP\tGT:COV:GT_CONF\t1/1:0,52:39.80')
record2 = vcf_record.VcfRecord('ref_42\t12\tid_2\tC\tG\t42.42\tPASS\tKMER=31;SVLEN=0;SVTYPE=SNP\tGT:COV:GT_CONF\t1/1:0,52:39.80')
record3 = vcf_record.VcfRecord('ref_42\t15\tid_2\tC\tG\t42.42\tPASS\tKMER=31;SVLEN=0;SVTYPE=SNP\tGT:COV:GT_CONF\t1/1:0,52:39.80')
record4 = vcf_record.VcfRecord('ref_42\t19\tid_2\tCCCCC\tG\t42.42\tPASS\tKMER=31;SVLEN=0;SVTYPE=SNP\tGT:COV:GT_CONF\t1/1:0,52:39.80')
record5 = vcf_record.VcfRecord('ref_42\t23\tid_2\tC\tG\t42.42\tPASS\tKMER=31;SVLEN=0;SVTYPE=SNP\tGT:COV:GT_CONF\t1/1:0,52:39.80')
record_list = [record1, record2, record3, record4, record5]
cluster1 = vcf_record_cluster.VcfRecordCluster(vcf_record=record1, max_distance_between_variants=3)
self.assertTrue(cluster1.add_vcf_record(record2))
self.assertTrue(cluster1.add_vcf_record(record3))
cluster2 = vcf_record_cluster.VcfRecordCluster(vcf_record=record4, max_distance_between_variants=3)
self.assertTrue(cluster2.add_vcf_record(record5))
expected = [cluster1, cluster2]
got = vcf_clusterer.VcfClusterer._cluster_vcf_record_list(record_list, max_distance_between_variants=3)
self.assertEqual(expected, got)
cluster1.max_distance_between_variants=5
self.assertTrue(cluster1.add_vcf_record(record4))
self.assertTrue(cluster1.add_vcf_record(record5))
got = vcf_clusterer.VcfClusterer._cluster_vcf_record_list(record_list, max_distance_between_variants=5)
self.assertEqual([cluster1], got)
def test_start_and_end(self):
'''test start_and_end'''
cluster = vcf_record_cluster.VcfRecordCluster(
max_distance_between_variants=3)
self.assertEqual((None, None), cluster.start_and_end())
record1 = vcf_record.VcfRecord(
'ref_42\t11\tid_1\tA\tG\t42.42\tPASS\tKMER=31;SVLEN=0;SVTYPE=SNP\tGT:COV:GT_CONF\t1/1:0,52:39.80'
)
self.assertTrue(cluster.add_vcf_record(record1))
self.assertEqual((10, 10), cluster.start_and_end())
record2 = vcf_record.VcfRecord(
'ref_42\t12\tid_2\tC\tG\t42.42\tPASS\tKMER=31;SVLEN=0;SVTYPE=SNP\tGT:COV:GT_CONF\t1/1:0,52:39.80'
)
self.assertTrue(cluster.add_vcf_record(record2))
self.assertEqual((10, 11), cluster.start_and_end())
def test_cluster_vcf_record_list(self):
"""test _cluster_vcf_record_list"""
record1 = vcf_record.VcfRecord(
"ref_42\t11\tid_1\tA\tG\t42.42\tPASS\tKMER=31;SVLEN=0;SVTYPE=SNP\tGT:COV:GT_CONF\t1/1:0,52:39.80"
)
record2 = vcf_record.VcfRecord(
"ref_42\t12\tid_2\tC\tG\t42.42\tPASS\tKMER=31;SVLEN=0;SVTYPE=SNP\tGT:COV:GT_CONF\t1/1:0,52:39.80"
)
record3 = vcf_record.VcfRecord(
"ref_42\t15\tid_2\tC\tG\t42.42\tPASS\tKMER=31;SVLEN=0;SVTYPE=SNP\tGT:COV:GT_CONF\t1/1:0,52:39.80"
)
record4 = vcf_record.VcfRecord(
"ref_42\t19\tid_2\tCCCCC\tG\t42.42\tPASS\tKMER=31;SVLEN=0;SVTYPE=SNP\tGT:COV:GT_CONF\t1/1:0,52:39.80"
)
record5 = vcf_record.VcfRecord(
"ref_42\t23\tid_2\tC\tG\t42.42\tPASS\tKMER=31;SVLEN=0;SVTYPE=SNP\tGT:COV:GT_CONF\t1/1:0,52:39.80"
)
record_list = [record1, record2, record3, record4, record5]
cluster1 = vcf_record_cluster.VcfRecordCluster(vcf_record=record1,
cluster_boundary_size=3)
self.assertTrue(cluster1.add_vcf_record(record2))
self.assertTrue(cluster1.add_vcf_record(record3))
cluster2 = vcf_record_cluster.VcfRecordCluster(vcf_record=record4,
cluster_boundary_size=3)
self.assertTrue(cluster2.add_vcf_record(record5))
expected = [cluster1, cluster2]
got = vcf_clusterer.VcfClusterer._cluster_vcf_record_list(
record_list, cluster_boundary_size=3)
self.assertEqual(expected, got)
cluster1.cluster_boundary_size = 5
self.assertTrue(cluster1.add_vcf_record(record4))
self.assertTrue(cluster1.add_vcf_record(record5))
got = vcf_clusterer.VcfClusterer._cluster_vcf_record_list(
record_list, cluster_boundary_size=5)
self.assertEqual([cluster1], got)
def test_make_separate_indels_and_one_alt_with_all_snps_no_combinations(
self):
'''test make_separate_indels_and_one_alt_with_all_snps_no_combinations'''
ref_seq = pyfastaq.sequences.Fasta('ref', 'AGCTAGGTCAG')
snp1 = vcf_record.VcfRecord('ref\t4\t.\tT\tA\t.\t.\t.\t.')
snp2 = vcf_record.VcfRecord('ref\t9\t.\tC\tG\t.\t.\t.\t.')
deletion = vcf_record.VcfRecord('ref\t3\t.\tCTAGGTCA\tG\t.\t.\t.\t.')
insertion = vcf_record.VcfRecord('ref\t5\t.\tA\tATT\t.\t.\t.\t.')
cluster = vcf_record_cluster.VcfRecordCluster(
vcf_record=deletion, max_distance_between_variants=1)
self.assertTrue(cluster.add_vcf_record(snp1))
self.assertTrue(cluster.add_vcf_record(snp2))
self.assertTrue(cluster.add_vcf_record(insertion))
got = cluster.make_separate_indels_and_one_alt_with_all_snps_no_combinations(
ref_seq)
expected = vcf_record.VcfRecord(
'ref\t3\t.\tCTAGGTCA\tG,CTATTGGTCA,CAAGGTGA\t.\tPASS\t.')
self.assertEqual(expected, got)
def test_make_one_merged_vcf_record_for_gramtools(self):
'''test make_one_vcf_merged_record_for_gramtools'''
# 12345678901234567890
ref_seq = 'AGCTATCTGCGTATTCGATC'
record1 = vcf_record.VcfRecord(
'ref\t10\t.\tC\tG\t42.42\t.\tSVTYPE=SNP\tGT\t1/1')
cluster = vcf_record_cluster.VcfRecordCluster(
vcf_record=record1, max_distance_between_variants=2)
# If there's only one record, then we should just get that one back,
# but should have FILTER = PASS
expected = copy.copy(record1)
expected.FILTER = 'PASS'
self.assertEqual(
expected,
cluster.make_one_merged_vcf_record_for_gramtools(ref_seq))
# Test one record, but two alleles
record2 = vcf_record.VcfRecord(
'ref\t12\t.\tT\tC,A\t42.42\tPASS\tSVTYPE=SNP\tGT\t1/1')
cluster = vcf_record_cluster.VcfRecordCluster(
vcf_record=record2, max_distance_between_variants=2)
self.assertEqual(
record2, cluster.make_one_merged_vcf_record_for_gramtools(ref_seq))
# Two records, SNPs at different positions
self.assertTrue(cluster.add_vcf_record(record1))
expected = vcf_record.VcfRecord(
'ref\t10\t.\tCGT\tCGA,CGC,GGA,GGC,GGT\t.\tPASS\tSVTYPE=COMPLEX')
self.assertEqual(
expected,
cluster.make_one_merged_vcf_record_for_gramtools(ref_seq))
# Add in a deletion to the previous two SNPs, starting a earlier and ending
# later, to also check flanking regions get added.
record3 = vcf_record.VcfRecord(
'ref\t8\t.\tTGCGTAT\tT\t42.42\tPASS\tSVTYPE=COMPLEX\tGT\t1/1')
self.assertTrue(cluster.add_vcf_record(record3))
expected = vcf_record.VcfRecord(
'ref\t8\t.\tTGCGTAT\tT,TGCGAAT,TGCGCAT,TGGGAAT,TGGGCAT,TGGGTAT\t.\tPASS\tSVTYPE=COMPLEX'
)
self.assertEqual(
expected,
cluster.make_one_merged_vcf_record_for_gramtools(ref_seq))
# Add an indel to all the previous variants.
record4 = vcf_record.VcfRecord(
'ref\t9\t.\tGCGT\tGAAAAC\t42.42\tPASS\tSVTYPE=COMPLEX\tGT\t1/1')
self.assertTrue(cluster.add_vcf_record(record4))
expected = vcf_record.VcfRecord(
'ref\t8\t.\tTGCGTAT\tT,TGAAAACAT,TGCGAAT,TGCGCAT,TGGGAAT,TGGGCAT,TGGGTAT\t.\tPASS\tSVTYPE=COMPLEX'
)
self.assertEqual(
expected,
cluster.make_one_merged_vcf_record_for_gramtools(ref_seq))
# Test insertion next to SNP
record5 = vcf_record.VcfRecord(
'ref\t3\t.\tC\tCG\t42.42\tPASS\tSVTPYPE=INDEL\tGT\t1/1')
record6 = vcf_record.VcfRecord(
'ref\t4\t.\tT\tA\t42.42\tPASS\tSVTPYPE=SNP\tGT\t1/1')
cluster = vcf_record_cluster.VcfRecordCluster(
vcf_record=record5, max_distance_between_variants=1)
self.assertTrue(cluster.add_vcf_record(record6))
expected = vcf_record.VcfRecord(
'ref\t3\t.\tCT\tCA,CGA,CGT\t.\tPASS\tSVTYPE=COMPLEX')
self.assertEqual(
expected,
cluster.make_one_merged_vcf_record_for_gramtools(ref_seq))
