def test_partition_variant_reads_deletion():
alignment_file = load_bam("data/cancer-wgs-primary.chr12.bam")
chromosome = "chr12"
base1_location = 70091490
ref = "TTGTAGATGCTGCCTCTCC"
alt = ""
variant = Variant(contig=chromosome,
start=base1_location,
ref=ref,
alt=alt,
ensembl=ensembl_grch38)
read_collector = ReadCollector()
read_evidence = read_collector.read_evidence_for_variant(
alignment_file=alignment_file, variant=variant)
assert len(read_evidence.alt_reads) > 1
for variant_read in read_evidence.alt_reads:
eq_(variant_read.allele, alt)
def test_partition_variant_reads_snv():
alignment_file = load_bam("data/cancer-wgs-primary.chr12.bam")
chromosome = "chr12"
base1_location = 65857041
ref = "G"
alt = "C"
variant = Variant(contig=chromosome,
start=base1_location,
ref=ref,
alt=alt,
ensembl=ensembl_grch38)
read_collector = ReadCollector()
read_evidence = read_collector.read_evidence_for_variant(
alignment_file=alignment_file, variant=variant)
alt_reads = read_evidence.alt_reads
assert len(alt_reads) > 1
for variant_read in alt_reads:
eq_(variant_read.allele, alt)
def test_group_unique_sequences():
samfile = load_bam("data/cancer-wgs-primary.chr12.bam")
chromosome = "chr12"
base1_location = 65857041
ref = "G"
alt = "C"
variant = Variant(contig=chromosome,
start=base1_location,
ref=ref,
alt=alt,
ensembl="hg38")
read_collector = ReadCollector()
variant_reads = read_collector.allele_reads_supporting_variant(
alignment_file=samfile, variant=variant)
print("%d variant reads: %s" % (len(variant_reads), variant_reads))
groups = group_unique_sequences(variant_reads,
max_prefix_size=30,
max_suffix_size=30)
print("%d unique sequences: %s" % (len(groups), groups))
# there are some redundant reads, so we expect that the number of
# unique entries should be less than the total read partitions
assert len(variant_reads) > len(groups)
def test_translate_variant_collection():
variants = load_vcf("data/b16.f10/b16.vcf")
samfile = load_bam("data/b16.f10/b16.combined.sorted.bam")
read_evidence_gen = ReadCollector().read_evidence_generator(
variants,
samfile)
translation_gen = ProteinSequenceCreator().translate_variants(read_evidence_gen)
translations = list(translation_gen)
eq_(
len(translations),
4,
"Expected %d translated variants but got %d: %s" % (
len(variants),
len(translations),
translations))