def test_assemble_transcript_fragments_snv():
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=ensembl_grch38)
variant_reads = reads_supporting_variant(
variant=variant,
samfile=samfile,
chromosome=chromosome,)
sequences = iterative_overlap_assembly(
initial_variant_sequences_from_reads(variant_reads),
min_overlap_size=30)
assert len(sequences) > 0
max_read_length = max(len(r) for r in variant_reads)
for s in sequences:
print("%s%s%s weight=%d length=%d" % (
s.prefix,
s.alt,
s.suffix,
len(s.reads),
len(s.sequence)))
eq_(s.alt, alt)
assert len(s) > max_read_length, \
"Expected assembled sequences to be longer than read length (%d)" % (
max_read_length,)
def test_assemble_transcript_fragments_snv():
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=ensembl_grch38)
variant_reads = reads_supporting_variant(
variant=variant,
samfile=samfile,
chromosome=chromosome,
)
sequences = iterative_overlap_assembly(
initial_variant_sequences_from_reads(variant_reads),
min_overlap_size=30)
assert len(sequences) > 0
max_read_length = max(len(r) for r in variant_reads)
for s in sequences:
print("%s%s%s weight=%d length=%d" %
(s.prefix, s.alt, s.suffix, len(s.reads), len(s.sequence)))
eq_(s.alt, alt)
if len(s.read_names) > 1:
# expect sequences supported by more than one read to be greater
# than the read length
assert len(s) > max_read_length, \
"Expected assembled sequences to be longer than read length (%d)" % (
max_read_length,)
def test_assembly_of_simple_sequence_from_mock_reads():
# Read sequences:
# AAAAA|CC|TTTTT
# AAAAA|CC|TTTTT
# GAAAAA|CC|TTTTTG
# AAAA|CC|TTTT
reads = [
# two identical reads with sequence AAAAA|CC|TTTTT
AlleleRead(prefix="A" * 5, allele="CC", suffix="T" * 5, name="dup1"),
AlleleRead(prefix="A" * 5, allele="CC", suffix="T" * 5, name="dup2"),
# longer sequence GAAAAA|CC|TTTTTG
AlleleRead(prefix="G" + "A" * 5,
allele="CC",
suffix="T" * 5 + "G",
name="longer"),
# shorter sequence AAAA|CC|TTTT
AlleleRead(prefix="A" * 4, allele="CC", suffix="T" * 4,
name="shorter"),
]
expected_variant_sequence = VariantSequence(prefix="G" + "A" * 5,
alt="CC",
suffix="T" * 5 + "G",
reads=reads)
initial_variant_sequences = initial_variant_sequences_from_reads(reads)
# expecting one fewer sequence than reads since two of the reads are
# duplicates
eq_(len(initial_variant_sequences), len(reads) - 1)
# calling into either iterative_overlap_assembly or greedy_merge should
# give same results
for fn in [greedy_merge, iterative_overlap_assembly]:
assembled_variant_sequences = fn(initial_variant_sequences,
min_overlap_size=1)
# since no reads contradict each other then we should get back a single
# assembled sequence
eq_(
len(assembled_variant_sequences), 1,
"Unexpected number of variant sequences: %s" %
(assembled_variant_sequences, ))
assembled_variant_sequence = assembled_variant_sequences[0]
eq_(assembled_variant_sequence, expected_variant_sequence)
eq_(len(assembled_variant_sequence.reads), len(reads))
eq_(assembled_variant_sequence.min_coverage(), 1)
# 2 bases with 1/4 reads, 2 bases with 3/4 reads, remaining 10 bases with
# all 4/4 reads
expected_mean_coverage = (2 * 1 + 2 * 3 + 10 * 4) / 14
eq_(assembled_variant_sequence.mean_coverage(), expected_mean_coverage)
def test_assembly_of_simple_sequence_from_mock_reads():
#
# Read sequences:
# AAAAA|CC|TTTTT
# AAAAA|CC|TTTTT
# GAAAAA|CC|TTTTTG
# AAAA|CC|TTTT
reads = [
# two identical reads with sequence AAAAA|CC|TTTTT
AlleleRead(prefix="A" * 5, allele="CC", suffix="T" * 5, name="dup1"),
AlleleRead(prefix="A" * 5, allele="CC", suffix="T" * 5, name="dup2"),
# longer sequence GAAAAA|CC|TTTTTG
AlleleRead(prefix="G" + "A" * 5, allele="CC", suffix="T" * 5 + "G", name="longer"),
# shorter sequence AAAA|CC|TTTT
AlleleRead(prefix="A" * 4, allele="CC", suffix="T" * 4, name="shorter"),
]
expected_variant_sequence = VariantSequence(
prefix="G" + "A" * 5, alt="CC", suffix="T" * 5 + "G", reads=reads)
initial_variant_sequences = initial_variant_sequences_from_reads(reads)
# expecting one fewer sequence than reads since two of the reads are
# duplicates
eq_(len(initial_variant_sequences), len(reads) - 1)
assembled_variant_sequences = iterative_overlap_assembly(
initial_variant_sequences,
min_overlap_size=1)
# since no reads contradict each other then we should get back a single
# assembled sequence
eq_(len(assembled_variant_sequences),
1,
"Unexpected number of variant sequences: %s" % (assembled_variant_sequences,))
assembled_variant_sequence = assembled_variant_sequences[0]
eq_(assembled_variant_sequence, expected_variant_sequence)
eq_(len(assembled_variant_sequence.reads), len(reads))
eq_(assembled_variant_sequence.min_coverage(), 1)
# 2 bases with 1/4 reads, 2 bases with 3/4 reads, remaining 10 bases with
# all 4/4 reads
expected_mean_coverage = (2 * 1 + 2 * 3 + 10 * 4) / 14
eq_(assembled_variant_sequence.mean_coverage(), expected_mean_coverage)