def test_variant_sequence_contains():
# AA|C|T
vs_longer_prefix = VariantSequence(prefix="AA",
alt="C",
suffix="T",
reads=[
AlleleRead(prefix="AA",
allele="C",
suffix="T",
name="longer_prefix")
])
# A|C|TT
vs_longer_suffix = VariantSequence(prefix="A",
alt="C",
suffix="TT",
reads=[
AlleleRead(prefix="A",
allele="C",
suffix="TT",
name="longer_suffix")
])
# A|C|T
vs_short = VariantSequence(
prefix="A",
alt="C",
suffix="T",
reads=[AlleleRead(prefix="A", allele="C", suffix="T", name="short")])
# two longer sequences contain the shorter subsequence
assert vs_longer_prefix.contains(vs_short), \
"Expected %s to contain %s" % (vs_longer_prefix, vs_short)
assert vs_longer_suffix.contains(vs_short), \
"Expected %s to contain %s" % (vs_longer_suffix, vs_short)
# other pairs do not contain each other
assert not vs_longer_prefix.contains(vs_longer_suffix), \
"Expected %s to not contain %s" % (vs_longer_prefix, vs_longer_suffix)
assert not vs_longer_suffix.contains(vs_longer_prefix), \
"Expected %s to not contain %s" % (vs_longer_suffix, vs_longer_prefix)
assert not vs_short.contains(vs_longer_prefix), \
"Expected %s to not contain %s" % (vs_short, vs_longer_prefix)
assert not vs_short.contains(vs_longer_suffix), \
"Expected %s to not contain %s" % (vs_short, vs_longer_suffix)
# Sequences above has 'C' allele whereas this one has 'G'
# A|G|T
vs_different_allele = VariantSequence(
prefix="A",
alt="G",
suffix="T",
reads=[AlleleRead(prefix="A", allele="G", suffix="T", name="short")])
for vs in [vs_longer_suffix, vs_longer_prefix, vs_short]:
assert not vs.contains(vs_different_allele), \
"Expected %s to not contain %s" % (vs, vs_different_allele)
assert not vs_different_allele.contains(vs), \
"Expected %s to not contain %s" % (vs_different_allele, vs)
def test_variant_sequence_min_coverage():
# 1: AA|C|TT
# 2: AA|C|T
# 3: A|C|TT
reads = [
AlleleRead(prefix="AA", allele="C", suffix="TT", name="1"),
AlleleRead(prefix="AA", allele="C", suffix="T", name="2"),
AlleleRead(prefix="A", allele="C", suffix="TT", name="3")
]
vs = VariantSequence(prefix="AA", alt="C", suffix="TT", reads=reads)
eq_(vs.min_coverage(), 2)
def test_allele_count_dataframe():
variant = Variant("test_contig", 50, "C", "G")
reads = [
AlleleRead(prefix="AAA", allele="C", suffix="TTT", name="C1"),
AlleleRead(prefix="AAC", allele="C", suffix="TTA", name="C2"),
AlleleRead(prefix="AAA", allele="G", suffix="TTT", name="G1"),
]
df = allele_counts_dataframe([(variant, reads)])
assert len(df) == 1, "Wrong number of rows in DataFrame: %s" % (df, )
row = df.iloc[0]
eq_(row.n_ref, 2)
eq_(row.n_alt, 1)
eq_(row.n_other, 0)
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_variant_sequence_mean_coverage():
# 1: AA|C|TT
# 2: AA|C|T
# 3: A|C|TT
reads = [
AlleleRead(prefix="AA", allele="C", suffix="TT", name="1"),
AlleleRead(prefix="AA", allele="C", suffix="T", name="2"),
AlleleRead(prefix="A", allele="C", suffix="TT", name="3")
]
vs = VariantSequence(prefix="AA", alt="C", suffix="TT", reads=reads)
# count the number of times a nucleotide in the sequences above
# is contained in a read
expected_mean_coverage = (2 + 3 + 3 + 3 + 2) / 5
eq_(vs.mean_coverage(), expected_mean_coverage)
def test_variant_sequence_trim_by_coverage():
reads = [
AlleleRead(prefix="AA", allele="C", suffix="T", name="1"),
AlleleRead(prefix="A", allele="C", suffix="T", name="2")
]
vs = VariantSequence(prefix="AA", alt="C", suffix="T", reads=reads)
# every nucleotide is spanned by one read
eq_(vs.trim_by_coverage(1), vs)
vs_expected_trim_by_2 = VariantSequence(prefix="A",
alt="C",
suffix="T",
reads=reads)
eq_(vs.trim_by_coverage(2), vs_expected_trim_by_2)
def test_variant_sequence_read_names():
vs = VariantSequence(prefix="A",
alt="C",
suffix="T",
reads=[
AlleleRead(prefix="A",
allele="C",
suffix="T",
name="1"),
AlleleRead(prefix="A",
allele="C",
suffix="T",
name="2")
])
eq_(vs.read_names, {"1", "2"})
def test_partitioned_read_sequences_deletion():
"""
test_partitioned_read_sequences_deletion : Test that read gets correctly
partitioned for chr1:4 TT>T where the sequence for chr1 is assumed to
be "ACCTTG"
"""
# chr1_seq = "ACCTTG"
chromosome = "chromosome"
location = 4
ref = "TT"
alt = "T"
variant = Variant(chromosome,
location,
ref,
alt,
normalize_contig_name=False)
read = make_read(seq="ACCTG", cigar="4M1D1M", mdtag="4^T1")
samfile = DummySamFile(reads=[read])
variant_reads = reads_supporting_variant(samfile=samfile,
chromosome=chromosome,
variant=variant)
print(variant_reads)
assert len(variant_reads) == 1
variant_read = variant_reads[0]
expected = AlleleRead(name=read.qname,
prefix="ACCT",
allele="",
suffix="G")
eq_(variant_read, expected)
def test_variant_sequence_overlaps():
# AAA|GG|TT
vs_3A = VariantSequence(
prefix="AAA",
alt="GG",
suffix="TT",
reads=[AlleleRead(prefix="AAA", allele="GG", suffix="TT", name="1")])
# AA|GG|TT
vs_2A = VariantSequence(
prefix="AA",
alt="GG",
suffix="TT",
reads=[AlleleRead(prefix="AA", allele="GG", suffix="TT", name="1")])
for min_overlap_size in [1, 2, 3, 4, 5, 6]:
assert vs_3A.left_overlaps(vs_2A, min_overlap_size=min_overlap_size), \
"Expected %s to overlap %s from left (min overlap size=%d)" % (
vs_3A, vs_2A, min_overlap_size)
assert not vs_2A.left_overlaps(vs_3A, min_overlap_size=min_overlap_size), \
"Expected %s to not overlap %s from left (min overlap size=%d)" % (
vs_2A, vs_3A, min_overlap_size)
assert not vs_3A.left_overlaps(vs_2A, min_overlap_size=7), \
"Unexpected overlap between %s and %s for min_overlap_size=7" % (
vs_3A, vs_2A)
def make_inputs_for_tp53_201_variant(
cdna_prefix="ATG",
cdna_suffix="AGGAGCCGCAGTCAGAT",
n_bad_nucleotides_at_start=0,
mismatches_before_variant=0,
mismatches_after_variant=14, # the read is that much longer than the reference (17 vs 3)
reference_context_size=3):
"""
Parameters
----------
cdna_prefix : str
Transcript nucleotides before the variant that we're pretending
got detected from RNA-seq reads.
cdna_suffix : str
Transcript nucleotides after the variant that we're pretending
got detected from RNA-seq reads.
n_bad_nucleotides_at_start : int
Number of nucleotides we expect to get trimmed from the
beginning of the variant sequence while matching to a reference context.
mismatches_before_variant : int
Expected number of nucleotide mismatches in the result before
the variant locus.
reference_context_size : int
Number of nucleotides before the variant locus to try matching
against a reference transcript.
"""
# TP53-201 is an isoform of TP53 which seems to lack untranslated
# regions so the sequence is:
# First exon: chr17 7,676,594 - 7,676,521
# ATG|GAG|GAG|CCG|CAG|TCA|GAT...
# -M-|-E-|-E-|-P-|-Q-|-S-|-D-
# we're assuming a variant
# chr17. 7,676,591 C>T which changes GAG (E) > AAG (K)
variant = Variant("chr17", 7676591, "C", "T", "GRCh38")
# TP53-201
transcript = variant.ensembl.transcripts_by_name("TP53-201")[0]
effect = variant.effect_on_transcript(transcript)
eq_(effect.__class__.__name__, "Substitution")
eq_(effect.aa_ref, "E")
eq_(effect.aa_alt, "K")
cdna_alt = "A"
# genomic DNA is the reverse complement of the cDNA
# for TP53-001 since it's on the negative strand
gdna_prefix = reverse_complement_dna(cdna_suffix)
gdna_alt = reverse_complement_dna(cdna_alt)
gdna_suffix = reverse_complement_dna(cdna_prefix)
# variant sequence supported by two reads
# one fully spanning the variant sequence
# and another missing the last nucleotide
fully_overlapping_read = AlleleRead(prefix=gdna_prefix,
allele=gdna_alt,
suffix=gdna_suffix,
name="full-overlap")
# testing the prefix and allele to make sure they have the expected
# TP53-201 sequence but the suffix might change depending on what's
# passed in as cdna_prefix
if cdna_suffix == "AGGAGCCGCAGTCAGAT":
eq_(fully_overlapping_read.prefix, "ATCTGACTGCGGCTCCT")
eq_(fully_overlapping_read.allele, "T")
partially_overlapping_read = AlleleRead(prefix=gdna_prefix,
allele=gdna_alt,
suffix=gdna_suffix[:-1],
name="partial-overlap")
if cdna_suffix == "AGGAGCCGCAGTCAGAT":
eq_(partially_overlapping_read.prefix, "ATCTGACTGCGGCTCCT")
eq_(partially_overlapping_read.allele, "T")
variant_sequence = VariantSequence(
prefix=gdna_prefix,
alt=gdna_alt,
suffix=gdna_suffix,
reads=[fully_overlapping_read, partially_overlapping_read])
assert isinstance(variant_sequence, VariantSequence)
prefix_length = len(cdna_prefix) - n_bad_nucleotides_at_start
reference_coding_sequence_key = ReferenceCodingSequenceKey.from_variant_and_transcript(
variant=variant,
transcript=transcript,
context_size=reference_context_size)
assert isinstance(reference_coding_sequence_key,
ReferenceCodingSequenceKey)
reference_context = ReferenceContext.from_reference_coding_sequence_key(
key=reference_coding_sequence_key,
variant=variant,
transcripts=[transcript])
assert isinstance(reference_context, ReferenceContext)
expected = VariantSequenceInReadingFrame(
cdna_sequence=cdna_prefix[-prefix_length:] + cdna_alt + cdna_suffix,
offset_to_first_complete_codon=prefix_length % 3,
variant_cdna_interval_start=prefix_length,
variant_cdna_interval_end=prefix_length + 1,
reference_cdna_sequence_before_variant="ATG"[-prefix_length:],
reference_cdna_sequence_after_variant=
"AGGAGCCGCAGTCAGAT"[:reference_context_size],
number_mismatches_before_variant=mismatches_before_variant,
number_mismatches_after_variant=mismatches_after_variant)
assert isinstance(expected, VariantSequenceInReadingFrame)
return variant_sequence, reference_context, expected
def test_allele_read_from_single_read_at_locus_trim_N_nucleotides():
read_at_locus = make_read_at_locus(prefix="NCCN", alt="A", suffix="TNNA")
allele_read = AlleleRead.from_locus_read(read_at_locus, n_ref=1)
print(allele_read)
expected = AlleleRead(prefix="", allele="A", suffix="T", name="dummy")
eq_(allele_read, expected)
def test_allele_read_from_single_read_at_locus_trim_N_nucleotides():
read_at_locus = make_read_at_locus(prefix="NCCN", alt="A", suffix="TNNA")
allele_read = AlleleRead.from_locus_read(read_at_locus, n_ref=1)
print(allele_read)
expected = AlleleRead(prefix="", allele="A", suffix="T", name="dummy")
eq_(allele_read, expected)