def test_locus_reads_insertion():
"""
test_partitioned_read_sequences_insertion : Test that read gets correctly
partitioned for chr1:4 T>TG
where the sequence for chr1 is assumed to be "ACCTTG"
and the variant sequence is "ACCTGTG"
"""
variant = Variant(
"chromosome", 4, ref="T", alt="TG", normalize_contig_name=False)
pysam_read = make_read(seq="ACCTGTG", cigar="4M1I2M", mdtag="6")
samfile = DummySamFile(reads=[pysam_read])
reads = list(locus_read_generator(
samfile=samfile,
chromosome="chromosome",
base1_position_before_variant=variant.start,
base1_position_after_variant=variant.start + 1))
print(reads)
assert len(reads) == 1, \
"Expected to get back one read but instead got %d" % (
len(reads),)
read = reads[0]
expected = LocusRead(
name=pysam_read.qname,
sequence=pysam_read.query_sequence,
# expect the inserted nucleotide to be missing a corresponding
# ref position
reference_positions=[0, 1, 2, 3, None, 4, 5],
quality_scores=pysam_read.query_qualities,
base0_read_position_before_variant=3,
base0_read_position_after_variant=5)
assert_equal_fields(read, expected)
def test_locus_reads_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"
"""
# normalization of this variant will turn it into the deletion of
# "T" at base-1 position 5
variant = Variant(
"chromosome", 4, ref="TT", alt="T", normalize_contig_name=False)
print(variant)
pysam_read = make_read(seq="ACCTG", cigar="4M1D1M", mdtag="4^T1")
samfile = DummySamFile(reads=[pysam_read])
reads = list(locus_read_generator(
samfile=samfile,
chromosome="chromosome",
base1_position_before_variant=variant.start - 1,
base1_position_after_variant=variant.start + 1))
print(reads)
assert len(reads) == 1, \
"Expected to get back one read but instead got %d" % (
len(reads),)
read = reads[0]
expected = LocusRead(
name=pysam_read.qname,
sequence=pysam_read.query_sequence,
reference_positions=[0, 1, 2, 3, 5],
quality_scores=pysam_read.query_qualities,
base0_read_position_before_variant=3,
base0_read_position_after_variant=4)
assert_equal_fields(read, expected)
def test_locus_reads_substitution_longer():
# test C>GG subsitution at second nucleotide of reference sequence "ACCTTG",
# the alignment is interpreted as a C>G variant followed by an insertion of
# another G
variant = Variant(
"chromosome", 2, ref="C", alt="GG", normalize_contig_name=False)
print(variant)
pysam_read = make_read(seq="AGGCTTG", cigar="2M1I4M", mdtag="1C4")
samfile = DummySamFile(reads=[pysam_read])
reads = list(locus_read_generator(
samfile=samfile,
chromosome="chromosome",
base1_position_before_variant=1,
base1_position_after_variant=3))
print(reads)
assert len(reads) == 1, \
"Expected to get back one read but instead got %d" % (
len(reads),)
read = reads[0]
expected = LocusRead(
name=pysam_read.qname,
sequence=pysam_read.query_sequence,
reference_positions=[0, 1, None, 2, 3, 4, 5],
quality_scores=pysam_read.query_qualities,
base0_read_position_before_variant=0,
base0_read_position_after_variant=3)
assert_equal_fields(read, expected)
def test_locus_reads_substitution_shorter():
# test CC>G subsitution at 2nd and 3rd nucleotides of reference sequence
# "ACCTTG", for which the alignment is interpreted as a C>G variant
# followed by the deletion of a C
variant = Variant(
"chromosome", 2, ref="CC", alt="G", normalize_contig_name=False)
print(variant)
pysam_read = make_read(seq="AGTTG", cigar="2M1D3M", mdtag="1C^C4")
samfile = DummySamFile(reads=[pysam_read])
reads = list(locus_read_generator(
samfile=samfile,
chromosome="chromosome",
base1_position_before_variant=1,
base1_position_after_variant=4))
assert len(reads) == 1, \
"Expected to get back one read but instead got %d" % (
len(reads),)
print(reads)
read = reads[0]
expected = LocusRead(
name=pysam_read.qname,
sequence=pysam_read.query_sequence,
reference_positions=[0, 1, 3, 4, 5],
quality_scores=pysam_read.query_qualities,
base0_read_position_before_variant=0,
base0_read_position_after_variant=2)
assert_equal_fields(read, expected)
def test_locus_reads_snv():
"""
test_partitioned_read_sequences_snv : Test that read gets correctly
partitioned for chr1:4 T>G where the sequence for chr1 is assumed
to be "ACCTTG"
"""
# chr1_seq = "ACCTTG"
variant = Variant("chromosome",
4,
ref="T",
alt="G",
normalize_contig_name=False)
pysam_read = make_read(seq="ACCGTG", cigar="6M", mdtag="3G2")
samfile = DummySamFile(reads=[pysam_read])
reads = list(
locus_read_generator(samfile=samfile,
chromosome="chromosome",
base1_position_before_variant=variant.start - 1,
base1_position_after_variant=variant.start + 1))
print(reads)
assert len(reads) == 1, \
"Expected to get back one read but instead got %d" % (
len(reads),)
read = reads[0]
expected = LocusRead(name=pysam_read.qname,
sequence=pysam_read.query_sequence,
reference_positions=[0, 1, 2, 3, 4, 5],
quality_scores=pysam_read.query_qualities,
base0_read_position_before_variant=2,
base0_read_position_after_variant=4)
assert_equal_fields(read, expected)
def test_locus_reads_substitution_longer():
# test C>GG subsitution at second nucleotide of reference sequence "ACCTTG",
# the alignment is interpreted as a C>G variant followed by an insertion of
# another G
variant = Variant("chromosome",
2,
ref="C",
alt="GG",
normalize_contig_name=False)
print(variant)
pysam_read = make_read(seq="AGGCTTG", cigar="2M1I4M", mdtag="1C4")
samfile = DummySamFile(reads=[pysam_read])
reads = list(
locus_read_generator(samfile=samfile,
chromosome="chromosome",
base1_position_before_variant=1,
base1_position_after_variant=3))
print(reads)
assert len(reads) == 1, \
"Expected to get back one read but instead got %d" % (
len(reads),)
read = reads[0]
expected = LocusRead(name=pysam_read.qname,
sequence=pysam_read.query_sequence,
reference_positions=[0, 1, None, 2, 3, 4, 5],
quality_scores=pysam_read.query_qualities,
base0_read_position_before_variant=0,
base0_read_position_after_variant=3)
assert_equal_fields(read, expected)
def test_locus_reads_substitution_shorter():
# test CC>G subsitution at 2nd and 3rd nucleotides of reference sequence
# "ACCTTG", for which the alignment is interpreted as a C>G variant
# followed by the deletion of a C
variant = Variant("chromosome",
2,
ref="CC",
alt="G",
normalize_contig_name=False)
print(variant)
pysam_read = make_read(seq="AGTTG", cigar="2M1D3M", mdtag="1C^C4")
samfile = DummySamFile(reads=[pysam_read])
reads = list(
locus_read_generator(samfile=samfile,
chromosome="chromosome",
base1_position_before_variant=1,
base1_position_after_variant=4))
assert len(reads) == 1, \
"Expected to get back one read but instead got %d" % (
len(reads),)
print(reads)
read = reads[0]
expected = LocusRead(name=pysam_read.qname,
sequence=pysam_read.query_sequence,
reference_positions=[0, 1, 3, 4, 5],
quality_scores=pysam_read.query_qualities,
base0_read_position_before_variant=0,
base0_read_position_after_variant=2)
assert_equal_fields(read, expected)
def test_locus_reads_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"
"""
# normalization of this variant will turn it into the deletion of
# "T" at base-1 position 5
variant = Variant("1", 4, ref="TT", alt="T")
pysam_read = make_pysam_read(seq="ACCTG", cigar="4M1D1M", mdtag="4^T1")
samfile = MockAlignmentFile(references={"chromosome"}, reads=[pysam_read])
read_creator = ReadCollector()
reads = read_creator.get_locus_reads(samfile, "chromosome",
variant.start - 1, variant.start)
print(reads)
assert len(reads) == 1, \
"Expected to get back one read but instead got %d" % (
len(reads),)
read = reads[0]
expected = LocusRead(
name=pysam_read.qname,
sequence=pysam_read.query_sequence,
reference_positions=[0, 1, 2, 3, 5],
quality_scores=pysam_read.query_qualities,
# missing would have gone after 4th nucleotide in the read
read_base0_start_inclusive=4,
read_base0_end_exclusive=4,
reference_base0_start_inclusive=4,
reference_base0_end_exclusive=5)
assert_equal_fields(read, expected)
def test_locus_reads_insertion():
"""
test_partitioned_read_sequences_insertion : Test that read gets correctly
partitioned for chr1:4 T>TG
where the sequence for chr1 is assumed to be "ACCTTG"
and the variant sequence is "ACCTGTG"
"""
variant = Variant("1", 4, ref="T", alt="TG")
pysam_read = make_pysam_read(seq="ACCTGTG", cigar="4M1I2M", mdtag="6")
samfile = MockAlignmentFile(references={"chromosome"}, reads=[pysam_read])
read_creator = ReadCollector()
reads = read_creator.get_locus_reads(samfile, "chromosome", variant.start,
variant.start)
print(reads)
assert len(reads) == 1, \
"Expected to get back one read but instead got %d" % (
len(reads),)
read = reads[0]
expected = LocusRead(
name=pysam_read.qname,
sequence=pysam_read.query_sequence,
# expect the inserted nucleotide to be missing a corresponding
# ref position
reference_positions=[0, 1, 2, 3, None, 4, 5],
quality_scores=pysam_read.query_qualities,
read_base0_start_inclusive=4,
read_base0_end_exclusive=5,
reference_base0_start_inclusive=4,
reference_base0_end_exclusive=4)
print("Actual: %s" % (read, ))
print("Expected: %s" % (expected, ))
assert_equal_fields(read, expected)
def test_locus_reads_substitution_shorter():
# test CC>G subsitution at 2nd and 3rd nucleotides of reference sequence
# "ACCTTG", for which the alignment is interpreted as a C>G variant
# followed by the deletion of a C
variant = Variant("1", 2, ref="CC", alt="G")
print(variant)
pysam_read = make_pysam_read(seq="AGTTG", cigar="2M1D3M", mdtag="1C^C4")
samfile = MockAlignmentFile(references={"chromosome"}, reads=[pysam_read])
read_creator = ReadCollector()
reads = read_creator.get_locus_reads(samfile, "chromosome", 1, 3)
assert len(reads) == 1, \
"Expected to get back one read but instead got %d" % (
len(reads),)
print(reads)
read = reads[0]
expected = LocusRead(name=pysam_read.qname,
sequence=pysam_read.query_sequence,
reference_positions=[0, 1, 3, 4, 5],
quality_scores=pysam_read.query_qualities,
read_base0_start_inclusive=1,
read_base0_end_exclusive=2,
reference_base0_start_inclusive=1,
reference_base0_end_exclusive=3)
assert_equal_fields(read, expected)
def test_locus_reads_snv():
"""
test_partitioned_read_sequences_snv : Test that read gets correctly
partitioned for chr1:4 T>G where the sequence for chr1 is assumed
to be "ACCTTG"
"""
# chr1_seq = "ACCTTG"
variant = Variant("1", 4, ref="T", alt="G")
pysam_read = make_pysam_read(seq="ACCGTG", cigar="6M", mdtag="3G2")
samfile = MockAlignmentFile(references=("chromosome", ),
reads=[pysam_read])
read_creator = ReadCollector()
reads = read_creator.get_locus_reads(samfile, "chromosome",
variant.start - 1, variant.start)
print(reads)
assert len(reads) == 1, \
"Expected to get back one read but instead got %d" % (
len(reads),)
read = reads[0]
expected = LocusRead(name=pysam_read.qname,
sequence=pysam_read.query_sequence,
reference_positions=[0, 1, 2, 3, 4, 5],
quality_scores=pysam_read.query_qualities,
reference_base0_start_inclusive=3,
reference_base0_end_exclusive=4,
read_base0_start_inclusive=3,
read_base0_end_exclusive=4)
assert_equal_fields(read, expected)
def test_locus_reads_substitution_longer():
# test C>GG subsitution at second nucleotide of reference sequence "ACCTTG",
# the alignment is interpreted as a C>G variant followed by an insertion of
# another G
variant = Variant("1", 2, ref="C", alt="GG")
print(variant)
pysam_read = make_pysam_read(seq="AGGCTTG", cigar="2M1I4M", mdtag="1C4")
samfile = MockAlignmentFile(references={"chromosome"}, reads=[pysam_read])
read_creator = ReadCollector()
reads = read_creator.get_locus_reads(samfile, "chromosome", 1, 2)
print(reads)
assert len(reads) == 1, \
"Expected to get back one read but instead got %d" % (
len(reads),)
read = reads[0]
expected = LocusRead(name=pysam_read.qname,
sequence=pysam_read.query_sequence,
reference_positions=[0, 1, None, 2, 3, 4, 5],
quality_scores=pysam_read.query_qualities,
read_base0_start_inclusive=1,
read_base0_end_exclusive=3,
reference_base0_start_inclusive=1,
reference_base0_end_exclusive=2)
assert_equal_fields(read, expected)
def test_locus_reads_insertion():
"""
test_partitioned_read_sequences_insertion : Test that read gets correctly
partitioned for chr1:4 T>TG
where the sequence for chr1 is assumed to be "ACCTTG"
and the variant sequence is "ACCTGTG"
"""
variant = Variant("chromosome",
4,
ref="T",
alt="TG",
normalize_contig_name=False)
pysam_read = make_read(seq="ACCTGTG", cigar="4M1I2M", mdtag="6")
samfile = DummySamFile(reads=[pysam_read])
reads = list(
locus_read_generator(samfile=samfile,
chromosome="chromosome",
base1_position_before_variant=variant.start,
base1_position_after_variant=variant.start + 1))
print(reads)
assert len(reads) == 1, \
"Expected to get back one read but instead got %d" % (
len(reads),)
read = reads[0]
expected = LocusRead(
name=pysam_read.qname,
sequence=pysam_read.query_sequence,
# expect the inserted nucleotide to be missing a corresponding
# ref position
reference_positions=[0, 1, 2, 3, None, 4, 5],
quality_scores=pysam_read.query_qualities,
base0_read_position_before_variant=3,
base0_read_position_after_variant=5)
assert_equal_fields(read, expected)
