def test_find_multiple_single_base_deletion(self):
ref = ReferenceChromosome("TTAAAAAGAAAAT")
seq = Sequence(ref, "..*.....*....")
self.assertEqual(seq.variants, {
Variant(ref.chrom, 1, "TA", "T"),
Variant(ref.chrom, 7, "GA", "G")
})
def test_should_find_multiple_snps(self):
ref = ReferenceChromosome("AAAAAAAAAAAAA")
seq = Sequence(ref, ".C.........T.")
self.assertEqual(seq.variants, {
Variant(ref.chrom, 1, "A", "C"),
Variant(ref.chrom, 11, "A", "T")
})
def test_find_adjacent_insertion_and_snp(self):
ref = ReferenceChromosome("T*ATAAAAAAAT")
seq = Sequence(ref, ".CG.........")
self.assertEqual(seq.variants, {
Variant(ref.chrom, 0, "T", "TC"),
Variant(ref.chrom, 1, "A", "G")
})
def test_find_adjacent_snp_and_deletion(self):
ref = ReferenceChromosome("TTAAAAAAAAAT")
seq = Sequence(ref, ".G*.........")
self.assertEqual(seq.variants, {
Variant(ref.chrom, 1, "T", "G"),
Variant(ref.chrom, 1, "TA", "T")
})
def test_find_multiple_variants(self):
ref = ReferenceChromosome("TA*AAAGCTAACT")
seq = Sequence(ref, ".GC...T...**.")
self.assertEqual(
seq.variants, {
Variant(ref.chrom, 1, "A", "G"),
Variant(ref.chrom, 1, "A", "AC"),
Variant(ref.chrom, 5, "G", "T"),
Variant(ref.chrom, 8, "AAC", "A")
})
def __get_expected_calls_from_haplotypes(ascii_strings, reference):
if len(ascii_strings) != 2:
raise weCallException(
"Expected calls have to be defined as a diploid.")
if not all(len(str) == reference.length_with_deletions()
for str in ascii_strings):
raise weCallException(
"Ascii haplotypes have to be of the same length as the reference")
vars_from_hap1 = Sequence(reference, ascii_strings[0]).variants
vars_from_hap2 = Sequence(reference, ascii_strings[1]).variants
calls = {}
for var in vars_from_hap1.intersection(vars_from_hap2):
calls[var] = GenotypeCall("1/1")
for var in vars_from_hap1.symmetric_difference(vars_from_hap2):
calls[var] = GenotypeCall("0/1")
return calls
def build_annotated_pair(fwd, rev, n_fwd, n_rev, mapping_quality, insert_size,
read_id, read_flags, cigar_string, read_start,
read_mate_start):
fwd_reference = ReferenceChromosome(fwd.reference_string, fwd.pos_from)
rev_reference = ReferenceChromosome(rev.reference_string, rev.pos_from)
fwd_sequence = Sequence(fwd_reference,
fwd.sequence_string.replace(",", ".").upper(),
cigar_string)
rev_sequence = Sequence(rev_reference,
rev.sequence_string.replace(",", ".").upper(),
cigar_string)
fwd_quality = SequenceQuality(fwd.quality_string)
rev_quality = SequenceQuality(rev.quality_string)
fwd_read_sequence = ReadSequence(fwd_sequence, fwd_quality,
mapping_quality, insert_size, read_id,
read_flags, read_start, read_mate_start)
rev_read_sequence = ReadSequence(rev_sequence, rev_quality,
mapping_quality, insert_size, read_id,
read_flags, read_start, read_mate_start)
return [
ReadPairWithCoverage(fwd_read_sequence, rev_read_sequence, n_fwd,
n_rev)
]
def build_annotated_seq(self, n_fwd, n_rev, mapping_quality, insert_size,
read_id, read_flags, cigar_string, read_start,
read_mate_start):
reference = ReferenceChromosome(self.reference_string, self.pos_from)
sequence = Sequence(reference,
self.sequence_string.replace(",", ".").upper(),
cigar_string)
quality = SequenceQuality(self.quality_string)
read_sequence = ReadSequence(sequence, quality, mapping_quality,
insert_size, read_id, read_flags,
read_start, read_mate_start)
if n_fwd is not None:
return [ReadSequenceWithCoverage(read_sequence, n_fwd, n_rev)]
elif self.is_reverse_seq():
return [ReadSequenceWithCoverage(read_sequence, 0, 1)]
elif self.is_forward_seq():
return [ReadSequenceWithCoverage(read_sequence, 1, 0)]
else:
raise weCallException(
"Raw sequence: {} is neither forward or reverse".format(self))
def test_should_find_multi_base_insertion(self):
ref = ReferenceChromosome("CT**AAAAAAAAT")
seq = Sequence(ref, "..GC.........")
self.assertEqual(seq.variants, {Variant(ref.chrom, 1, "T", "TGC")})
def test_finds_snp(self):
ref = ReferenceChromosome("AAAAAAAAAAAAA")
seq = Sequence(ref, ".C...........")
self.assertEqual(seq.variants, {Variant(ref.chrom, 1, "A", "C")})
def test_should_not_find_deletion_on_left_edge(self):
ref = ReferenceChromosome("TAGCAAAAAAAT")
seq = Sequence(ref, "*...........")
print((seq.variants))
self.assertEqual(len(seq.variants), 0)
def test_should_not_find_long_deletion_on_right_edge(self):
ref = ReferenceChromosome("TTAGCAAAAAACT")
seq = Sequence(ref, "..........***")
self.assertEqual(len(seq.variants), 0)
def test_should_get_empty_cigar(self):
ref = ReferenceChromosome("")
seq = Sequence(ref, "")
self.assertEqual(str(seq.cigar), "")
def test_find_multi_base_deletion_with_deletion_in_reference(self):
ref = ReferenceChromosome("TTA*AAAAAAAAT")
seq = Sequence(ref, "..**.........")
self.assertEqual(seq.variants, {Variant(ref.chrom, 1, "TA", "T")})
def test_finds_snp_at_the_ref_start(self):
ref = ReferenceChromosome("CATAAAAAAAA")
seq = Sequence(ref, "T..........")
self.assertEqual(seq.variants, {Variant(ref.chrom, 0, "C", "T")})
def test_finds_snp_at_the_ref_end(self):
ref = ReferenceChromosome("CATAAAAAAAT")
seq = Sequence(ref, "..........C")
self.assertEqual(seq.variants, {Variant(ref.chrom, 10, "T", "C")})
def test_finds_snp_after_asterix(self):
ref = ReferenceChromosome("T*CATAAAAAAAA")
seq = Sequence(ref, ".*.C.........")
self.assertEqual(seq.variants, {Variant(ref.chrom, 2, "A", "C")})
def test_should_get_correct_cigar_for_dots(self):
ref = ReferenceChromosome("CCAA")
seq = Sequence(ref, "....")
self.assertEqual(str(seq.cigar), "4M")
def test_should_get_correct_cigar_for_snp(self):
ref = ReferenceChromosome("TTT")
seq = Sequence(ref, ".G.")
self.assertEqual(str(seq.cigar), "3M")
def test_should_get_correct_cigar_for_multiple_events(self):
ref = ReferenceChromosome("CCC***AAATTT")
seq = Sequence(ref, "A*.T*T...**C")
self.assertEqual(str(seq.cigar), "1M1D1M2I3M2D1M")
def test_should_get_correct_cigar_for_padding_and_insertion(self):
ref = ReferenceChromosome("T*T")
seq = Sequence(ref, ".C.")
self.assertEqual(str(seq.cigar), "1M1I1M")
