def test_should_interpret_trailing_whitespace_to_override_pos_to_when_seq_has_insertion(
self):
ref = ReferenceChromosome("C*GA")
annotated_seqs = sequence_builder(ref, ".C ")
read_lists = [builder.build_reads(0, {}) for builder in annotated_seqs]
reads = [read for read_list in read_lists for read in read_list]
self.assertEqual(reads[0].rlen, 2)
def test_should_build_with_custom_quality_with_ins(self):
ref = ReferenceChromosome("AA**A")
annotated_seqs = sequence_builder(ref, "..CC.", quality_string="31220")
read_lists = [builder.build_reads(0, {}) for builder in annotated_seqs]
reads = [read for read_list in read_lists for read in read_list]
self.assertEqual(
reads[0].qual, self.ascii_codes["3"] + self.ascii_codes["1"] +
self.ascii_codes["2"] * 2 + self.ascii_codes["0"])
def test_should_build_correct_sequence_with_insertion_at_the_end(self):
ref = ReferenceChromosome("CCC**")
builders = sequence_builder(ref, "...TT")
read_lists = [builder.build_reads(0, {}) for builder in builders]
reads = [read for read_list in read_lists for read in read_list]
self.assertEqual(reads[0].pos, 0)
self.assertEqual(reads[0].rlen, 5)
self.assertEqual(reads[0].seq, "CCCTT")
def test_should_interpret_trailing_whitespace_to_override_positions_for_complex_ref_and_seq(
self):
ref = ReferenceChromosome("ACCC*G*A")
annotated_seqs = sequence_builder(ref, ".**.C ")
read_lists = [builder.build_reads(0, {}) for builder in annotated_seqs]
reads = [read for read_list in read_lists for read in read_list]
self.assertEqual(reads[0].pos, 0)
self.assertEqual(reads[0].rlen, 3)
def test_should_interpret_trailing_whitespace_to_override_pos_to(self):
ref = ReferenceChromosome("CATG")
annotated_seqs = sequence_builder(ref, ".C ")
read_lists = [builder.build_reads(0, {}) for builder in annotated_seqs]
reads = [read for read_list in read_lists for read in read_list]
self.assertEqual(len(reads), 1)
self.assertEqual(reads[0].pos, 0)
self.assertEqual(reads[0].seq, "CC")
def test_should_build_with_custom_quality_with_del(self):
ref = ReferenceChromosome("AAAAA")
annotated_seqs = sequence_builder(ref, "..*..", quality_string="31 00")
read_lists = [builder.build_reads(0, {}) for builder in annotated_seqs]
reads = [read for read_list in read_lists for read in read_list]
reads.sort(key=lambda x: (x.pos, x.seq, x.qual, x.cigarstring, x.mapq))
self.assertEqual(
reads[0].qual, self.ascii_codes["3"] + self.ascii_codes["1"] +
self.ascii_codes["0"] * 2)
def test_should_build_correct_sequence_without_any_whitespace(self):
ref = ReferenceChromosome("C*CC")
annotated_seqs = sequence_builder(ref, ".*.T")
read_lists = [builder.build_reads(0, {}) for builder in annotated_seqs]
reads = [read for read_list in read_lists for read in read_list]
self.assertEqual(len(reads), 1)
self.assertEqual(reads[0].pos, 0)
self.assertEqual(reads[0].rlen, 3)
self.assertEqual(reads[0].seq, "CCT")
def test_should_interpret_leading_whitespace_to_override_pos_from_when_ref_has_deletion(
self):
ref = ReferenceChromosome("C*TG")
annotated_seqs = sequence_builder(ref, " C.")
read_lists = [builder.build_reads(0, {}) for builder in annotated_seqs]
reads = [read for read_list in read_lists for read in read_list]
self.assertEqual(len(reads), 1)
self.assertEqual(reads[0].pos, 1)
self.assertEqual(reads[0].seq, "CG")
def test_should_build_two_complex_seqs_defined_on_single_line(self):
ref = ReferenceChromosome("AA*CC*TGTAAGG")
annotated_seqs = sequence_builder(ref, " .G. ,c,*, ")
read_lists = [builder.build_reads(0, {}) for builder in annotated_seqs]
reads = [read for read_list in read_lists for read in read_list]
reads.sort(key=lambda x: (x.pos, x.seq, x.qual, x.cigarstring, x.mapq))
self.assertEqual(len(reads), 2)
self.assertEqual(reads[0].pos, 1)
self.assertEqual(reads[0].seq, "AGC")
self.assertEqual(reads[1].pos, 4)
self.assertEqual(reads[1].seq, "TCTA")
def test_should_build_with_custom_quality_and_sequence_shorter_than_reference(
self):
ref = ReferenceChromosome("AAAAAAAAAAAA")
builders = sequence_builder(ref,
" ..*.. ",
quality_string=" 31 0 ")
read_lists = [builder.build_reads(0, {}) for builder in builders]
reads = [read for read_list in read_lists for read in read_list]
self.assertEqual(
reads[0].qual, self.ascii_codes["3"] + self.ascii_codes["1"] +
self.ascii_codes["0"] + self.default_qual)
def add_sequence(self,
seq_string,
quality_string=None,
n_fwd=None,
n_rev=None,
mapping_quality=HIGH_QUALITY,
insert_size=None,
read_id=None,
read_flags=None,
cigar_string=None,
read_start=None,
read_mate_start=None):
self._read_sequences_with_coverage.extend(
sequence_builder(self.reference, seq_string, quality_string, n_fwd,
n_rev, mapping_quality, insert_size, read_id,
read_flags, cigar_string, read_start,
read_mate_start))
return self
def test_should_translate_reverse_seq_into_correct_annotations(self):
ref = ReferenceChromosome("CCTG")
annotated_seq = sequence_builder(ref, ",,c,")[0]
self.assertEqual(annotated_seq.n_fwd, 0)
self.assertEqual(annotated_seq.n_rev, 1)
def test_should_raise_when_assigning_qual_to_deletion(self):
with self.assertRaisesRegex(
weCallException,
"Cannot assign base quality to a deleted base."):
sequence_builder(ReferenceChromosome("AAAA"), ".*..", " 1 ")
def test_should_translate_reverse_seq_into_correct_sequence(self):
ref = ReferenceChromosome("AAACCTG*TAA")
builders = sequence_builder(ref, " ,,c,*, ")
read_lists = [builder.build_reads(0, {}) for builder in builders]
reads = [read for read_list in read_lists for read in read_list]
self.assertEqual(reads[0].seq, 'CCCGT')
def test_should_raise_for_invalid_char_in_seq(self):
with self.assertRaisesRegex(weCallException,
"Illegal character in sequence .*'"):
sequence_builder(ReferenceChromosome("TAAAA"), "..&..")
def test_should_build_with_default_quality_for_None(self):
ref = ReferenceChromosome("AAAAA")
annotated_seqs = sequence_builder(ref, ".....")
read_lists = [builder.build_reads(0, {}) for builder in annotated_seqs]
reads = [read for read_list in read_lists for read in read_list]
self.assertEqual(reads[0].qual, self.default_qual * 5)
def test_should_raise_when_quality_string_too_long_due_to_insertions(self):
with self.assertRaisesRegex(
weCallException,
"Quality string has to be of the same length as reference."):
sequence_builder(ReferenceChromosome("TA**A"), "..TT.", "123")
def test_should_raise_when_quality_assigned_to_gap(self):
with self.assertRaisesRegex(
weCallException, "Cannot assign base quality inside a gap."):
sequence_builder(ReferenceChromosome("TAAAA*A"), "... ..",
"12 34 ")
def test_should_raise_when_quality_string_too_short_multisequence(self):
with self.assertRaisesRegex(
weCallException,
"Quality string has to be of the same length as reference."):
sequence_builder(ReferenceChromosome("TAAAA*A"), "... ..",
"12 4")
def test_should_raise_for_dot_in_reverse_seq(self):
with self.assertRaisesRegex(weCallException,
"Illegal character in sequence .*"):
sequence_builder(ReferenceChromosome("TAAAA"), ",,c.,")
