def test_trim_read(self, window, cigar, start, read_length, expected_cigar,
expected_position, expected_read_length, comment):
read = test_utils.make_read('A' * read_length,
start=start,
cigar=cigar,
quals=[30] * read_length)
region = ranges.parse_literal(window)
output = realigner.trim_read(read, region)
self.assertEqual(expected_cigar,
cigar_utils.format_cigar_units(
output.alignment.cigar),
msg='Wrong cigar for case: {}'.format(comment))
# Start position of the alignment.
self.assertEqual(output.alignment.position.position,
expected_position,
msg='Wrong position for case: {}'.format(comment))
# Read sequence.
self.assertLen(
output.aligned_sequence,
expected_read_length,
msg='Wrong length of aligned_sequence for case: {}'.format(
comment))
# Base quality scores.
self.assertLen(
output.aligned_quality,
expected_read_length,
msg='Wrong length of aligned_quality for case: {}'.format(
comment))
def test_trim_cigar(self, cigar, ref_trim, ref_length, expected_cigar,
expected_read_trim, expected_read_length, comment):
read = test_utils.make_read('AAAATAAAATAAAATAAAATA',
start=100,
cigar=cigar)
output_cigar, output_read_trim, output_read_length = realigner.trim_cigar(
read.alignment.cigar, ref_trim, ref_length)
self.assertEqual(cigar_utils.format_cigar_units(output_cigar),
expected_cigar,
msg='Wrong cigar for: {}'.format(comment))
self.assertEqual(output_read_trim,
expected_read_trim,
msg='Wrong read trim for: {}'.format(comment))
self.assertEqual(output_read_length,
expected_read_length,
msg='Wrong read length for: {}'.format(comment))
self.assertEqual(cigar_utils.format_cigar_units(read.alignment.cigar),
cigar,
msg='Cigar in original read was mutated.')
def test_to_cigar_units(self, to_convert, expected):
# We can convert the raw form.
to_convert = list(to_convert)
expected = list(expected)
actual = cigar.to_cigar_units(to_convert)
self.assertEqual(actual, expected)
# We can also convert the string form by formatting actual.
self.assertEqual(
cigar.to_cigar_units(cigar.format_cigar_units(actual)), expected)
def test_to_cigar_units(self, to_convert, expected):
# We can convert the raw form.
to_convert = list(to_convert)
expected = list(expected)
actual = cigar.to_cigar_units(to_convert)
self.assertEqual(actual, expected)
# We can also convert the string form by formatting actual.
self.assertEqual(
cigar.to_cigar_units(cigar.format_cigar_units(actual)), expected)
def test_align_to_haplotype(self, read_seq, prefix, suffix, haplotypes,
expected_cigars):
test_read = test_utils.make_read(read_seq, start=1)
reads = [test_read]
# Align to each haplotype in turn.
for i in range(len(haplotypes)):
aligned_reads = self.reads_realigner.align_to_haplotype(
haplotypes[i], haplotypes, prefix, suffix, reads, 'test', 1)
self.assertEqual(len(reads), len(aligned_reads))
self.assertEqual(
cigar_utils.format_cigar_units(
aligned_reads[0].alignment.cigar), expected_cigars[i])
def test_split_reads(self, read_seq, cigar, expected_cigars,
expected_sequences, expected_positions):
test_read = test_utils.make_read(read_seq, cigar=cigar, start=1)
reads = realigner.split_reads([test_read])
for i in range(len(reads)):
# Check sequences
self.assertEqual(reads[i].aligned_sequence, expected_sequences[i])
# Check cigars
self.assertEqual(
cigar_utils.format_cigar_units(reads[i].alignment.cigar),
expected_cigars[i])
# Check reference positions
self.assertEqual(reads[i].alignment.position.position,
expected_positions[i])
self.assertLen(reads, len(expected_sequences))
def test_align_to_haplotype_stress_tests(self, alt_allele,
ref_buffer_length,
read_buffer_length):
"""Testing what happens when read and reference sequences are shorter."""
# Start with long prefix and suffix to enable cutting it down as necessary
whole_prefix = 'AGTGATCTAGTCCTTTTTGTTGTGCAAAAGGAAGTGCTAAAATCAGAATGAGAACCATGGTCACCTGACATAGAC'
whole_suffix = 'ATCCATGTTCAAGTACTAATTCTGGGCAAGACACTGTTCTAAGTGCTATGAATATATTACCTCATTTAATCATCT'
ref_prefix = whole_prefix[-ref_buffer_length:]
ref_suffix = whole_suffix[:ref_buffer_length]
# Make two haplotypes.
ref_allele = ''
haplotypes = [ref_allele, alt_allele]
# Simulate one read from the reference and one from the alt haplotype.
read_prefix = ref_prefix[-read_buffer_length:]
read_suffix = ref_suffix[:read_buffer_length]
expected_cigars = [
# Aligning to ref haplotype: Insertion.
'{}M{}I{}M'.format(len(read_prefix), len(alt_allele),
len(read_suffix)),
# Aligning to alt haplotype: All matching.
'{}M'.format(
len(read_prefix) + len(alt_allele) + len(read_suffix))
]
reads = [
test_utils.make_read(read_prefix + alt_allele + read_suffix,
start=1)
]
# Align to each haplotype in turn.
for i in range(len(haplotypes)):
aligned_reads = self.reads_realigner.align_to_haplotype(
haplotypes[i], haplotypes, ref_prefix, ref_suffix, reads,
'test', 1)
self.assertEqual(len(reads), len(aligned_reads))
self.assertEqual(
cigar_utils.format_cigar_units(
aligned_reads[0].alignment.cigar), expected_cigars[i])
def test_format_cigar_units(self, cigar_units, expected): self.assertEqual(cigar.format_cigar_units(cigar_units), expected)
def test_format_cigar_units(self, cigar_units, expected): self.assertEqual(cigar.format_cigar_units(cigar_units), expected)
