def test_calls_correct_reference_between_clusters_with_uncalled_indel_between(
self):
chrom = "1"
driver = SVCDriver(self)
driver.with_ref_sequence(
"AAAAAAAATAACGCACGCCCCATAAAAAAATTTTTTTTTTT",
chrom=chrom).with_read(
" ..*....................... ",
n_fwd=10,
n_rev=10).with_read(
".......................*............ ",
n_fwd=1,
n_rev=1).with_read(
".......................T.. ",
n_fwd=10,
n_rev=10).with_output_ref_calls(
True).with_max_cluster_distance(5)
expect = driver.call()
vcf_expect = expect.with_output_vcf()
vcf_expect.has_reference_calls(ChromInterval(chrom, 0, 8))
vcf_expect.has_record_for_variant(Variant(chrom, 8, "TA", "T"))
vcf_expect.has_reference_calls(ChromInterval(chrom, 10, 23))
vcf_expect.has_record_for_variant(Variant(chrom, 23, "A", "T"))
vcf_expect.has_reference_calls(ChromInterval(chrom, 24, 41))
def test_calls_reference_on_location_with_low_quality_variant_support(
self):
chrom = "1"
driver = SVCDriver(self)
driver.with_ref_sequence(
"AAAAAAAATAACGCACGCCCCATAAAAAAATTTTTTTTTTT",
chrom=chrom).with_read(
" ..*....................... ", n_fwd=2,
n_rev=1).with_read(
".................T.....T......... ",
" 1 ",
n_fwd=1,
n_rev=1).with_read(
".......................T.. ",
n_fwd=1,
n_rev=0).with_output_ref_calls(True)
expect = driver.call()
vcf_expect = expect.with_output_vcf()
vcf_expect.has_reference_calls(ChromInterval(chrom, 0, 8))
vcf_expect.has_record_for_variant(Variant(chrom, 8, "TA", "T"))
vcf_expect.has_reference_calls(ChromInterval(chrom, 10, 23))
vcf_expect.has_record_for_variant(Variant(chrom, 23, "A", "T"))
vcf_expect.has_reference_calls(ChromInterval(chrom, 24, 41))
def calls_variants_in_bed_region(self,
ref,
sequence_list,
expected_ascii_haplotypes=None,
expected_variant_stubs=None,
bed_regions=[],
compress=False):
bed_filename = os.path.join(self.work_dir, "test.bed")
with BEDWriterContextManager(bed_filename) as bed_writer:
# TODO - link chromosomes
for region in bed_regions:
bed_writer.write_chrom_interval(
ChromInterval(DEFAULT_CHROM, region.start, region.end))
if compress:
indexer = BEDIndexer(bed_filename)
indexer.index()
bed_filename = indexer.compressed_filename
self.calls_variants(ref,
sequence_list,
expected_ascii_haplotypes,
expected_variant_stubs,
n_fwd=10,
n_rev=10,
config_dict={
"regions": bed_filename,
"allowMNPCalls": "True"
})
def test_should_write_line_to_stream(self):
output_stream = MockStream()
writer = BEDWriter(output_stream)
writer.write_chrom_interval(ChromInterval("20", 1, 2))
# Then
self.assertEqual(output_stream.lines, ["20\t1\t2\n"])
def __init__(self,
chrom,
start,
end,
label=None,
score=None,
strand=None,
build=None):
self.chrom_interval = ChromInterval(chrom, start, end)
self.build = build
self.label = label
self.score = score
self.strand = strand
def test_bed_extension_is_not_required(self):
region_filename = os.path.join(self.work_dir, "bed.txt")
with BEDWriterContextManager(region_filename) as bed:
bed.write_chrom_interval(ChromInterval("1", 0, 29))
svc = SVCDriver(self).with_ref_sequence(
"ACGTACGTACGTACGTACGTACGT", chrom="1"
).with_read(
"....G...................", n_rev=10, n_fwd=10
).with_region_string(region_filename)
expect = svc.call()
expect.with_output_vcf() \
.record_count(1)
def setUp(self):
BaseTest.setUp(self)
self.bed_filename = os.path.join(self.work_dir, "_.bed")
self.log_filename = os.path.join(self.work_dir, "_.log")
chrom = "1"
with BEDWriterContextManager(self.bed_filename) as bed_file:
bed_file.write_chrom_interval(ChromInterval(chrom, 0, 42))
self.output_vcf = os.path.join(self.work_dir, "output.vcf")
self.svc_driver = SVCDriver(self)
self.svc_driver.with_ref_sequence(
"AAAAAAAAAAACGCACCCCCCATAAAAAAAATTTTTTTTTTT", chrom=chrom)
self.svc_driver.with_read(" ..............C............. ",
chrom=chrom)
self.svc_driver.with_log_timings(True)
self.svc_driver.with_region_string(self.bed_filename)
self.svc_driver.with_log_filename(self.log_filename)
self.svc_driver.with_output_vcf_filename(self.output_vcf)
def test_should_overlap_mnp_at_region_end(self):
mnp = variant.Variant('1', 15, 'ACGT', 'GCGC')
self.assertTrue(mnp.overlap(ChromInterval('1', 15, 16)))
def has_reference_calls_for_region(self, chrom, start, end):
return self.has_reference_calls(ChromInterval(chrom, start, end))
def test_should_write_tab_delimited_region(self):
region = ChromInterval("20", 1, 2)
output_line = bed_line_from_chrom_interval(region)
self.assertEqual(output_line, "20\t1\t2")
def chrom_interval(self):
return ChromInterval(self.chrom, self.pos_from, self.pos_to)
def test_should_not_overlap_mnp_after_region(self):
mnp = variant.Variant('1', 15, 'ACGT', 'GCGC')
self.assertFalse(mnp.overlap(ChromInterval('1', 19, 20)))
def overlap(self, chrom_interval):
return chrom_interval.overlap(
ChromInterval(self.chrom, self.pos_from, self.pos_to))
def test_should_overlap_insertion_at_region_end(self):
ins = variant.Variant('1', 15, 'A', 'AAAAA')
self.assertTrue(ins.overlap(ChromInterval('1', 15, 16)))
def test_should_not_overlap_deletion_after_region(self):
deletion = variant.Variant('1', 15, 'AAAAA', 'A')
self.assertFalse(deletion.overlap(ChromInterval('1', 20, 21)))
def test_should_not_overlap_insertion_before_region(self):
ins = variant.Variant('1', 15, 'A', 'AAAAA')
self.assertFalse(ins.overlap(ChromInterval('1', 16, 20)))
def test_should_overlap_deletion_at_region_end(self):
deletion = variant.Variant('1', 15, 'AAAAA', 'A')
self.assertTrue(deletion.overlap(ChromInterval('1', 15, 16)))