def test_end_sortsAndIndexes(self):
#pylint: disable=no-member
with TempDirectory() as input_dir, TempDirectory() as output_dir:
input_bam_filename = os.path.join(input_dir.path, "input.bam")
make_bam_file(input_bam_filename, [build_read()])
output_bam_filename = os.path.join(output_dir.path, "output.bam")
mock_log = MockLog()
handler = readhandler.WriteReadHandler(input_bam_filename,
output_bam_filename,
log_method=mock_log.log)
read1 = build_read(query_name="read1",
reference_id=0,
reference_start=20)
read2 = build_read(query_name="read2",
reference_id=0,
reference_start=10)
handler.begin()
handler.handle(read1, None, None)
handler.handle(read2, None, None)
handler.end()
actual_files = sorted(os.listdir(output_dir.path))
self.assertEquals(["output.bam", "output.bam.bai"], actual_files)
actual_bam = pysam.AlignmentFile(output_bam_filename, "rb")
actual_reads = [read for read in actual_bam.fetch()]
actual_bam.close()
self.assertEquals(2, len(actual_reads))
self.assertEquals("read2", actual_reads[0].query_name)
self.assertEquals("read1", actual_reads[1].query_name)
def test_end_sortsAndIndexes(self):
#pylint: disable=no-member
with TempDirectory() as input_dir, TempDirectory() as output_dir:
input_bam_filename = os.path.join(input_dir.path, "input.bam")
make_bam_file(input_bam_filename, [build_read()])
output_bam_filename = os.path.join(output_dir.path, "output.bam")
mock_log = MockLog()
handler = readhandler.WriteReadHandler(input_bam_filename,
output_bam_filename,
log_method=mock_log.log)
read1 = build_read(query_name="read1",
reference_id=0,
reference_start=20)
read2 = build_read(query_name="read2",
reference_id=0,
reference_start=10)
handler.begin()
handler.handle(read1, None, None)
handler.handle(read2, None, None)
handler.end()
actual_files = sorted(os.listdir(output_dir.path))
self.assertEquals(["output.bam", "output.bam.bai"], actual_files)
actual_bam = pysam.AlignmentFile(output_bam_filename, "rb")
actual_reads = [read for read in actual_bam.fetch()]
actual_bam.close()
self.assertEquals(2, len(actual_reads))
self.assertEquals("read2", actual_reads[0].query_name)
self.assertEquals("read1", actual_reads[1].query_name)
def test_main(self):
primer_file_content = \
'''Customer TargetID|Chr|Sense Start|Antisense Start|Sense Sequence|Antisense Sequence
primer1|1|101|200|AAGG|CCTT
primer2|2|501|600|CGCG|ATAT
'''.replace("|", "\t")
CIGAR_10M = ((0,10),)
readA1 = build_read(query_name = "readA",
query_sequence="AGCTTAGCTA",
flag = 99,
reference_id = 0,
reference_start = 100,
cigar = CIGAR_10M,
next_reference_id =0,
next_reference_start=190,
template_length=80)
readA2 = build_read(query_name = "readA",
query_sequence="AGCTTAGCTA",
flag = 147,
reference_id = 0,
reference_start = 190,
cigar = CIGAR_10M,
next_reference_id = 0,
next_reference_start=100,
template_length=80)
readB1 = build_read(query_name = "readB",
query_sequence="AGCTTAGCTA",
flag = 0,
reference_id = 1,
reference_start = 242,
cigar = CIGAR_10M,
next_reference_id = 0,
next_reference_start=0,
template_length=0)
with TempDirectory() as input_dir, TempDirectory() as output_dir:
input_bam_filename = os.path.join(input_dir.path, "input.bam")
output_bam_filename = os.path.join(output_dir.path, "output.bam")
input_primers_filename = self._create_file(input_dir.path,
'primers.txt',
primer_file_content)
make_bam_file(input_bam_filename, [readA1, readA2, readB1])
clipper.main(["katana",
input_primers_filename,
input_bam_filename,
output_bam_filename])
actual = self._bam_to_sam(output_bam_filename)
self.assertRegexpMatches(actual[0], "readA.*chr1.*105.*4S6M.*191")
self.assertRegexpMatches(actual[1], "readA.*chr1.*191.*6M4S.*105")
self.assertEquals(2, len(actual))
def test_main(self):
primer_file_content = \
'''Customer TargetID|Chr|Sense Start|Antisense Start|Sense Sequence|Antisense Sequence
primer1|1|101|200|AAGG|CCTT
primer2|2|501|600|CGCG|ATAT
'''.replace("|", "\t")
CIGAR_10M = ((0, 10), )
readA1 = build_read(query_name="readA",
query_sequence="AGCTTAGCTA",
flag=99,
reference_id=0,
reference_start=100,
cigar=CIGAR_10M,
next_reference_id=0,
next_reference_start=190,
template_length=80)
readA2 = build_read(query_name="readA",
query_sequence="AGCTTAGCTA",
flag=147,
reference_id=0,
reference_start=190,
cigar=CIGAR_10M,
next_reference_id=0,
next_reference_start=100,
template_length=80)
readB1 = build_read(query_name="readB",
query_sequence="AGCTTAGCTA",
flag=0,
reference_id=1,
reference_start=242,
cigar=CIGAR_10M,
next_reference_id=0,
next_reference_start=0,
template_length=0)
with TempDirectory() as input_dir, TempDirectory() as output_dir:
input_bam_filename = os.path.join(input_dir.path, "input.bam")
output_bam_filename = os.path.join(output_dir.path, "output.bam")
input_primers_filename = self._create_file(input_dir.path,
'primers.txt',
primer_file_content)
make_bam_file(input_bam_filename, [readA1, readA2, readB1])
clipper.main([
"katana", input_primers_filename, input_bam_filename,
output_bam_filename
])
actual = self._bam_to_sam(output_bam_filename)
self.assertRegexpMatches(actual[0], "readA.*chr1.*105.*4S6M.*191")
self.assertRegexpMatches(actual[1], "readA.*chr1.*191.*6M4S.*105")
self.assertEquals(2, len(actual))