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))
def test_examples(self):
with TempDirectory() as output_dir:
input_bam = "chr10.pten.bam"
output_bam = "chr10.pten.clipped.bam"
output_bai = output_bam + ".bai"
input_primer_filename = os.path.join(INPUT_DIR, "primers.txt")
input_bam_filename = os.path.join(INPUT_DIR, input_bam)
expect_bam_filename = os.path.join(INPUT_DIR, output_bam)
expect_bai_filename = os.path.join(INPUT_DIR, output_bai)
output_bam_filename = os.path.join(output_dir.path, output_bam)
output_bai_filename = os.path.join(output_dir.path, output_bai)
clipper.main(["program_name",
input_primer_filename,
input_bam_filename,
output_bam_filename])
self.assertTrue(filecmp.cmp(expect_bam_filename,
output_bam_filename),
"{} does not match expected".format(output_bam))
self.assertTrue(filecmp.cmp(expect_bai_filename,
output_bai_filename),
"{} does not match expected".format(output_bai))
def test_examples(self):
with TempDirectory() as output_dir:
input_bam = "chr10.pten.bam"
output_bam = "chr10.pten.clipped.bam"
output_bai = output_bam + ".bai"
input_primer_filename = os.path.join(INPUT_DIR, "primers.txt")
input_bam_filename = os.path.join(INPUT_DIR, input_bam)
expect_bam_filename = os.path.join(INPUT_DIR, output_bam)
expect_bai_filename = os.path.join(INPUT_DIR, output_bai)
output_bam_filename = os.path.join(output_dir.path, output_bam)
output_bai_filename = os.path.join(output_dir.path, output_bai)
clipper.main([
"program_name", input_primer_filename, input_bam_filename,
output_bam_filename
])
self.assertTrue(
filecmp.cmp(expect_bam_filename, output_bam_filename),
"{} does not match expected".format(output_bam))
self.assertTrue(
filecmp.cmp(expect_bai_filename, output_bai_filename),
"{} does not match expected".format(output_bai))
"""Katana entry point""" import sys from katana.clipper import main main(sys.argv)
"""Katana entry point""" import sys from katana.clipper import main main(sys.argv)
