def test_partition_bmtagger(self):
outMatch = [
os.path.join(self.tempDir, 'outMatch.{}.fastq'.format(n))
for n in '12'
]
outNoMatch = [
os.path.join(self.tempDir, 'outNoMatch.{}.fastq'.format(n))
for n in '12'
]
myInputDir = util.file.get_test_input_path(self)
args = taxon_filter.parser_partition_bmtagger(
argparse.ArgumentParser()).parse_args([
os.path.join(myInputDir, 'in1.fastq'),
os.path.join(myInputDir, 'in2.fastq'),
os.path.join(self.tempDir, 'humanChr1Subset'),
os.path.join(self.tempDir,
'humanChr9Subset'), '--outMatch', outMatch[0],
outMatch[1], '--outNoMatch', outNoMatch[0], outNoMatch[1]
])
args.func_main(args)
# Compare to expected
for case in ['Match.1', 'Match.2', 'NoMatch.1', 'NoMatch.2']:
assert_equal_contents(
self, os.path.join(self.tempDir, 'out' + case + '.fastq'),
os.path.join(myInputDir, 'expected.' + case + '.fastq'))
def test_deplete_bmtagger(self):
myInputDir = util.file.get_test_input_path(self)
args = taxon_filter.parser_partition_bmtagger(argparse.ArgumentParser()).parse_args(
[os.path.join(myInputDir, 'in1.fastq'), os.path.join(myInputDir, 'in2.fastq'), os.path.join(
self.tempDir, 'humanChr1Subset'), os.path.join(self.tempDir, 'humanChr9Subset'), '--outNoMatch',
os.path.join(self.tempDir, 'deplete.1.fastq'), os.path.join(self.tempDir, 'deplete.2.fastq')])
args.func_main(args)
# Compare to expected
for case in ['1', '2']:
assert_equal_contents(self, os.path.join(self.tempDir, 'deplete.' + case + '.fastq'),
os.path.join(myInputDir, 'expected.NoMatch.' + case + '.fastq'))
def test_partition_bmtagger(self):
outMatch = [os.path.join(self.tempDir, 'outMatch.{}.fastq'.format(n)) for n in '12']
outNoMatch = [os.path.join(self.tempDir, 'outNoMatch.{}.fastq'.format(n)) for n in '12']
myInputDir = util.file.get_test_input_path(self)
args = taxon_filter.parser_partition_bmtagger(argparse.ArgumentParser()).parse_args(
[os.path.join(myInputDir, 'in1.fastq'), os.path.join(myInputDir, 'in2.fastq'), os.path.join(
self.tempDir, 'humanChr1Subset'), os.path.join(self.tempDir, 'humanChr9Subset'), '--outMatch',
outMatch[0], outMatch[1], '--outNoMatch', outNoMatch[0], outNoMatch[1]])
args.func_main(args)
# Compare to expected
for case in ['Match.1', 'Match.2', 'NoMatch.1', 'NoMatch.2']:
assert_equal_contents(self, os.path.join(self.tempDir, 'out' + case + '.fastq'),
os.path.join(myInputDir, 'expected.' + case + '.fastq'))
