def test_purge_unmated_sra(self):
myInputDir = util.file.get_test_input_path(self)
inFastq1 = os.path.join(myInputDir, "in_sra1.fastq")
inFastq2 = os.path.join(myInputDir, "in_sra2.fastq")
outFastq1 = util.file.mkstempfname(".fastq")
outFastq2 = util.file.mkstempfname(".fastq")
parser = read_utils.parser_purge_unmated(argparse.ArgumentParser())
args = parser.parse_args(["--regex", "^@(\S+).[1|2] .*", inFastq1, inFastq2, outFastq1, outFastq2])
args.func_main(args)
# The expected outputs are identical to the previous case.
expected1Fastq = os.path.join(myInputDir, "expected1.fastq")
expected2Fastq = os.path.join(myInputDir, "expected2.fastq")
self.assertEqualContents(outFastq1, expected1Fastq)
self.assertEqualContents(outFastq2, expected2Fastq)
def test_purge_unmated(self):
myInputDir = util.file.get_test_input_path(self)
inFastq1 = os.path.join(myInputDir, "in1.fastq")
inFastq2 = os.path.join(myInputDir, "in2.fastq")
outFastq1 = util.file.mkstempfname(".fastq")
outFastq2 = util.file.mkstempfname(".fastq")
parser = read_utils.parser_purge_unmated(argparse.ArgumentParser())
args = parser.parse_args([inFastq1, inFastq2, outFastq1, outFastq2])
args.func_main(args)
# Check that results match expected
expected1Fastq = os.path.join(myInputDir, "expected1.fastq")
expected2Fastq = os.path.join(myInputDir, "expected2.fastq")
self.assertEqualContents(outFastq1, expected1Fastq)
self.assertEqualContents(outFastq2, expected2Fastq)
def test_purge_unmated(self):
myInputDir = util.file.get_test_input_path(self)
inFastq1 = os.path.join(myInputDir, 'in1.fastq')
inFastq2 = os.path.join(myInputDir, 'in2.fastq')
outFastq1 = util.file.mkstempfname('.fastq')
outFastq2 = util.file.mkstempfname('.fastq')
parser = read_utils.parser_purge_unmated(argparse.ArgumentParser())
args = parser.parse_args([inFastq1, inFastq2, outFastq1, outFastq2])
args.func_main(args)
# Check that results match expected
expected1Fastq = os.path.join(myInputDir, 'expected1.fastq')
expected2Fastq = os.path.join(myInputDir, 'expected2.fastq')
self.assertEqualContents(outFastq1, expected1Fastq)
self.assertEqualContents(outFastq2, expected2Fastq)
def test_purge_unmated_sra(self):
myInputDir = util.file.get_test_input_path(self)
inFastq1 = os.path.join(myInputDir, 'in_sra1.fastq')
inFastq2 = os.path.join(myInputDir, 'in_sra2.fastq')
outFastq1 = util.file.mkstempfname('.fastq')
outFastq2 = util.file.mkstempfname('.fastq')
parser = read_utils.parser_purge_unmated(argparse.ArgumentParser())
args = parser.parse_args(['--regex', '^@(\S+).[1|2] .*', inFastq1, inFastq2, outFastq1, outFastq2])
args.func_main(args)
# The expected outputs are identical to the previous case.
expected1Fastq = os.path.join(myInputDir, 'expected1.fastq')
expected2Fastq = os.path.join(myInputDir, 'expected2.fastq')
self.assertEqualContents(outFastq1, expected1Fastq)
self.assertEqualContents(outFastq2, expected2Fastq)
def test_purge_unmated(self) :
myInputDir = util.file.get_test_input_path(self)
inFastq1 = os.path.join(myInputDir, 'in1.fastq')
inFastq2 = os.path.join(myInputDir, 'in2.fastq')
outFastq1 = util.file.mkstempfname('.fastq')
outFastq2 = util.file.mkstempfname('.fastq')
parser = read_utils.parser_purge_unmated()
args = parser.parse_args([inFastq1, inFastq2, outFastq1, outFastq2])
read_utils.main_purge_unmated(args)
# Check that results match expected
expected1Fastq = os.path.join(myInputDir, 'expected1.fastq')
expected2Fastq = os.path.join(myInputDir, 'expected2.fastq')
self.assertEqualContents(outFastq1, expected1Fastq)
self.assertEqualContents(outFastq2, expected2Fastq)
