def test_fasta(self):
'Test splitting fasta file.'
myInputDir = util.file.get_test_input_path(self)
inFasta = os.path.join(myInputDir, 'in.fasta')
outPrefix = util.file.mkstempfname()
# Split
parser = read_utils.parser_split_reads(argparse.ArgumentParser())
args = parser.parse_args([inFasta, outPrefix, '--numChunks', '2', '--format', 'fasta'])
args.func_main(args)
# Check that results match expected
expectedFasta1 = os.path.join(myInputDir, 'expected.fasta.01')
expectedFasta2 = os.path.join(myInputDir, 'expected.fasta.02')
self.assertEqualContents(outPrefix + '01', expectedFasta1)
self.assertEqualContents(outPrefix + '02', expectedFasta2)
def test_fasta(self):
"Test splitting fasta file."
myInputDir = util.file.get_test_input_path(self)
inFasta = os.path.join(myInputDir, "in.fasta")
outPrefix = util.file.mkstempfname()
# Split
parser = read_utils.parser_split_reads(argparse.ArgumentParser())
args = parser.parse_args([inFasta, outPrefix, "--numChunks", "2", "--format", "fasta"])
args.func_main(args)
# Check that results match expected
expectedFasta1 = os.path.join(myInputDir, "expected.fasta.01")
expectedFasta2 = os.path.join(myInputDir, "expected.fasta.02")
self.assertEqualContents(outPrefix + "01", expectedFasta1)
self.assertEqualContents(outPrefix + "02", expectedFasta2)
def test_max_reads(self):
"Test splitting fastq using --maxReads option, with indexLen 1."
myInputDir = util.file.get_test_input_path(self)
inFastq = os.path.join(myInputDir, "in.fastq")
outPrefix = util.file.mkstempfname()
# Split
parser = read_utils.parser_split_reads(argparse.ArgumentParser())
args = parser.parse_args([inFastq, outPrefix, "--maxReads", "4", "--indexLen", "1"])
args.func_main(args)
# Check that results match expected
expectedFastq1 = os.path.join(myInputDir, "expected.fastq.1")
expectedFastq2 = os.path.join(myInputDir, "expected.fastq.2")
self.assertEqualContents(outPrefix + "1", expectedFastq1)
self.assertEqualContents(outPrefix + "2", expectedFastq2)
def test_max_reads(self):
'Test splitting fastq using --maxReads option, with indexLen 1.'
myInputDir = util.file.get_test_input_path(self)
inFastq = os.path.join(myInputDir, 'in.fastq')
outPrefix = util.file.mkstempfname()
# Split
parser = read_utils.parser_split_reads(argparse.ArgumentParser())
args = parser.parse_args([inFastq, outPrefix, '--maxReads', '4', '--indexLen', '1'])
args.func_main(args)
# Check that results match expected
expectedFastq1 = os.path.join(myInputDir, 'expected.fastq.1')
expectedFastq2 = os.path.join(myInputDir, 'expected.fastq.2')
self.assertEqualContents(outPrefix + '1', expectedFastq1)
self.assertEqualContents(outPrefix + '2', expectedFastq2)
def test_fasta(self):
'Test splitting fasta file.'
myInputDir = util.file.get_test_input_path(self)
inFasta = os.path.join(myInputDir, 'in.fasta')
outPrefix = util.file.mkstempfname()
# Split
parser = read_utils.parser_split_reads(argparse.ArgumentParser())
args = parser.parse_args(
[inFasta, outPrefix, '--numChunks', '2', '--format', 'fasta'])
args.func_main(args)
# Check that results match expected
expectedFasta1 = os.path.join(myInputDir, 'expected.fasta.01')
expectedFasta2 = os.path.join(myInputDir, 'expected.fasta.02')
self.assertEqualContents(outPrefix + '01', expectedFasta1)
self.assertEqualContents(outPrefix + '02', expectedFasta2)
def test_max_reads(self):
'Test splitting fastq using --maxReads option, with indexLen 1.'
myInputDir = util.file.get_test_input_path(self)
inFastq = os.path.join(myInputDir, 'in.fastq')
outPrefix = util.file.mkstempfname()
# Split
parser = read_utils.parser_split_reads(argparse.ArgumentParser())
args = parser.parse_args(
[inFastq, outPrefix, '--maxReads', '4', '--indexLen', '1'])
args.func_main(args)
# Check that results match expected
expectedFastq1 = os.path.join(myInputDir, 'expected.fastq.1')
expectedFastq2 = os.path.join(myInputDir, 'expected.fastq.2')
self.assertEqualContents(outPrefix + '1', expectedFastq1)
self.assertEqualContents(outPrefix + '2', expectedFastq2)
def test_num_chunks(self):
"Test spliting fastq.gz using --numChunks option, with default indexLen."
myInputDir = util.file.get_test_input_path(self)
inFastq = os.path.join(myInputDir, "in.fastq.gz")
outPrefix = util.file.mkstempfname()
# Split
parser = read_utils.parser_split_reads(argparse.ArgumentParser())
args = parser.parse_args([inFastq, outPrefix, "--numChunks", "3"])
args.func_main(args)
# Check that results match expected
expectedFastq1 = os.path.join(myInputDir, "expected.fastq.01")
expectedFastq2 = os.path.join(myInputDir, "expected.fastq.02")
expectedFastq3 = os.path.join(myInputDir, "expected.fastq.03")
self.assertEqualContents(outPrefix + "01", expectedFastq1)
self.assertEqualContents(outPrefix + "02", expectedFastq2)
self.assertEqualContents(outPrefix + "03", expectedFastq3)
def test_num_chunks(self):
'Test spliting fastq.gz using --numChunks option, with default indexLen.'
myInputDir = util.file.get_test_input_path(self)
inFastq = os.path.join(myInputDir, 'in.fastq.gz')
outPrefix = util.file.mkstempfname()
# Split
parser = read_utils.parser_split_reads(argparse.ArgumentParser())
args = parser.parse_args([inFastq, outPrefix, '--numChunks', '3'])
args.func_main(args)
# Check that results match expected
expectedFastq1 = os.path.join(myInputDir, 'expected.fastq.01')
expectedFastq2 = os.path.join(myInputDir, 'expected.fastq.02')
expectedFastq3 = os.path.join(myInputDir, 'expected.fastq.03')
self.assertEqualContents(outPrefix + '01', expectedFastq1)
self.assertEqualContents(outPrefix + '02', expectedFastq2)
self.assertEqualContents(outPrefix + '03', expectedFastq3)
def test_num_chunks(self):
'Test spliting fastq.gz using --numChunks option, with default indexLen.'
myInputDir = util.file.get_test_input_path(self)
inFastq = os.path.join(myInputDir, 'in.fastq.gz')
outPrefix = util.file.mkstempfname()
# Split
parser = read_utils.parser_split_reads(argparse.ArgumentParser())
args = parser.parse_args([inFastq, outPrefix, '--numChunks', '3'])
args.func_main(args)
# Check that results match expected
expectedFastq1 = os.path.join(myInputDir, 'expected.fastq.01')
expectedFastq2 = os.path.join(myInputDir, 'expected.fastq.02')
expectedFastq3 = os.path.join(myInputDir, 'expected.fastq.03')
self.assertEqualContents(outPrefix + '01', expectedFastq1)
self.assertEqualContents(outPrefix + '02', expectedFastq2)
self.assertEqualContents(outPrefix + '03', expectedFastq3)
