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)