Imported Upstream version 3.11.0
Sascha Steinbiss
8 years ago
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version = '3.10.1'
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version = '3.11.0'
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parser = argparse.ArgumentParser(
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description = description,
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usage = 'fastaq interleave <infile_1> <infile_2> <outfile>')
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parser.add_argument('--suffix1', help='Suffix to add to all names from infile_1 (if suffix not already present)')
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parser.add_argument('--suffix2', help='Suffix to add to all names from infile_2 (if suffix not already present)')
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parser.add_argument('infile_1', help='Name of first input file')
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parser.add_argument('infile_2', help='Name of second input file')
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parser.add_argument('outfile', help='Name of output file of interleaved reads')
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options = parser.parse_args()
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tasks.interleave(options.infile_1, options.infile_2, options.outfile)
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tasks.interleave(
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options.infile_1,
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options.infile_2,
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options.outfile,
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suffix1=options.suffix1,
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suffix2=options.suffix2
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)
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| 353 | 353 |
utils.close(fout)
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def interleave(infile_1, infile_2, outfile):
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def interleave(infile_1, infile_2, outfile, suffix1=None, suffix2=None):
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'''Makes interleaved file from two sequence files. If used, will append suffix1 onto end
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of every sequence name in infile_1, unless it already ends with suffix1. Similar for sufffix2.'''
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seq_reader_1 = sequences.file_reader(infile_1)
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seq_reader_2 = sequences.file_reader(infile_2)
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f_out = utils.open_file_write(outfile)
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except:
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utils.close(f_out)
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raise Error('Error getting mate for sequence', seq_1.id, ' ... cannot continue')
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if suffix1 is not None and not seq_1.id.endswith(suffix1):
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seq_1.id += suffix1
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if suffix2 is not None and not seq_2.id.endswith(suffix2):
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seq_2.id += suffix2
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print(seq_1, file=f_out)
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print(seq_2, file=f_out)
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>1/1
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ACGTA
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>1/2
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ACGTA
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>2/1
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A
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>2/2
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C
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tmp)
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self.assertTrue(filecmp.cmp(os.path.join(data_dir, 'sequences_test_interleaved.fa'), tmp))
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| 225 | 225 |
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tasks.interleave(os.path.join(data_dir, 'sequences_test_deinterleaved_no_suffixes_1.fa'),
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os.path.join(data_dir, 'sequences_test_deinterleaved_no_suffixes_2.fa'),
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tmp, suffix1='/1', suffix2='/2')
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self.assertTrue(filecmp.cmp(os.path.join(data_dir, 'sequences_test_interleaved_with_suffixes.fa'), tmp))
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with self.assertRaises(tasks.Error):
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tasks.interleave(os.path.join(data_dir, 'sequences_test_deinterleaved_bad_1.fa'),
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os.path.join(data_dir, 'sequences_test_deinterleaved_bad_2.fa'),
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setup(
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name='pyfastaq',
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version='3.10.1',
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version='3.11.0',
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description='Script to manipulate FASTA and FASTQ files, plus API for developers',
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packages = find_packages(),
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author='Martin Hunt',
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