def run(description): parser = argparse.ArgumentParser( description='Renames sequences in a file, calling them 1,2,3... etc', usage='fastaq enumerate_names [options] <infile> <outfile>') parser.add_argument('--start_index', type=int, help='Starting number [%(default)s]', default=1) parser.add_argument( '--rename_file', help='If used, will write a file of old name to new name') parser.add_argument( '--keep_suffix', action='store_true', help='Use this to keep a /1 or /2 suffix at the end of each name') parser.add_argument('--suffix', help='Add the given string to the end of every name', default=None) parser.add_argument('infile', help='Name of fasta/q file to be read') parser.add_argument('outfile', help='Name of output fasta/q file') options = parser.parse_args() tasks.enumerate_names(options.infile, options.outfile, start_index=options.start_index, keep_illumina_suffix=options.keep_suffix, rename_file=options.rename_file, suffix=options.suffix)
def test_enumerate_names(self): '''Test enomereate_names works with all options''' outfile = 'tmp.enumerate_seqs.fa' rename_out = outfile + '.rename' tasks.enumerate_names( os.path.join(data_dir, 'sequences_test_enumerate_names.fa'), outfile) self.assertTrue( filecmp.cmp( os.path.join(data_dir, 'sequences_test_enumerate_names.fa.out.start.1'), outfile)) tasks.enumerate_names(os.path.join( data_dir, 'sequences_test_enumerate_names.fa'), outfile, rename_file=rename_out) self.assertTrue( filecmp.cmp( os.path.join(data_dir, 'sequences_test_enumerate_names.fa.out.start.1'), outfile)) self.assertTrue( filecmp.cmp( os.path.join( data_dir, 'sequences_test_enumerate_names.fa.out.start.1.rename_file' ), rename_out)) tasks.enumerate_names(os.path.join( data_dir, 'sequences_test_enumerate_names.fa'), outfile, start_index=2) self.assertTrue( filecmp.cmp( os.path.join(data_dir, 'sequences_test_enumerate_names.fa.out.start.2'), outfile)) tasks.enumerate_names(os.path.join( data_dir, 'sequences_test_enumerate_names.fa'), outfile, keep_illumina_suffix=True) self.assertTrue( filecmp.cmp( os.path.join( data_dir, 'sequences_test_enumerate_names.fa.out.keep_suffix'), outfile)) tasks.enumerate_names(os.path.join( data_dir, 'sequences_test_enumerate_names.fa'), outfile, suffix='.SUFFIX') self.assertTrue( filecmp.cmp(os.path.join( data_dir, 'sequences_test_enumerate_names.fa.out.add_suffix'), outfile, shallow=False)) os.unlink(outfile) os.unlink(rename_out)
def run(description): parser = argparse.ArgumentParser( description = 'Renames sequences in a file, calling them 1,2,3... etc', usage = 'fastaq enumerate_names [options] <infile> <outfile>') parser.add_argument('--start_index', type=int, help='Starting number [%(default)s]', default=1) parser.add_argument('--rename_file', help='If used, will write a file of old name to new name') parser.add_argument('--keep_suffix', action='store_true', help='Use this to keep a /1 or /2 suffix at the end of each name') parser.add_argument('--suffix', help='Add the given string to the end of every name', default=None) parser.add_argument('infile', help='Name of fasta/q file to be read') parser.add_argument('outfile', help='Name of output fasta/q file') options = parser.parse_args() tasks.enumerate_names(options.infile, options.outfile, start_index=options.start_index, keep_illumina_suffix=options.keep_suffix, rename_file=options.rename_file, suffix=options.suffix)
def test_enumerate_names(self): '''Test enomereate_names works with all options''' outfile = 'tmp.enumerate_seqs.fa' rename_out = outfile + '.rename' tasks.enumerate_names(os.path.join(data_dir, 'sequences_test_enumerate_names.fa'), outfile) self.assertTrue(filecmp.cmp(os.path.join(data_dir, 'sequences_test_enumerate_names.fa.out.start.1'), outfile)) tasks.enumerate_names(os.path.join(data_dir, 'sequences_test_enumerate_names.fa'), outfile, rename_file=rename_out) self.assertTrue(filecmp.cmp(os.path.join(data_dir, 'sequences_test_enumerate_names.fa.out.start.1'), outfile)) self.assertTrue(filecmp.cmp(os.path.join(data_dir, 'sequences_test_enumerate_names.fa.out.start.1.rename_file'), rename_out)) tasks.enumerate_names(os.path.join(data_dir, 'sequences_test_enumerate_names.fa'), outfile, start_index=2) self.assertTrue(filecmp.cmp(os.path.join(data_dir, 'sequences_test_enumerate_names.fa.out.start.2'), outfile)) tasks.enumerate_names(os.path.join(data_dir, 'sequences_test_enumerate_names.fa'), outfile, keep_illumina_suffix=True) self.assertTrue(filecmp.cmp(os.path.join(data_dir, 'sequences_test_enumerate_names.fa.out.keep_suffix'), outfile)) tasks.enumerate_names(os.path.join(data_dir, 'sequences_test_enumerate_names.fa'), outfile, suffix='.SUFFIX') self.assertTrue(filecmp.cmp(os.path.join(data_dir, 'sequences_test_enumerate_names.fa.out.add_suffix'), outfile, shallow=False)) os.unlink(outfile) os.unlink(rename_out)