def test_bad_chars_from_threshold(self): """bad_chars_from_threshold selects correct chars as bad """ self.assertEqual(bad_chars_from_threshold('B'), {}.fromkeys(list('@AB'))) self.assertEqual(bad_chars_from_threshold(''),{}) self.assertEqual(bad_chars_from_threshold('~'), {}.fromkeys(list(get_illumina_qual_chars()))) self.assertEqual(bad_chars_from_threshold('@'),{'@':None})
make_option('-o', '--output_dir', help='the output directory'), make_option('-b', '--barcode_length', type='int', help='length of the barcode'), ] script_info['optional_options'] = [ make_option('--barcode_in_header', action='store_true', help='pass if barcode is in the header index' + ' field (rather than at the beginning of the sequence)', default=False), make_option( '--barcode_qual_c', type='choice', choices=list(get_illumina_qual_chars()), help='if no barcode quality string is available, score each base with' + ' this quality [default: %default]', default='b') ] script_info['version'] = __version__ def main(): option_parser, opts, args =\ parse_command_line_parameters(**script_info) input_fps = opts.input_fps output_dir = opts.output_dir create_dir(output_dir) barcode_length = opts.barcode_length
("","Generate fastq files from the gzipped lanes 1 and 2 (read 1 data) where barcodes are contained as the first tweleve bases of the sequences.","process_qseq.py -i ./s_1_1_sequence.txt.gz,./s_2_1_sequence.txt.gz -b 12 -o ./fastq/") ] script_info['output_description']= "" script_info['required_options'] = [ make_option('-i','--input_fps',type='existing_filepaths', help='the input filepaths (either iseq or gzipped iseq format; comma-separated if more than one). See Processing Illumina Data tutorial for a description of the iseq file type.'), make_option('-o','--output_dir',help='the output directory'), make_option('-b','--barcode_length',type='int', help='length of the barcode'), ] script_info['optional_options'] = [ make_option('--barcode_in_header',action='store_true', help='pass if barcode is in the header index'+\ ' field (rather than at the beginning of the sequence)',default=False), make_option('--barcode_qual_c',type='choice', choices=list(get_illumina_qual_chars()), help='if no barcode quality string is available, score each base with'+\ ' this quality [default: %default]',default='b') ] script_info['version'] = __version__ def main(): option_parser, opts, args =\ parse_command_line_parameters(**script_info) input_fps = opts.input_fps output_dir = opts.output_dir create_dir(output_dir) barcode_length = opts.barcode_length barcode_in_header = opts.barcode_in_header barcode_qual_c = opts.barcode_qual_c