def main(): option_parser, opts, args = parse_command_line_parameters(**script_info) technical_lengths = get_technical_lengths( open(opts.input_map, 'U'), opts.debug) if opts.use_sfftools: set_sff_trimpoints_with_sfftools( opts.libdir, technical_lengths, opts.sffinfo_path, opts.sfffile_path, opts.debug) else: set_sff_trimpoints(opts.libdir, technical_lengths)
def main(): option_parser, opts, args = parse_command_line_parameters(**script_info) technical_lengths = get_technical_lengths(open(opts.input_map, 'U'), opts.debug) if opts.use_sfftools: set_sff_trimpoints_with_sfftools(opts.libdir, technical_lengths, opts.sffinfo_path, opts.sfffile_path, opts.debug) else: set_sff_trimpoints(opts.libdir, technical_lengths)
def test_set_sff_trimpoints(self): _, orig_reads = parse_binary_sff(open(self.sff_fp), True) orig_reads = list(orig_reads) set_sff_trimpoints(self.sff_dir, {'F6AVWTA01': 10}) _, reads = parse_binary_sff(open(self.sff_fp), True) for read, orig_read in zip(reads, orig_reads): self.assertEqual(read['clip_qual_left'], 11) # Check that eveything else is the same between original # reads and trimmed reads. orig_read['clip_qual_left'] = 11 self.assertEqual(read, orig_read)