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_with_sfftools(self):
_, orig_reads = parse_binary_sff(open(self.sff_fp), True)
orig_reads = list(orig_reads)
set_sff_trimpoints_with_sfftools(self.sff_dir, {'F6AVWTA01': 10})
# check trimpoint file
for line in open(self.sff_fp + '.trim'):
toks = line.split()
trim_start = int(toks[1])
trim_end = int(toks[2])
self.assertTrue(trim_start <= trim_end)
self.assertEqual(trim_start, 11)
# Check resultant SFF file
_, 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)
def test_set_sff_trimpoints_with_sfftools(self):
_, orig_reads = parse_binary_sff(open(self.sff_fp), True)
orig_reads = list(orig_reads)
set_sff_trimpoints_with_sfftools(self.sff_dir, {'F6AVWTA01': 10})
# check trimpoint file
for line in open(self.sff_fp + '.trim'):
toks = line.split()
trim_start = int(toks[1])
trim_end = int(toks[2])
self.assertTrue(trim_start <= trim_end)
self.assertEqual(trim_start, 11)
# Check resultant SFF file
_, 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)
