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
