def main():
option_parser, opts, args =\
parse_command_line_parameters(suppress_verbose=True, **script_info)
mapping_fp = opts.mapping_fp
has_barcodes = not opts.not_barcoded
variable_len_barcodes = opts.variable_len_barcodes
output_dir = opts.output_dir + "/"
char_replace = opts.char_replace
verbose = opts.verbose
disable_primer_check = opts.disable_primer_check
added_demultiplex_field = opts.added_demultiplex_field
suppress_html = opts.suppress_html
# Create output directory, check path/access to mapping file
create_dir(output_dir)
# Test for valid replacement characters
valid_replacement_chars = digits + letters + "_" + "."
if char_replace not in valid_replacement_chars:
option_parser.error('-c option requires alphanumeric, period, or ' +
'underscore character.')
if len(char_replace) != 1:
option_parser.error('-c parameter must be a single character.')
check_mapping_file(mapping_fp, output_dir, has_barcodes, char_replace,
verbose, variable_len_barcodes, disable_primer_check,
added_demultiplex_field, suppress_html)
def main():
option_parser, opts, args =\
parse_command_line_parameters(suppress_verbose=True, **script_info)
mapping_fp = opts.mapping_fp
has_barcodes = not opts.not_barcoded
variable_len_barcodes = opts.variable_len_barcodes
output_dir = opts.output_dir + "/"
char_replace = opts.char_replace
verbose = opts.verbose
disable_primer_check = opts.disable_primer_check
added_demultiplex_field = opts.added_demultiplex_field
# Create output directory, check path/access to mapping file
create_dir(output_dir)
# Test for valid replacement characters
valid_replacement_chars = digits + letters + "_" + "."
if char_replace not in valid_replacement_chars:
option_parser.error('-c option requires alphanumeric, period, or '+\
'underscore character.')
if len(char_replace) != 1:
option_parser.error('-c parameter must be a single character.')
check_mapping_file(mapping_fp, output_dir, has_barcodes, char_replace,\
verbose, variable_len_barcodes,
disable_primer_check, added_demultiplex_field)
def main():
option_parser, opts, args =\
parse_command_line_parameters(suppress_verbose=True, **script_info)
infile_name = opts.map_fname
has_barcodes = not opts.not_barcoded
output_dir = opts.output_dir
char_replace = opts.char_replace
var_len_barcodes = opts.variable_len_barcodes
verbose = opts.verbose
disable_primer_check = opts.disable_primer_check
added_demultiplex_field = opts.added_demultiplex_field
valid_replacement_chars=digits+letters+"_"
if char_replace not in valid_replacement_chars:
option_parser.error('-c option requires alphanumeric or '+\
'underscore character')
if len(char_replace) != 1:
option_parser.error('-c parameter must be a single character.')
check_mapping_file(infile_name, output_dir, has_barcodes, char_replace,\
verbose, var_len_barcodes, disable_primer_check, added_demultiplex_field)