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)
Exemple #2
0
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)