comparison data_manager_build_alfa_indexes/data_manager/data_manager_build_alfa_indexes.py @ 4:6f0be85be8fb draft

Uploaded

3:4ada30780811

def generate_alfa_indexes(path_to_alfa, gtf_file_name):
    logging.info("____________________________________________________________")
    logging.info("*** Generating alfa indexes from %s" % gtf_file_name)
    alfa_result = subprocess.Popen(['python', path_to_alfa + 'ALFA.py', '-a',  gtf_file_name], stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
    alfa_out, alfa_err = alfa_result.communicate()
    if alfa_err != None and not re.search('### End of program', alfa_err):
        msg = 'Generation Failed due an alfa error: %s' % (alfa_err)
        logging.critical(msg)
        sys.exit(msg)

def main():
    options, args = get_arg()
    galaxy_root_dir = args[0]

    path_to_alfa = os.path.join(galaxy_root_dir, 'tools/alfa/')
    path_to_tmp_dir = os.path.join(galaxy_root_dir, 'database/tmp/')

    if options.output_filename == None:
        msg = 'No json output file specified'
        logging.critical(msg)

4:6f0be85be8fb

def generate_alfa_indexes(path_to_alfa, gtf_file_name):
    logging.info("____________________________________________________________")
    logging.info("*** Generating alfa indexes from %s" % gtf_file_name)
    alfa_result = subprocess.Popen(['python', path_to_alfa, '-a',  gtf_file_name], stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
    alfa_out, alfa_err = alfa_result.communicate()
    if alfa_err != None and not re.search('### End of program', alfa_err):
        msg = 'Generation Failed due an alfa error: %s' % (alfa_err)
        logging.critical(msg)
        sys.exit(msg)

def main():
    options, args = get_arg()
    galaxy_root_dir = args[0]
    tool_dir = args[1]

    path_to_alfa = os.path.join(tool_dir, 'ALFA.py')
    path_to_tmp_dir = os.path.join(galaxy_root_dir, 'database/tmp/')

    if options.output_filename == None:
        msg = 'No json output file specified'
        logging.critical(msg)