segmentsGenerator.py

import sys
import logging
from argparse import ArgumentParser, RawTextHelpFormatter

from lib.SegGraphCreator import createSegments



description = \
    "Description:\n\n" + \
    "This subcommand breaks the preprocessed transcriptome into a set of maximal L-disjoint" + \
    "segments (prepares the segments library)."
parser = ArgumentParser(description=description, formatter_class=RawTextHelpFormatter,
                        add_help=False)
parser.add_argument("-l", "--max-overlap", help="to create L-disjoint segments (typically equals to read length)",
                    required=True)
parser.add_argument("-o", "--output-name", help="specify name prefix of output files", required=False)
parser.add_argument("-ioe", "--events-annotation", nargs='*',
                    help="specify events annotation file(s) (.ioe file(s) generated by SUPPA)", required=False)
parser.add_argument("-m", "--mode", nargs='?', choices=['strict', 'flex'], default='flex',
                    help="specify mode for mapping segments to events", required=False)
parser.add_argument("-wd", "--work-dir", help="specify directory where the preprocessed annotation files " + \
                    "exist (same output directory used in the preprocess subcommand)")


def main():
    args = parser.parse_args()

    # Setting logging preferences
    logger = logging.getLogger(__name__)

    #print(args)
    if not args.output_name:
        args.output_name = "segs_"+args.max_overlap
    createSegments(int(args.max_overlap), args.work_dir, args.output_name, args.events_annotation, False, args.mode)

    logger.info("Done")
    
if __name__ == '__main__':
    main()