annotate extract_data_for_profrep.py @ 5:ad3bbf392135 draft

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#!/usr/bin/env python3

import zipfile
import tempfile
import argparse
from shutil import copyfile
import os
import configuration


def main(args):

    RE_ARCHIVE = args.re_archive
    OUTPUT_CLS = args.output_cls
    OUTPUT_READS_ALL = args.output_reads_all
    OUTPUT_ANNOTATION = args.output_annotation

    if not os.path.isabs(OUTPUT_CLS):
        OUTPUT_CLS = os.path.join(os.getcwd(), OUTPUT_CLS)

    if not os.path.isabs(OUTPUT_READS_ALL):
        OUTPUt_READS_ALL = os.path.join(os.getcwd(), OUTPUT_READS_ALL)

    if not os.path.isabs(OUTPUT_ANNOTATION):
        OUTPUT_ANNOTATION = os.path.join(os.getcwd(), OUTPUT_ANNOTATION)

    with tempfile.TemporaryDirectory() as dirpath:
        with zipfile.ZipFile(RE_ARCHIVE, 'r') as re_archive:
            re_archive.extractall(dirpath)
        copyfile(os.path.join(dirpath, configuration.HITSORT_CLS), OUTPUT_CLS)
        copyfile(
            os.path.join(dirpath, configuration.READS_ALL), OUTPUT_READS_ALL)
        copyfile(
            os.path.join(dirpath, configuration.ANNOTATION), OUTPUT_ANNOTATION)


if __name__ == '__main__':

    # Command line arguments
    parser = argparse.ArgumentParser()
    parser.add_argument('-ar',
                        '--re_archive',
                        type=str,
                        required=True,
                        help='RepeatExplorer output data archive')
    parser.add_argument('-oc',
                        '--output_cls',
                        type=str,
                        default="output_hitsort_cls",
                        help='Output cls file of all clusters')
    parser.add_argument('-or',
                        '--output_reads_all',
                        type=str,
                        default="output_reads_all",
                        help='Output file of all reads sequences')
    parser.add_argument('-oa',
                        '--output_annotation',
                        type=str,
                        default="output_annotation",
                        help='Output file of clusters annotation')
    args = parser.parse_args()
    main(args)