RegGTFExtractor.py

#!/usr/bin/env python3

import argparse
from Modules.Ensembl.Ensembl import Ensembl
from Modules.ucsc.ucsc import UcscGtf
from Modules.Uniquifier import UniqueFilter
from Modules.SaveResults import ResultSaver
import os


def check_for_local_folder(wd):

    if not os.path.isdir(os.path.join(wd+"/EnsemblData")):

        os.mkdir(os.path.join(wd+"/EnsemblData"))

    if not os.path.isdir(os.path.join(wd+"/UCSCData" )):
        os.mkdir(os.path.join(wd+"/UCSCData" ))


def main_script(org, wd, tissuetype=None):

    check_for_local_folder(wd)
    ucsc = UcscGtf(org, wd)
    ense = Ensembl(org, wd)
    print("Getting Unique Results")
    unique_filter = UniqueFilter(ense.get_gtf(), ucsc.get_gtf(), tissuetype)
    ResultSaver(unique_filter.get_results(), org, tissuetype, wd)


if __name__ == '__main__':
    parser = argparse.ArgumentParser(description='GTF-Generator from UCSC Table Browser and Ensembl Regulatory Build' )
    parser.add_argument('organism', help='Source organism [ homo_sapiens or mus_musculus ]', action='store', nargs='?', type=str)
    parser.add_argument('--tissue', help='Tissue- or Celltype(s)', action='store', nargs='*', type=str)
    parser.add_argument('--wd', help='Working directory. default: "."', action='store', default='.', type=str)
    args = vars(parser.parse_args())
    if args["organism"]:
        print("Working Dir: " + args["wd"])
        main_script(args["organism"], args["wd"], args["tissue"])
    else:
        print("No Arguments found -> See ./RegGTFExtractor.py -h for help.")