RegGTFExtractor.py

"""

RegGTFExtractor.py extracts regulatory-data from Ensembl and UCSC databases
and converts the output to a GTF-formatted file.

@author: Sebastian Beyvers
@contact: sebastian.beyvers@med.uni-giessen.de

"""

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


def check_for_local_folder(wd):

    # Check if local folder exists and create if missing when no data_dir is specified
    # input_parameter: wd = working directory
    # return_value: None

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

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

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

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

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

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


def check_for_data_dir(data_dir):

    # Check if local folder exists and create if missing when data_dir as parameter is specified
    # input_parameter: data_dir = data directory
    # return_value: None

    if not os.path.isdir(os.path.join(data_dir)):
        os.mkdir(os.path.join(data_dir))

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

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

    if not os.path.isdir(os.path.join(data_dir+"/temp")):
        os.mkdir(os.path.join(data_dir+"/temp"))


def check_filter(tissue_cmd, org, wd):

    # Checks if filter-celltype is in Json types for organism
    # input_parameter: tissue_cmd: Filtered tissuetypes; org = organism; wd = working directory
    # return_value: boolean if selected filter is in config

    path_to_config = os.path.join(wd + "/config/celltypes_" + org + ".json")
    tissues_config = []
    if not tissue_cmd:
        return False
    with open(path_to_config) as input_file:
        data = json.loads(input_file.read())
        for x in data:
            tissues_config.append(x["type"])

    if any(tissue in tissues_config for tissue in tissue_cmd):
        return True

    else:
        return False


def check_organism(org):

    # Checks the organism input and decides if chrossmapping is necessary
    # input_parameter: org = input organism (parameter)
    # return_value: tuple with values = (organism_alias (string), boolean if chrossmapping is needed)

    if org == "hg38":
        return "homo_sapiens", False
    if org == "hg19":
        print("Older assembly Version detected: hg19 -> Crossmapping result from hg38")
        return "homo_sapiens", True
    elif org == "mm10":
        return "mus_musculus", False
    elif org == "mm9":
        print("Older assembly Version detected: mm9 -> Crossmapping result from mm10")
        return "mus_musculus", True


def main_script(organism, wd, data_dir, out, tissuetype=None):

    # main function
    # input_parameter: all parameters from argparse

    (org,  x_mappable) = check_organism(organism)
    if not data_dir:
        check_for_local_folder(wd)
    else:
        check_for_data_dir(data_dir)
    if check_filter(tissuetype, org, wd):
        tissues = tissuetype
        print("Filter detected !")
    else:
        tissues = None
        print("Filter not detected !")

    # Get UCSC Data
    ucsc = UcscGtf(org, wd, data_dir)
    # Gen Ensembl Data
    ense = Ensembl(org, wd, data_dir)
    print("Getting Unique Results")
    unique_filter = UniqueFilter(ense.get_gtf(), ucsc.get_gtf(), tissues)
    if data_dir:
        ResultSaver(unique_filter.get_results(), organism, data_dir, x_mappable, True, tissues, out)
        if x_mappable:
            CrossMapper(organism, data_dir, out, True)
    else:
        ResultSaver(unique_filter.get_results(), organism, wd, x_mappable, False, tissues, out)
        if x_mappable:
            CrossMapper(organism, wd, out, False)


if __name__ == '__main__':

    # argument parser

    parser = argparse.ArgumentParser(description='GTF-Generator from UCSC Table Browser and Ensembl Regulatory Build' )
    parser.add_argument('organism', help='Source organism [ hg19 | hg38 or mm9 | mm10 ]', 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=os.getcwd(), type=str)
    parser.add_argument('--dir', help='Data directory. default: "working_directory"', action='store', default="", type=str)
    parser.add_argument('--out', help='Output directory: default: "."', action='store', default=".", type=str)
    args = vars(parser.parse_args())

    # Check if organism exists

    if args["organism"]:
        if args["organism"] in ["hg19", "hg38", "mm9", "mm10"]:
            print("Working Dir: " + args["wd"])
            main_script(args["organism"], args["wd"], args["dir"],  args["out"], args["tissue"])
        else:
            print("Invalid Organism: " + args["organism"] + " see -h for help")
    else:
        print("No Arguments found -> See python3 ./RegGTFExtractor.py -h for help.")