convertbed.py

#!/usr/bin/env python

import argparse
import Core
import Annotation
import os


def check_file(filename):
    """
    Chech for the existance of the input filename.
    :param filename: filename to check.
    :return:
    """
    return os.path.exists(os.path.abspath(filename))


# USAGE : ./convertbed.py -file Data/GSE42308.txt -out gello.bed -gene DENR
parser = argparse.ArgumentParser()
parser.add_argument("-file", help="File name that contains average beta values.")
parser.add_argument("-out", help="File name that will be stored as BED file.")
parser.add_argument("-gene", help="Name of gene that BED file will be created for")
args = vars(parser.parse_args())

file = os.path.abspath(args["file"])
out = os.path.abspath(args["out"])

if check_file(file):
    annotations = Annotation.Annotator()
    parse = Core.ParseFile(file)
    probe_list = annotations.get_probes_from_gene(args["gene"])

    for i, sam in enumerate(parse.get_samples()):
        print("%d\t%s" % (i, sam.name))

    selected_sample = input("please select the sample to export from > ")

    Core.probes_to_bed(out, probe_list, Core.get_sample_by_no(parse.get_samples(), selected_sample))
    print("Done.")

else:
    print("File does not exist.")