Validator.py

import os


class Validator:

    """
        Class to validate and sort the gtf-output-file.
        @author: Sebastian Beyvers
        @contact: sebastian.beyvers@med.uni-giessen.de

    """

    def __init__(self, out_file):

        # Constructor
        # input_parameter: out_file = path to output file

        self.out_file = out_file
        self.sort_file()
        self.test_read_file()

    def sort_file(self):

        # function that utilizes linux sort to sort the output by chromosome and start coordinate,
        # this improves handling in tools like IGV

        command = "sort -V -k1,1 -k4,4n -o "+self.out_file+" "+self.out_file
        os.system(command)

    def test_read_file(self):

        # Method to test the output file-format

        with open(self.out_file) as outfile:
            line = outfile.readline()

            if line:
                if len(line.split("\t")) == 9:
                    print("Validation complete no errors found !")
                else:
                    print("Incorrect output Format: Try again after deleting data folder.")
            else:
                print("Outputfile not in correct Format: Try again after deleting data Folder.")
                exit(1)

# Debug
# v = Validator("/home/basti/Schreibtisch/test_hg38.gtf")