CatRecodedVCF.py

#!/usr/bin/env python2.7
import os
import argparse
import logging
import sys
import subprocess as sp

from Utils import configure_logging

def configure_argparser(argparser_obj):

    def file_type(arg_string):
        """
        This function check both the existance of input file and the file size
        :param arg_string: file name as string
        :return: file name as string
        """
        if not os.path.exists(arg_string):
            err_msg = "%s does not exist! " \
                      "Please provide a valid file!" % arg_string
            raise argparse.ArgumentTypeError(err_msg)

        return arg_string

    # Path to VCF input file
    argparser_obj.add_argument("-i",
                               action="store",
                               type=file_type,
                               nargs='+',
                               dest="input_files",
                               required=True,
                               help="Space-delimited list of RecodedVCF files to combine")

    # Path to VCF input file
    argparser_obj.add_argument("--output",
                               action="store",
                               type=str,
                               dest="out_file",
                               required=True,
                               help="Path to recoded output file.")
    # Verbosity level
    argparser_obj.add_argument("-v",
                               action='count',
                               dest='verbosity_level',
                               required=False,
                               default=0,
                               help="Increase verbosity of the program."
                                    "Multiple -v's increase the verbosity level:\n"
                                    "0 = Errors\n"
                                    "1 = Errors + Warnings\n"
                                    "2 = Errors + Warnings + Info\n"
                                    "3 = Errors + Warnings + Info + Debug")

def get_header_string(input_file):
    # Return header line from a file
    with open(input_file, "r") as fh:
        header = fh.readline().rstrip()
    return header

def check_input_columns(input_files):
    # Check to make sure column headers are all the same.
    # Return header if so. Throw error if not.
    header_string = None
    for input_file in input_files:

        # Get header line from next file
        first_line = get_header_string(input_file)

        # Set header string to be first
        if header_string is None:
            header_string = first_line
            continue

        # Check to make sure columns are in same order
        if first_line != header_string:
            logging.error("Input files do not contain same columns in same order!")
            logging.error("Expected:\n%s" % header_string)
            logging.error("Received from %s:\n%s" % (input_file, first_line))
            raise IOError("Input files much have same number of columns in same order!")

def main():

    # Configure argparser
    argparser = argparse.ArgumentParser(prog="CatRecodeVCF")
    configure_argparser(argparser)

    # Parse the arguments
    args = argparser.parse_args()

    # Configure logging
    configure_logging(args.verbosity_level)

    try:
        # Check to make sure all input files have same columns in same order
        check_input_columns(args.input_files)

        # Run command to concat all tables together
        cmd = "awk 'FNR==1 && NR!=1{next;}{print}' %s > %s" % (" ".join(args.input_files), args.out_file)
        proc = sp.Popen(cmd, stdout=sp.PIPE, stderr=sp.PIPE, shell=True)
        out, err = proc.communicate()

        # Check to make sure no errors received
        if len(err) != 0:
            logging.error("CatRecodeVCF failed! Received following error message:\n%s" % err)
            exit(1)

    except KeyboardInterrupt:
        logging.error("(Main) Keyboard interrupt!")
        raise

    except BaseException, e:
        # Report any errors that arise
        logging.error("(Main) CatRecodeVCF failed!")
        if e.message != "":
            logging.error("Received the following error message:\n%s" % e.message)
        raise

if __name__ == "__main__":
    sys.exit(main())