#!/usr/bin/env python
######################################################################
#                  Copyright (c) 2016 Northrop Grumman.
#                          All rights reserved.
######################################################################
from __future__ import print_function
import sys
import os

from argparse import ArgumentParser


def get_fcs_marker_list(marker_file):
    with open(marker_file, "r") as mrkrs:
        useless_first_line = mrkrs.readline()
        channels = []
        markers = []
        for lines in mrkrs:
            stuff = lines.strip().split("\t")
            channels.append(stuff[1].strip("\""))
            markers.append(stuff[2].strip("\""))
    fcs_markers = [
        "\t".join(channels),
        "\t".join(markers)
    ]
    return(fcs_markers)


def print_fcs_headers(files, filenames, outfile, tool_dir):
    headers = {}
    tool = "/".join([tool_dir, "getFCSheader.R"])
    for eachfile in files:
        tmp_output = "tmp_fcs_headers.txt"
        run_command = " ". join(["Rscript --slave --vanilla", tool, "--args", eachfile, tmp_output])
        os.system(run_command)
        headers[eachfile] = get_fcs_marker_list(tmp_output)

    with open(outfile, "w") as outf:
        for i, flc in enumerate(files):
            outf.write("\t".join([filenames[i], "channels", headers[flc][0]]) + "\n")
        for j, flm in enumerate(files):
            outf.write("\t".join([filenames[j], "markers", headers[flm][1]]) + "\n")
    return


if __name__ == "__main__":
    parser = ArgumentParser(
             prog="GetFCSHeaders",
             description="Gets the headers of all files in given set.")

    parser.add_argument(
            '-i',
            dest="input_files",
            required=True,
            action='append',
            help="File location for the text files.")

    parser.add_argument(
            '-n',
            dest="file_names",
            required=True,
            action='append',
            help="File names.")

    parser.add_argument(
            '-t',
            dest="tool_dir",
            required=True,
            help="Path to the tool directory")

    parser.add_argument(
            '-o',
            dest="output_file",
            required=True,
            help="Name of the output file.")

    args = parser.parse_args()
    input_files = [f for f in args.input_files]
    file_names = [fn for fn in args.file_names]
    print_fcs_headers(input_files, file_names, args.output_file, args.tool_dir)
    sys.exit(0)