sleuth.py

#!/usr/bin/env python3

#############################################################################
#    Copyright 2020 Simon Andrews
#
#    This program is free software: you can redistribute it and/or modify
#    it under the terms of the GNU General Public License as published by
#    the Free Software Foundation, either version 3 of the License, or
#    (at your option) any later version.
#
#    This program is distributed in the hope that it will be useful,
#    but WITHOUT ANY WARRANTY; without even the implied warranty of
#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
#    GNU General Public License for more details.
#
#    You should have received a copy of the GNU General Public License
#    along with this program.  If not, see <https://www.gnu.org/licenses/>.
#
############################################################################

import argparse
import os
import subprocess
import sys

VERSION = 1.2

def process_file(options):
    if not options.quiet:
        print(f"Calling SNPs on {options.bamfile}")
    
    outfile = run_snp_calling(options)

    if not options.quiet:
        print(f"Drawing graph")


    draw_graph(outfile,options)


def run_snp_calling(options):

    # Find the current location so we can set the classpath
    current = os.path.dirname(os.path.realpath(__file__))

    classpath = [current, current+"/htsjdk.jar", current+"/commons_compress.jar"]

    joined_classpath = ":".join(classpath)

    if sys.platform.startswith("win"):
        joined_classpath = ";".join(classpath)

    outfile = options.bamfile

    if outfile.endswith(".bam"):
        outfile = outfile[:-4]
    
    outfile = outfile+"_sleuth.txt"

    quiet_value = "false"

    if options.quiet:
        quiet_value = "true"

    command_options = [options.java,"-cp",joined_classpath,f'-Dquiet={quiet_value}',"uk/ac/babraham/CellLineSleuth/CellLineSleuthApplication",options.snpfile, options.bamfile,outfile]

    #print(f"Command options are {command_options}")

    subprocess.run(command_options, check=True)

    return outfile

def draw_graph(infile, options):

    current = os.path.dirname(os.path.realpath(__file__))

    format = "png"

    if options.svg:
        format = "svg"

    subprocess.run([options.rscript,current+"/R/create_sleuth_graph.R",infile,format], check=True, stdout=subprocess.DEVNULL, stderr=subprocess.DEVNULL)


def read_options():
    parser = argparse.ArgumentParser(description="Identify human cell lines")

    parser.add_argument('--quiet', dest="quiet", action='store_true', default=False, help="Supress all but essential messages")
    parser.add_argument('--version', action='version', version=f"Cell Line Sleuth v{VERSION}")
    parser.add_argument('--java', type=str, help="Location of the java binary", default="java")
    parser.add_argument('--rscript', type=str, help="Location of the Rscript binary", default="Rscript")
    parser.add_argument('--svg', dest="svg", action='store_true', default=False, help="Write graph in SVG format")
    parser.add_argument('snpfile', type=str, help="The SNP file generated by cosmic_diagnosic_snps.py")
    parser.add_argument('bamfile', type=str, help="The BAM file aligned to GRCh38 to analyse")

    options = parser.parse_args()

    #TODO: Test java and R

    return options

def main():

    options = read_options()
    process_file(options)


if __name__ == "__main__":
    main()