view qualimap_bamqc.py @ 0:d87d6c0c27f5 draft

planemo upload for repository https://github.com/zipho/qualimap2 commit fb67f375d3ae592c62f73d647d8afa19b79037c0

#!/usr/bin/env python
from __future__ import print_function
import argparse
from subprocess import check_call, CalledProcessError
import shlex
import sys
import logging
log = logging.getLogger( __name__ )

def qualimap_bamqc( bam_filename, genomecov_file, out_dir, pdf_file, jv_mem_size):
    #qualimap bamqc -bam R.bam.sorted_dedup.bam_realigned.bam -oc ./test.genomecov  -outdir ./Kaust_kxdr/variants/qualimap/bamqc_report --outfile test.pdf --java-mem-size=16G
    cmdline_str = "qualimap bamqc -bam {} -oc {} -outdir {} --outfile {} --java-mem-size={}".format( bam_filename,
                                                                                                     genomecov_file,
                                                                                                     out_dir,
                                                                                                     pdf_file,
                                                                                                     jv_mem_size)
    cmdline = newSplit(cmdline_str)
    try:
        check_call(cmdline)
    except CalledProcessError:
        print("Error running the qualimap bamqc", file=sys.stderr)

def newSplit(value):
    lex = shlex.shlex(value)
    lex.quotes = '"'
    lex.whitespace_split = True
    lex.commenters = ''
    return list(lex)

def main():
    parser = argparse.ArgumentParser(description="Generate Bam Quality Statistics")
    parser.add_argument('--input_file')
    parser.add_argument('--out_genome_file', default="bam_stats.genomecov")
    parser.add_argument('--out_dir',  default="/tmp/bamstats")
    parser.add_argument('--out_pdf_file', default="bam_stats.pdf")
    parser.add_argument('--java_mem_size', default="8G" )

    args = parser.parse_args()
   
    qualimap_bamqc(args.input_file, args.out_genome_file, args.out_dir, args.out_pdf_file, args.java_mem_size)

if __name__ == "__main__": main()