Mercurial > repos > scottx611x > qualimap2_bamqc
view qualimap_bamqc.py @ 41:e856fda6f375 draft
planemo upload for repository https://github.com/scottx611x/qualimap2 commit dc78b7c4b1780b316ca4aba2be247969ac1100ec-dirty
author | scottx611x |
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date | Fri, 27 Jul 2018 11:53:29 -0400 |
parents | 98944e914637 |
children | c53375e61b33 |
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#!/usr/bin/env python from __future__ import print_function import argparse import os from subprocess import check_call, CalledProcessError import shutil import sys def qualimap_bamqc(bam_filename, genomecov_file, out_dir, jv_mem_size): qualimap_command = [ "qualimap", "bamqc", "-bam " + bam_filename, "-oc " + genomecov_file, "-outdir " + out_dir, "--java-mem-size=" + jv_mem_size ] try: check_call(qualimap_command) except CalledProcessError: print("Error running the qualimap bamqc", file=sys.stderr) def main(): parser = argparse.ArgumentParser( description="Generate Bam Quality Statistics" ) parser.add_argument('--input_file') parser.add_argument('--out_genome_file') parser.add_argument('--out_dir') parser.add_argument('--out_zip') parser.add_argument('--out_html') parser.add_argument('--out_results') parser.add_argument('--java_mem_size') args = parser.parse_args() print(args) qualimap_bamqc( args.input_file, args.out_genome_file, args.out_dir, args.java_mem_size ) shutil.make_archive( 'raw_data_qualimapReport', 'zip', os.path.join(args.out_dir,'raw_data_qualimapReport') ) shutil.move("raw_data_qualimapReport.zip", args.out_zip) shutil.move( os.path.join(args.out_dir, "genome_results.txt"), args.out_results ) shutil.move( os.path.join(args.out_dir, "qualimapReport.html"), args.out_html ) if __name__ == "__main__": main()