comparison qualimap_bamqc.py @ 30:418ee04dd1b2 draft

planemo upload for repository https://github.com/scottx611x/qualimap2 commit dc78b7c4b1780b316ca4aba2be247969ac1100ec-dirty

29:71af3fbe85be

#!/usr/bin/env python
from __future__ import print_function
import argparse
from subprocess import check_call, CalledProcessError
import os
import shutil
import sys


def qualimap_bamqc(bam_filename, genomecov_file, jv_mem_size):
    qualimap_command = [
        "qualimap", "bamqc",
        "-bam " + bam_filename,
        "-oc " + genomecov_file,
        "-outdir .",
        "--java-mem-size=" + jv_mem_size
    ]

    try:
        check_call(qualimap_command)

        args.input_file,
        args.out_genome_file,
        args.java_mem_size
    )

    print(os.listdir("../"))

    shutil.make_archive(
        'raw_data_qualimapReport',
        'zip',
        os.path.join("../", 'raw_data_qualimapReport')
    )


if __name__ == "__main__":
    main()

30:418ee04dd1b2

#!/usr/bin/env python
from __future__ import print_function
import argparse
from subprocess import check_call, CalledProcessError
import shutil
import sys

OUTPUT_DIR = "qualimap_results"


def qualimap_bamqc(bam_filename, genomecov_file, jv_mem_size):
    qualimap_command = [
        "qualimap", "bamqc",
        "-bam " + bam_filename,
        "-oc " + genomecov_file,
        "-outdir " + OUTPUT_DIR,
        "--java-mem-size=" + jv_mem_size
    ]

    try:
        check_call(qualimap_command)

        args.input_file,
        args.out_genome_file,
        args.java_mem_size
    )

    shutil.move(OUTPUT_DIR + "/genome_results.txt", "genome_results.txt")
    shutil.move(OUTPUT_DIR + "/qualimapReport.html", "qualimapReport.html")
    shutil.make_archive(
        'raw_data_qualimapReport',
        'zip',
        OUTPUT_DIR + '/raw_data_qualimapReport'
    )


if __name__ == "__main__":
    main()