comparison qualimap_bamqc.py @ 37:407b6a65c867 draft

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

36:0e6aeed62025

import argparse
import os
from subprocess import check_call, CalledProcessError
import shutil
import sys

OUTPUT_DIR = "qualimap_results"


def qualimap_bamqc(bam_filename, genomecov_file, out_dir, jv_mem_size):
    qualimap_command = [
        "qualimap", "bamqc",

    parser.add_argument('--out_dir')
    parser.add_argument('--java_mem_size')

    args = parser.parse_args()

    qualimap_bamqc(
        args.input_file,
        args.out_genome_file,
        args.out_dir,
        args.java_mem_size
    )

    print(os.listdir(os.getcwd()))
    print(os.listdir(args.out_dir))

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

    print(os.listdir(os.getcwd()))
    print(os.listdir(args.out_dir))

if __name__ == "__main__":
    main()

37:407b6a65c867

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",

    parser.add_argument('--out_dir')
    parser.add_argument('--java_mem_size')

    args = parser.parse_args()

    output_dir = os.path.dirname(args.out_genome_file)

    qualimap_bamqc(
        args.input_file,
        args.out_genome_file,
        args.out_dir,
        args.java_mem_size
    )

    print(os.listdir(output_dir))

    shutil.make_archive(
        'raw_data_qualimapReport',
        'zip',
        args.out_dir + '/raw_data_qualimapReport'
    )

    [
        shutil.move(os.path.join(output_dir, file_name), file_name)
        for file_name in [
            "genome_results.txt",
            "qualimapReport.html",
            "raw_data_qualimapReport.zip"
        ]
    ]

    print(os.listdir(output_dir))

if __name__ == "__main__":
    main()