comparison tools/mira4_0/mira4_make_bam.py @ 31:fd95aaef8818 draft

planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit bc3d484c5cd68ddcf456db2fff489d584aa2034c

30:b506e3b779fa

import os
import sys
import shutil
import subprocess
import tempfile

def sys_exit(msg, err=1):
    sys.stderr.write(msg+"\n")
    sys.exit(err)

def run(cmd, log_handle):
    try:
        child = subprocess.Popen(cmd, shell=True,
                                 stdout=subprocess.PIPE,

if __name__ == "__main__":
    mira_convert, maf_file, fasta_file, bam_file = sys.argv[1:]
    msg = make_bam(mira_convert, maf_file, fasta_file, bam_file, sys.stdout)
    if msg:
        sys_exit(msg)

31:fd95aaef8818

import os
import sys
import shutil
import subprocess
import tempfile

def run(cmd, log_handle):
    try:
        child = subprocess.Popen(cmd, shell=True,
                                 stdout=subprocess.PIPE,

if __name__ == "__main__":
    mira_convert, maf_file, fasta_file, bam_file = sys.argv[1:]
    msg = make_bam(mira_convert, maf_file, fasta_file, bam_file, sys.stdout)
    if msg:
        sys.exit(msg)