comparison tools/sr_assembly/mira.py @ 6:3e7eca1f5d04 draft

MIRA wrapper v0.0.5 with <version_command> support and check for MIRA V3.4

5:216bf640baaf

import sys
import subprocess
import shutil
import time

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

def collect_output(temp, name):
    n3 = (temp, name, name, name)
    f = "%s/%s_assembly/%s_d_results" % (temp, name, name)
    if not os.path.isdir(f):

6:3e7eca1f5d04

import sys
import subprocess
import shutil
import time

WRAPPER_VER = "0.0.5" #Keep in sync with the XML file

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


def get_version():
    """Run MIRA to find its version number"""
    # At the commend line I would use: mira -v | head -n 1
    # however there is some pipe error when doing that here.
    try:
        child = subprocess.Popen(["mira", "-v"],
                                 stdout=subprocess.PIPE,
                                 stderr=subprocess.STDOUT)
    except Exception, err:
        sys.stderr.write("Error invoking command:\n%s\n\n%s\n" % (" ".join(cmd), err))
        sys.exit(1)
    ver, tmp = child.communicate()
    del child
    return ver.split("\n", 1)[0]


mira_ver = get_version()
if "V3.4." not in mira_ver:
    stop_err("This wrapper is for MIRA V3.4, not %s" % mira_ver)
if "-v" in sys.argv:
    print "MIRA wrapper version %s," % WRAPPER_VER
    print mira_ver
    sys.exit(0)


def collect_output(temp, name):
    n3 = (temp, name, name, name)
    f = "%s/%s_assembly/%s_d_results" % (temp, name, name)
    if not os.path.isdir(f):