comparison tools/mira4/mira4.py @ 18:381aa262c8cb draft

Uploaded v0.0.2 preview 10, override /tmp via environment variable

17:5bbaa930d7fa

import os
import sys
import subprocess
import shutil
import time

#Do we need any PYTHONPATH magic?
from mira4_make_bam import make_bam

WRAPPER_VER = "0.0.1" #Keep in sync with the XML file

except ValueError:
    threads = 1
assert 1 <= threads, threads


def log_manifest(manifest):
    """Write the manifest file to stderr."""
    sys.stderr.write("\n%s\nManifest file\n%s\n" % ("="*60, "="*60))
    with open(manifest) as h:
        for line in h:

temp = "."
#name, out_fasta, out_qual, out_ace, out_caf, out_wig, out_log = sys.argv[1:8]
name = "MIRA"
manifest, out_maf, out_bam, out_fasta, out_log = sys.argv[1:]

start_time = time.time()
#cmd_list =sys.argv[8:]
cmd_list = [mira_binary, "-t", str(threads), manifest]
cmd = " ".join(cmd_list)

18:381aa262c8cb

import os
import sys
import subprocess
import shutil
import time
import tempfile

#Do we need any PYTHONPATH magic?
from mira4_make_bam import make_bam

WRAPPER_VER = "0.0.1" #Keep in sync with the XML file

except ValueError:
    threads = 1
assert 1 <= threads, threads


def override_temp(manifest):
    """Override ``-DI:trt=/tmp`` in manifest with environment variable.

    Currently MIRA 4 does not allow envronment variables like ``$TMP``
    inside the manifest, which is a problem if you need to override
    the default at run time.

    The tool XML will ``/tmp`` and we replace that here with
    ``tempfile.gettempdir()`` which will respect $TMPDIR, $TEMP, $TMP
    as explained in the Python standard library documentation:
    http://docs.python.org/2/library/tempfile.html#tempfile.tempdir

    By default MIRA 4 would write its temporary files within the output
    folder, which is a problem if that is a network drive.
    """
    handle = open(manifest, "r")
    text = handle.read()
    handle.close()

    #At time of writing, this is at the end of a file,
    #but could be followed by a space in future...
    text = text.replace("-DI:trt=/tmp", "-DI:trt=" + tempfile.gettempdir())

    handle = open(manifest, "w")
    handle.write(text)
    handle.flush()
    handle.close()


def log_manifest(manifest):
    """Write the manifest file to stderr."""
    sys.stderr.write("\n%s\nManifest file\n%s\n" % ("="*60, "="*60))
    with open(manifest) as h:
        for line in h:

temp = "."
#name, out_fasta, out_qual, out_ace, out_caf, out_wig, out_log = sys.argv[1:8]
name = "MIRA"
manifest, out_maf, out_bam, out_fasta, out_log = sys.argv[1:]

override_temp(manifest)

start_time = time.time()
#cmd_list =sys.argv[8:]
cmd_list = [mira_binary, "-t", str(threads), manifest]
cmd = " ".join(cmd_list)