comparison tools/mira3/mira.py @ 28:e28d6015fc56 draft default tip

planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira3/ commit 89578746a1c5b29c84a173d8b2709f086f69a7b6

27:85b86f31327c

    """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.
    cmd = ["mira", "-v"]
    try:
        child = subprocess.Popen(cmd, universal_newlines=True,
                                 stdout=subprocess.PIPE,
                                 stderr=subprocess.STDOUT)
    except Exception as 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

    if not os.path.isdir(f):
        sys.exit("Missing output folder")
    if not os.listdir(f):
        sys.exit("Empty output folder")
    missing = []
    for old, new in [("%s/%s_out.unpadded.fasta" % (f, name), out_fasta),
                     ("%s/%s_out.unpadded.fasta.qual" % (f, name), out_qual),
                     ("%s/%s_out.wig" % (f, name), out_wig),
                     ("%s/%s_out.caf" % (f, name), out_caf),
                     ("%s/%s_out.ace" % (f, name), out_ace)]:
        if not os.path.isfile(old):
            missing.append(os.path.splitext(old)[-1])
        else:
            shutil.move(old, new)
    if missing:

# print(cmd)

handle = open(out_log, "w")
try:
    # Run MIRA
    child = subprocess.Popen(cmd_list, universal_newlines=True,
                             stdout=handle,
                             stderr=subprocess.STDOUT)
except Exception as err:
    sys.stderr.write("Error invoking command:\n%s\n\n%s\n" % (cmd, err))
    # TODO - call clean up?
    handle.write("Error invoking command:\n%s\n\n%s\n" % (cmd, err))
    handle.close()

28:e28d6015fc56

    """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.
    cmd = ["mira", "-v"]
    try:
        child = subprocess.Popen(
            cmd,
            universal_newlines=True,
            stdout=subprocess.PIPE,
            stderr=subprocess.STDOUT,
        )
    except Exception as 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

    if not os.path.isdir(f):
        sys.exit("Missing output folder")
    if not os.listdir(f):
        sys.exit("Empty output folder")
    missing = []
    for old, new in [
        ("%s/%s_out.unpadded.fasta" % (f, name), out_fasta),
        ("%s/%s_out.unpadded.fasta.qual" % (f, name), out_qual),
        ("%s/%s_out.wig" % (f, name), out_wig),
        ("%s/%s_out.caf" % (f, name), out_caf),
        ("%s/%s_out.ace" % (f, name), out_ace),
    ]:
        if not os.path.isfile(old):
            missing.append(os.path.splitext(old)[-1])
        else:
            shutil.move(old, new)
    if missing:

# print(cmd)

handle = open(out_log, "w")
try:
    # Run MIRA
    child = subprocess.Popen(
        cmd_list, universal_newlines=True, stdout=handle, stderr=subprocess.STDOUT
    )
except Exception as err:
    sys.stderr.write("Error invoking command:\n%s\n\n%s\n" % (cmd, err))
    # TODO - call clean up?
    handle.write("Error invoking command:\n%s\n\n%s\n" % (cmd, err))
    handle.close()