view tools/mira4_0/mira4_bait.py @ 39:bbf14bb9607b draft default tip

planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6

#!/usr/bin/env python
"""A simple wrapper script to call MIRA4's mirabait and collect its output."""

from __future__ import print_function

import os
import shutil
import subprocess
import sys
import time

WRAPPER_VER = "0.0.11"  # Keep in sync with the XML file


def get_version(mira_binary):
    """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_binary, "-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
    # Workaround for -v not working in mirabait 4.0RC4
    if "invalid option" in ver.split("\n", 1)[0]:
        for line in ver.split("\n", 1):
            if " version " in line:
                line = line.split()
                return line[line.index("version") + 1].rstrip(")")
        sys.exit("Could not determine MIRA version:\n%s" % ver)
    return ver.split("\n", 1)[0]


if "MIRA4" in os.environ:
    mira_path = os.environ["MIRA4"]
    mira_binary = os.path.join(mira_path, "mirabait")
    if not os.path.isfile(mira_binary):
        sys.exit(
            "Missing mirabait under $MIRA4, %r\nFolder contained: %s"
            % (mira_binary, ", ".join(os.listdir(mira_path)))
        )
else:
    sys.stderr.write(
        "DEBUG: Since $MIRA4 is not set, assuming mira binaries are on $PATH.\n"
    )
    mira_path = None
    mira_binary = "mirabait"

mira_ver = get_version(mira_binary)
if not mira_ver.strip().startswith("4.0"):
    sys.exit("This wrapper is for MIRA V4.0, not:\n%s" % mira_ver)
if "-v" in sys.argv or "--version" in sys.argv:
    print("%s, MIRA wrapper version %s" % (mira_ver, WRAPPER_VER))
    sys.exit(0)


(
    format,
    output_choice,
    strand_choice,
    kmer_length,
    min_occurance,
    bait_file,
    in_file,
    out_file,
) = sys.argv[1:]

if format.startswith("fastq"):
    format = "fastq"
elif format == "mira":
    format = "maf"
elif format != "fasta":
    sys.exit("Was not expected format %r" % format)

assert out_file.endswith(".dat")
out_file_stem = out_file[:-4]

cmd_list = [
    mira_binary,
    "-f",
    format,
    "-t",
    format,
    "-k",
    kmer_length,
    "-n",
    min_occurance,
    bait_file,
    in_file,
    out_file_stem,
]
if output_choice == "pos":
    pass
elif output_choice == "neg":
    # Invert the selection...
    cmd_list.insert(1, "-i")
else:
    sys.exit("Output choice should be 'pos' or 'neg', not %r" % output_choice)
if strand_choice == "both":
    pass
elif strand_choice == "fwd":
    # Ingore reverse strand...
    cmd_list.insert(1, "-r")
else:
    sys.exit("Strand choice should be 'both' or 'fwd', not %r" % strand_choice)

cmd = " ".join(cmd_list)
# print cmd
start_time = time.time()
try:
    # Run MIRA
    child = subprocess.Popen(
        cmd_list,
        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" % (cmd, err))
    sys.exit(1)
# Use .communicate as can get deadlocks with .wait(),
stdout, stderr = child.communicate()
assert stderr is None  # Due to way we ran with subprocess
run_time = time.time() - start_time
return_code = child.returncode
print("mirabait took %0.2f minutes" % (run_time / 60.0))

if return_code:
    sys.stderr.write(stdout)
    sys.exit("Return error code %i from command:\n%s" % (return_code, cmd), return_code)

# Capture output
out_tmp = out_file_stem + "." + format
if not os.path.isfile(out_tmp):
    sys.stderr.write(stdout)
    sys.exit("Missing output file from mirabait: %s" % out_tmp)
shutil.move(out_tmp, out_file)