vanheeringen-lab/gimmemotifs

#!/usr/bin/env python
# Copyright (c) 2009-2019 Simon van Heeringen <simon.vanheeringen@gmail.com>
#
# This module is free software. You can redistribute it and/or modify it under
# the terms of the MIT License, see the file COPYING included with this
# distribution.
import logging

from yaml import load

from gimmemotifs.tools import get_tool

logger = logging.getLogger("gimme.prediction")


def prediction(args):
    tool = args.tool
    infile = args.infile
    outfile = args.outfile
    paramfile = args.paramfile

    t = get_tool(tool)

    params = {}
    if paramfile:
        params = load(open(paramfile))

    (motifs, stdout, stderr) = t.run(infile, params)

    logger.error(stderr)
    logger.info(stdout)

    f = open(outfile, "w")
    for m in motifs:
        f.write(f"{m.to_pfm()}\n")
    f.close()