vanheeringen-lab/gimmemotifs

import os
from subprocess import PIPE, Popen

from .motifprogram import MotifProgram


class Dinamo(MotifProgram):

    """
    Predict motifs using DiNAMO.

    Reference: Saad et al., 2018, doi: 10.1186/s12859-018-2215-1
    """

    def __init__(self):
        self.name = "DiNAMO"
        self.cmd = "dinamo"
        self.use_width = True
        self.default_params = {"background": None, "number": 10, "width": 10}

    def _run_program(self, bin, fastafile, params=None):
        """
        Run DiNAMO and predict motifs from a FASTA file.

        Parameters
        ----------
        bin : str
            Command used to run the tool.

        fastafile : str
            Name of the FASTA input file.

        params : dict, optional
            Optional parameters. For some of the tools required parameters
            are passed using this dictionary.

        Returns
        -------
        motifs : list of Motif instances
            The predicted motifs.

        stdout : str
            Standard out of the tool.

        stderr : str
            Standard error of the tool.
        """
        params = self._parse_params(params, needs_background=True)

        outfile = os.path.join(self.tmpdir, "motifs.meme")
        stdout = ""
        stderr = ""

        cmd = (
            f"{bin} -pf {fastafile} -nf {params['background']} "
            f"-l {params['width']} -o {outfile}"
        )

        p = Popen(cmd, shell=True, stdout=PIPE, stderr=PIPE, cwd=self.tmpdir)
        out, err = p.communicate()
        stdout += out.decode()
        stderr += err.decode()

        motifs, stdout, stderr = self._read_and_label_motifs(
            outfile, stdout, stderr, fmt="meme"
        )

        return motifs, stdout, stderr