#(c) 2013-2014 by Authors
#This file is a part of Ragout program.
#Released under the BSD license (see LICENSE file)

"""
This module executes maf2synteny native binary
which recovers synteny blocks from multiple alignment
"""

import logging
import subprocess
import os

from ragout.shared.utils import which
from ragout.shared import config

logger = logging.getLogger()

M2S_EXEC = "ragout-maf2synteny"


def check_binary():
    """
    Checks if native binary is available
    """
    binary = which(M2S_EXEC)
    if not binary:
        logger.error("\"{0}\" native module not found".format(M2S_EXEC))
        return False
    return True


def make_synteny(maf_file, out_dir, min_blocks_list):
    """
    Builds synteny blocks from MAF file
    """
    if not check_binary():
        return False

    params_file = os.path.join(out_dir, "simpl_params.txt")
    _make_params_file(config.vals["maf2synteny"], params_file)
    cmdline = [M2S_EXEC, maf_file, out_dir, params_file]
    cmdline.extend(list(map(str, min_blocks_list)))
    try:
        subprocess.check_call(cmdline)
    except subprocess.CalledProcessError as e:
        logger.error("Some error inside native {0} module".format(M2S_EXEC))
        return False
    os.remove(params_file)

    return True

def _make_params_file(params, out_file):
    assert len(params)

    with open(out_file, "w") as f:
        for k, d in params:
            f.write("{0} {1}\n".format(k, d))