Revision 480a94cbe722741cd3f1c2d35549a5af06c3e774 authored by fenderglass on 18 July 2014, 18:59:24 UTC, committed by fenderglass on 18 July 2014, 18:59:24 UTC
1 parent 5bc5199
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#(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)))
    except subprocess.CalledProcessError as e:
        logger.error("Some error inside native {0} module".format(M2S_EXEC))
        return False

    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))
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