Revision 480a94cbe722741cd3f1c2d35549a5af06c3e774 authored by fenderglass on 18 July 2014, 18:59:24 UTC, committed by fenderglass on 18 July 2014, 18:59:24 UTC
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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 overlap native binary
which reconstructs overlap graph from contigs

import logging
import subprocess

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

logger = logging.getLogger()

OVERLAP_EXEC = "ragout-overlap"

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

def make_overlap_graph(contigs_file, dot_file):
    Builds assembly graph and outputs it in "dot" format
    """"Building overlap graph...")
    if not check_binary():
        return False

    cmdline = [OVERLAP_EXEC, contigs_file, dot_file,
    if config.vals["overlap"]["detect_kmer"]:

    except subprocess.CalledProcessError as e:
        logger.error("Some error inside native {0} module".format(OVERLAP_EXEC))
        return False

    return True
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