https://github.com/fenderglass/Ragout
Tip revision: f37511c1d5874812f7689d9036ce265d0dbd9b4b authored by Mikhail Kolmogorov on 29 September 2015, 00:25:49 UTC
minor docs change
minor docs change
Tip revision: f37511c
maf2synteny.py
#(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 and runnable
"""
binary = which(M2S_EXEC)
if not binary:
logger.error("\"{0}\" native module not found".format(M2S_EXEC))
return False
try:
devnull = open(os.devnull, "w")
subprocess.check_call([M2S_EXEC, "-h"], stderr=devnull)
except subprocess.CalledProcessError as e:
logger.error("Some error inside native {0} module: {1}"
.format(M2S_EXEC, e))
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, "-o", out_dir, "-s", params_file,
"-b", ",".join(map(str, min_blocks_list))]
logger.info("Running maf2synteny module")
proc = subprocess.Popen(cmdline, stderr=subprocess.PIPE)
for line in iter(proc.stderr.readline, ""):
logger.debug(line.strip())
ret_code = proc.wait()
if ret_code:
logger.error("Non-zero return code when calling {0} module: {1}"
.format(M2S_EXEC, ret_code))
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))