https://github.com/fenderglass/Ragout
Tip revision: a010582c8df9b28958e7447ae37bfca886c457de authored by Mikhail Kolmogorov on 18 March 2015, 01:59:36 UTC
non-negative tree lengths, dosumentationimproved
non-negative tree lengths, dosumentationimproved
Tip revision: a010582
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, "--help"], 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, out_dir, params_file]
cmdline.extend(list(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))