# -*- coding: utf-8 -*-
####################################################################################
# Integron_Finder - Integron Finder aims at detecting integrons in DNA sequences #
# by finding particular features of the integron: #
# - the attC sites #
# - the integrase #
# - and when possible attI site and promoters. #
# #
# Authors: Jean Cury, Bertrand Neron, Eduardo PC Rocha #
# Copyright (c) 2015 - 2018 Institut Pasteur, Paris and CNRS. #
# See the COPYRIGHT file for details #
# #
# integron_finder is free software: you can redistribute it and/or modify #
# it under the terms of the GNU General Public License as published by #
# the Free Software Foundation, either version 3 of the License, or #
# (at your option) any later version. #
# #
# integron_finder is distributed in the hope that it will be useful, #
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
# GNU General Public License for more details. #
# #
# You should have received a copy of the GNU General Public License #
# along with this program (COPYING file). #
# If not, see <http://www.gnu.org/licenses/>. #
####################################################################################
import os
from subprocess import call
import colorlog
from . import EmptyFileError
_log = colorlog.getLogger(__name__)
[docs]def find_integrase(replicon_id, prot_file, out_dir, cfg):
"""
Call Prodigal for Gene annotation and hmmer to find integrase, either with phage_int
HMM profile or with intI profile.
:param str replicon_id: The Replicon identifier to search integrase into
:param str prot_file: the path to the fasta file containing the translation of the replicon.
:param str out_dir: the relative path to the directory where prodigal outputs will be stored
:param cfg: the configuration
:type cfg: a :class:`integron_finder.config.Config` object
:returns: None, the results are written on the disk
"""
intI_hmm_out = os.path.join(out_dir, replicon_id + "_intI.res")
hmm_cmd = []
if not os.path.exists(prot_file):
msg = "The protein file: '{}' does not exists cannot perform hmmsearch on it.".format(prot_file)
_log.warning(msg)
raise RuntimeError(msg)
elif os.path.getsize(prot_file) == 0:
msg = "The protein file: '{}' is empty cannot perform hmmsearch on it.".format(prot_file)
_log.warning(msg)
raise EmptyFileError(msg)
if not os.path.isfile(intI_hmm_out):
hmm_cmd.append([cfg.hmmsearch,
"--cpu", str(cfg.cpu),
"--tblout", os.path.join(out_dir, replicon_id + "_intI_table.res"),
"-o", intI_hmm_out,
cfg.model_integrase,
prot_file])
phage_hmm_out = os.path.join(out_dir, replicon_id + "_phage_int.res")
if not os.path.isfile(phage_hmm_out):
hmm_cmd.append([cfg.hmmsearch,
"--cpu", str(cfg.cpu),
"--tblout", os.path.join(out_dir, replicon_id + "_phage_int_table.res"),
"-o", phage_hmm_out,
cfg.model_phage_int,
prot_file])
for cmd in hmm_cmd:
try:
_log.debug("run hmmsearch: {}".format(' '.join(cmd)))
returncode = call(cmd)
except Exception as err:
raise RuntimeError("{0} failed : {1}".format(' '.join(cmd), err))
if returncode != 0:
raise RuntimeError("{0} failed return code = {1}".format(' '.join(cmd), returncode))
