view commons/tools/PrepareBatches.py @ 18:94ab73e8a190

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#!/usr/bin/env python

# Copyright INRA (Institut National de la Recherche Agronomique)
# http://www.inra.fr
# http://urgi.versailles.inra.fr
#
# This software is governed by the CeCILL license under French law and
# abiding by the rules of distribution of free software.  You can  use, 
# modify and/ or redistribute the software under the terms of the CeCILL
# license as circulated by CEA, CNRS and INRIA at the following URL
# "http://www.cecill.info". 
#
# As a counterpart to the access to the source code and  rights to copy,
# modify and redistribute granted by the license, users are provided only
# with a limited warranty  and the software's author,  the holder of the
# economic rights,  and the successive licensors  have only  limited
# liability. 
#
# In this respect, the user's attention is drawn to the risks associated
# with loading,  using,  modifying and/or developing or reproducing the
# software by the user in light of its specific status of free software,
# that may mean  that it is complicated to manipulate,  and  that  also
# therefore means  that it is reserved for developers  and  experienced
# professionals having in-depth computer knowledge. Users are therefore
# encouraged to load and test the software's suitability as regards their
# requirements in conditions enabling the security of their systems and/or 
# data to be ensured and,  more generally, to use and operate it in the 
# same conditions as regards security. 
#
# The fact that you are presently reading this means that you have had
# knowledge of the CeCILL license and that you accept its terms.

import os
import sys
from ConfigParser import NoSectionError, NoOptionError
from commons.core.checker.CheckerUtils import CheckerUtils
from commons.core.checker.CheckerException import CheckerException
from commons.core.utils.FileUtils import FileUtils
from commons.core.seq.FastaUtils import FastaUtils

class PrepareBatches(object):
    
    def __init__(self, pipelineName, projectDir, projectName, iConfig, verbose):
        self._pipelineName = pipelineName
        self._projectDir = projectDir
        self._projectName = projectName
        self._iConfig = iConfig
        self._verbose = verbose
        
    def run(self):
        if self._verbose > 0:
            print "beginning of step 1"
            sys.stdout.flush()
        if FileUtils.isRessourceExists("%s_db" % self._projectName):
            print "ERROR: directory '%s_db' already exists" % self._projectName
            sys.exit(1)
        
        os.mkdir("%s_db" % self._projectName)
        os.chdir("%s_db" % self._projectName)
        genomeFastaFileName = "%s.fa" % self._projectName
        os.symlink("../%s" % genomeFastaFileName, genomeFastaFileName)
        sectionName = "prepare_batches"
        self._checkConfig(sectionName)  
        
        separator = "\n"
        inGenomeFileHandler = open(genomeFastaFileName, "r")
        try:
            CheckerUtils.checkHeaders(inGenomeFileHandler)
        except CheckerException, e:
            print "Error in file %s. Wrong headers are :" % genomeFastaFileName
            print separator.join(e.messages)
            print "Authorized characters are : a-z A-Z 0-9 - . : _\n"
            inGenomeFileHandler.close()
            sys.exit(1)
        inGenomeFileHandler.close()

        doClean = False
        if self._iConfig.get(sectionName, "clean") == "yes":
            doClean = True
        chunkFilePrefix = "%s_chunks" % self._projectName
        chunkLength = int(self._iConfig.get(sectionName, "chunk_length"))
        chunkOverlap = int(self._iConfig.get(sectionName, "chunk_overlap"))
        FastaUtils.dbChunks(genomeFastaFileName, chunkLength, chunkOverlap, 0, chunkFilePrefix, doClean, self._verbose)
        
        nbSeq = int(self._iConfig.get(sectionName, "nb_seq_per_batch"))
        FastaUtils.splitFastaFileInBatches("%s.fa" % chunkFilePrefix, nbSeq * chunkLength)

        if self._iConfig.get(sectionName, "clean") == "yes":
            FileUtils.removeFilesByPattern("%s.fa*" % self._projectName)
            
        os.chdir( ".." )
        if self._verbose > 0:
            print "step 1 finished successfully"
            sys.stdout.flush()

    def _checkConfig(self, sectionName):
        try:
            CheckerUtils.checkSectionInConfigFile(self._iConfig, sectionName)
        except NoSectionError:
            print "ERROR: the section %s must be in your configuration file" % sectionName
            sys.exit(1)
        try:
            CheckerUtils.checkOptionInSectionInConfigFile(self._iConfig, sectionName, "chunk_length")
        except NoOptionError:
            print "ERROR: the option 'chunk_length' must be defined in %s in your configuration file" % sectionName
            sys.exit(1)
        try:
            CheckerUtils.checkOptionInSectionInConfigFile(self._iConfig, sectionName, "chunk_overlap")
        except NoOptionError:
            print "ERROR: the option 'chunk_overlap' must be defined in %s in your configuration file" % sectionName
            sys.exit(1)
        try:
            CheckerUtils.checkOptionInSectionInConfigFile(self._iConfig, sectionName, "nb_seq_per_batch")
        except NoOptionError:
            print "ERROR: the option 'nb_seq_per_batch' must be defined in %s in your configuration file" % sectionName
            sys.exit(1)
        try:
            CheckerUtils.checkOptionInSectionInConfigFile(self._iConfig, sectionName, "resources")
        except NoOptionError:
            print "ERROR: the option 'resources' must be defined in %s in your configuration file" % sectionName
            sys.exit(1)
        try:
            CheckerUtils.checkOptionInSectionInConfigFile(self._iConfig, sectionName, "tmpDir")
        except NoOptionError:
            print "ERROR: the option 'tmpDir' must be defined in %s in your configuration file" % sectionName
            sys.exit(1)