annotate commons/tools/SplicerFromAnnotation.py @ 31:0ab839023fe4

Uploaded

#!/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
import ConfigParser

from commons.core.sql.DbMySql import DbMySql
from commons.core.utils.RepetOptionParser import RepetOptionParser
from commons.core.utils.FileUtils import FileUtils
from commons.core.parsing.FastaParser import FastaParser
from ConfigParser import MissingSectionHeaderError
from commons.core.sql.DbFactory import DbFactory
from commons.core.sql.TablePathAdaptator import TablePathAdaptator
from commons.core.LoggerFactory import LoggerFactory

#TODO: use configuration file

LOG_DEPTH = "repet.tools"

## Get 3 annotation files, using output from TEannot:
#- consensus with one or more full length copy, 
#- consensus with one or more full length fragment,
#- consensus without copy

class SplicerFromAnnotation(object):
    
    def __init__(self, inInfoFileName = "", tableName = "", verbose = 0):
        self._inInfoFileName = inInfoFileName
        self._tableName = tableName
        self._verbosity = verbose
        self._log = LoggerFactory.createLogger("%s.%s" % (LOG_DEPTH, self.__class__.__name__), self._verbosity)
        
    def _logAndRaise(self, errorMsg):
        self._log.error(errorMsg)
        raise Exception(errorMsg)
    
    def setAttributesFromCmdLine(self):
        desc = "Splice annotations from genome. These annotations are Full Length Copy or Full Length Fragment according to consensus."
        desc += "A TEs library and annotation are necessary. Connection to the database parameters are retrieved from the environment"
        
        examples = "\nExample : with a project called \"MyTEannotAnalysis\":\n"
        examples += "\t$ python SplicerFromAnnotation.py -i inputFastaFileName -C configFileName -t MyTEannotAnalysis_refTEs_seq "
        examples += "\n\t"
        examples += "\n\n"
        
        parser = RepetOptionParser(description = desc, epilog = examples)
        parser.add_option("-i", "--file",      dest = "inputFastaFileName",  action = "store", type = "string", help = "input file (mandatory) = output file with .splice)")
        parser.add_option("-C", "--config",    dest = "configFileName",     action = "store", type = "string", help = "config file name to set database connection", default = "")
        parser.add_option("-t", "--copyType",  dest = "copyType" ,          action = "store", type = "int", help = "type number [default: 1, 2] 1 is Full Length Copy", default = 1 )
        parser.add_option("-I", "--identity",  dest = "identity",           action= "store",   type = "float",  help = "identity between 0 and 100 [default: 80]", default = 80) 
        parser.add_option("-o", "--outputFile",dest = "outputFile",         action= "store", type = "string", help = "output fasta file (default=input File + '.splice')",  default = "")
        parser.add_option("-v", "--verbose",   dest = "verbose",             action = "store", type = "int",    help = "verbosity level (default=0)", default = 0)
        (options, args) = parser.parse_args()
        self._setAttributesFromOptions(options)
        
    def _setAttributesFromOptions(self, options):
        self.setConfigFileName(options.configFileName)
        self.setInputFileName(options.inputFastaFileName)
        self.setOutputFileName(options.outputFile)
        self.setIdentity(options.identity)
        self.setCopyType(options.copyType)
        self.setVerbose(options.verbose)
        
    def setCopyType(self, copyType):
        self._copyType = copyType
        
    def setIdentity(self,identity):
        self._identity=identity
        
    def setInputFileName(self, inputFastaFileName):
        self._inputFastaFileName = inputFastaFileName
        self._projectName= os.path.basename(self._inputFastaFileName)
        self._projectName = self._projectName.split('.')[0]
        self._fF=FastaParser(self._inputFastaFileName)
        self._fF.getInfos()
        self.genomeSize=self._fF.size
        self.nbSeqGenome=self._fF.nbSequences
        
    def setOutputFileName(self,outputFile):
        self._outputFileName = outputFile
        
    def setConfigFileName(self, configFileName):
        self._configFileName = configFileName
        configFileHandle = open(self._configFileName)
        config = ConfigParser.ConfigParser()
    
        try :
            config.readfp( configFileHandle )
        except MissingSectionHeaderError:
            self._logAndRaise("Config file " + self._configFileName + " must begin with a section header ")

        self.setup_env( config )
        
    def setVerbose(self, verbose):
        self._verbosity = verbose
   
    def setup_env(self, config):
        os.environ["REPET_HOST"] = config.get("repet_env", "repet_host")
        os.environ["REPET_USER"] = config.get("repet_env", "repet_user")
        os.environ["REPET_PW"] = config.get("repet_env", "repet_pw")
        os.environ["REPET_DB"] = config.get("repet_env", "repet_db")
        os.environ["REPET_PORT"] = config.get("repet_env", "repet_port")
        os.environ["REPET_JOB_MANAGER"] = config.get("repet_env", "repet_job_manager")

    def checkOptions(self):
        if self._inputFastaFileName != "":
            if not FileUtils.isRessourceExists(self._inputFastaFileName):
                self._logAndRaise("Input fasta file does not exist!")
        else:
            self._logAndRaise("No specified -i option! It is mandatory")
       
        if self._outputFileName =="":
            self._outputFileName = os.path.basename(self._inputFastaFileName)+'.splice'
        
        if self._copyType!=1 or self._copyType!=2:
            self._logAndRaise("Copy type must be only 1 or 2!")
        if self._configFileName != "":
            iDb = DbMySql(cfgFileName = self._configFileName)
            iDb.close()
        else:
            self._logAndRaise("No specified config file name!")

                    
    def run(self):
        LoggerFactory.setLevel(self._log, self._verbosity)
        self.checkOptions()
        
        msg = "START SplicerFromAnnotation"
        msg += "\n input info file: %s" % self._inputFastaFileName
        msg += "\n Copy type is: %s" % self._copyType
        msg += "\n identity is: %s" % self._identity
        msg += "\n host is: %s" % os.environ["REPET_HOST"]
        msg += "\n user is: %s" % os.environ["REPET_USER"]
        msg += "\n DB is: %s" % os.environ["REPET_DB"] 
        msg += "\n port is: %s" % os.environ["REPET_PORT"]
        self._log.debug("%s\n" % msg)
        
        cmd="PostAnalyzeTELib.py -a 3 -p %s_chr_allTEs_nr_noSSR_join_path -s %s_refTEs_seq -g %s" % (self._projectName,self._projectName,self.genomeSize)       
        os.system(cmd)
        
        cmd="GetSpecificTELibAccordingToAnnotation.py -i %s_chr_allTEs_nr_noSSR_join_path.annotStatsPerTE.tab -t %s_refTEs_seq -v 2" % (self._projectName,self._projectName)
        os.system(cmd) 

        if self._copyType == 1 :
            f = open("Splicer_inputFile_chr_allTEs_nr_noSSR_join_path.annotStatsPerTE_FullLengthCopy.txt", "r")
        else :
            f = open("Splicer_inputFile_chr_allTEs_nr_noSSR_join_path.annotStatsPerTE_FullLengthFrag.txt", "r")
        
        lines=f.readlines()[1:]
        if len(lines)>0:
            lConsensusHeader_copyType=[i.split('\t',1)[0] for i in lines] 
            db = DbFactory.createInstance()
            
            sql_cmd = "CREATE TABLE %s_annotationIdentitySup%d_path SELECT * FROM %s_chr_allTEs_nr_noSSR_join_path where identity >=%f" % ( self._projectName,int(self._identity),self._projectName,self._identity)
            db.execute( sql_cmd )
    
            iTPA = TablePathAdaptator(db, "%s_annotationIdentitySup%d_path" % (self._projectName, int(self._identity)))
            lAllDistinctPath=[]
            for consensusName in lConsensusHeader_copyType:
                lDistinctPath = iTPA.getIdListFromSubject(consensusName)
                lAllDistinctPath=lAllDistinctPath+lDistinctPath
            
            iTPA = TablePathAdaptator(db,"%s_chr_allTEs_nr_noSSR_join_path" % self._projectName)
            sql_cmd = "CREATE TABLE  %s_annotationToSplice_path LIKE %s_chr_allTEs_nr_noSSR_join_path" % ( self._projectName, self._projectName )
            db.execute( sql_cmd )

            for pathId in lAllDistinctPath:
                sql_cmd = "INSERT INTO %s_annotationToSplice_path SELECT * FROM %s_chr_allTEs_nr_noSSR_join_path where path =%d" % ( self._projectName, self._projectName, pathId )
                db.execute( sql_cmd )           
            db.close()
            
            cmd="SpliceTEsFromGenome.py -i %s_annotationToSplice_path -f path -g %s -o %s -C %s -v 2" % (self._projectName, self._inputFastaFileName, self._outputFileName, self._configFileName)       
            os.system(cmd)
            
        else : 
            msg = "There is no consensus in this copy type.\n"
            self._log.info(msg)
        f.close()     
        
        self._log.info("END SplicerFromAnnotation")
        return 0

if __name__ == '__main__':
    iGetTELib = SplicerFromAnnotation()
    iGetTELib.setAttributesFromCmdLine()
    iGetTELib.run()