18
+ − 1 #!/usr/bin/env python
+ − 2
+ − 3 # Copyright INRA (Institut National de la Recherche Agronomique)
+ − 4 # http://www.inra.fr
+ − 5 # http://urgi.versailles.inra.fr
+ − 6 #
+ − 7 # This software is governed by the CeCILL license under French law and
+ − 8 # abiding by the rules of distribution of free software. You can use,
+ − 9 # modify and/ or redistribute the software under the terms of the CeCILL
+ − 10 # license as circulated by CEA, CNRS and INRIA at the following URL
+ − 11 # "http://www.cecill.info".
+ − 12 #
+ − 13 # As a counterpart to the access to the source code and rights to copy,
+ − 14 # modify and redistribute granted by the license, users are provided only
+ − 15 # with a limited warranty and the software's author, the holder of the
+ − 16 # economic rights, and the successive licensors have only limited
+ − 17 # liability.
+ − 18 #
+ − 19 # In this respect, the user's attention is drawn to the risks associated
+ − 20 # with loading, using, modifying and/or developing or reproducing the
+ − 21 # software by the user in light of its specific status of free software,
+ − 22 # that may mean that it is complicated to manipulate, and that also
+ − 23 # therefore means that it is reserved for developers and experienced
+ − 24 # professionals having in-depth computer knowledge. Users are therefore
+ − 25 # encouraged to load and test the software's suitability as regards their
+ − 26 # requirements in conditions enabling the security of their systems and/or
+ − 27 # data to be ensured and, more generally, to use and operate it in the
+ − 28 # same conditions as regards security.
+ − 29 #
+ − 30 # The fact that you are presently reading this means that you have had
+ − 31 # knowledge of the CeCILL license and that you accept its terms.
+ − 32
+ − 33
+ − 34 import os
+ − 35 import sys
+ − 36 import ConfigParser
+ − 37
+ − 38 from commons.core.sql.DbMySql import DbMySql
+ − 39 from commons.core.utils.RepetOptionParser import RepetOptionParser
+ − 40 from commons.core.utils.FileUtils import FileUtils
+ − 41 from commons.core.parsing.FastaParser import FastaParser
+ − 42 from ConfigParser import MissingSectionHeaderError
+ − 43 from commons.core.sql.DbFactory import DbFactory
+ − 44 from commons.core.sql.TablePathAdaptator import TablePathAdaptator
+ − 45 from commons.core.LoggerFactory import LoggerFactory
+ − 46
+ − 47 #TODO: use configuration file
+ − 48
+ − 49 LOG_DEPTH = "repet.tools"
+ − 50
+ − 51 ## Get 3 annotation files, using output from TEannot:
+ − 52 #- consensus with one or more full length copy,
+ − 53 #- consensus with one or more full length fragment,
+ − 54 #- consensus without copy
+ − 55
+ − 56 class SplicerFromAnnotation(object):
+ − 57
+ − 58 def __init__(self, inInfoFileName = "", tableName = "", verbose = 0):
+ − 59 self._inInfoFileName = inInfoFileName
+ − 60 self._tableName = tableName
+ − 61 self._verbosity = verbose
+ − 62 self._log = LoggerFactory.createLogger("%s.%s" % (LOG_DEPTH, self.__class__.__name__), self._verbosity)
+ − 63
+ − 64 def _logAndRaise(self, errorMsg):
+ − 65 self._log.error(errorMsg)
+ − 66 raise Exception(errorMsg)
+ − 67
+ − 68 def setAttributesFromCmdLine(self):
+ − 69 desc = "Splice annotations from genome. These annotations are Full Length Copy or Full Length Fragment according to consensus."
+ − 70 desc += "A TEs library and annotation are necessary. Connection to the database parameters are retrieved from the environment"
+ − 71
+ − 72 examples = "\nExample : with a project called \"MyTEannotAnalysis\":\n"
+ − 73 examples += "\t$ python SplicerFromAnnotation.py -i inputFastaFileName -C configFileName -t MyTEannotAnalysis_refTEs_seq "
+ − 74 examples += "\n\t"
+ − 75 examples += "\n\n"
+ − 76
+ − 77 parser = RepetOptionParser(description = desc, epilog = examples)
+ − 78 parser.add_option("-i", "--file", dest = "inputFastaFileName", action = "store", type = "string", help = "input file (mandatory) = output file with .splice)")
+ − 79 parser.add_option("-C", "--config", dest = "configFileName", action = "store", type = "string", help = "config file name to set database connection", default = "")
+ − 80 parser.add_option("-t", "--copyType", dest = "copyType" , action = "store", type = "int", help = "type number [default: 1, 2] 1 is Full Length Copy", default = 1 )
+ − 81 parser.add_option("-I", "--identity", dest = "identity", action= "store", type = "float", help = "identity between 0 and 100 [default: 80]", default = 80)
+ − 82 parser.add_option("-o", "--outputFile",dest = "outputFile", action= "store", type = "string", help = "output fasta file (default=input File + '.splice')", default = "")
+ − 83 parser.add_option("-v", "--verbose", dest = "verbose", action = "store", type = "int", help = "verbosity level (default=0)", default = 0)
+ − 84 (options, args) = parser.parse_args()
+ − 85 self._setAttributesFromOptions(options)
+ − 86
+ − 87 def _setAttributesFromOptions(self, options):
+ − 88 self.setConfigFileName(options.configFileName)
+ − 89 self.setInputFileName(options.inputFastaFileName)
+ − 90 self.setOutputFileName(options.outputFile)
+ − 91 self.setIdentity(options.identity)
+ − 92 self.setCopyType(options.copyType)
+ − 93 self.setVerbose(options.verbose)
+ − 94
+ − 95 def setCopyType(self, copyType):
+ − 96 self._copyType = copyType
+ − 97
+ − 98 def setIdentity(self,identity):
+ − 99 self._identity=identity
+ − 100
+ − 101 def setInputFileName(self, inputFastaFileName):
+ − 102 self._inputFastaFileName = inputFastaFileName
+ − 103 self._projectName= os.path.basename(self._inputFastaFileName)
+ − 104 self._projectName = self._projectName.split('.')[0]
+ − 105 self._fF=FastaParser(self._inputFastaFileName)
+ − 106 self._fF.getInfos()
+ − 107 self.genomeSize=self._fF.size
+ − 108 self.nbSeqGenome=self._fF.nbSequences
+ − 109
+ − 110 def setOutputFileName(self,outputFile):
+ − 111 self._outputFileName = outputFile
+ − 112
+ − 113 def setConfigFileName(self, configFileName):
+ − 114 self._configFileName = configFileName
+ − 115 configFileHandle = open(self._configFileName)
+ − 116 config = ConfigParser.ConfigParser()
+ − 117
+ − 118 try :
+ − 119 config.readfp( configFileHandle )
+ − 120 except MissingSectionHeaderError:
+ − 121 self._logAndRaise("Config file " + self._configFileName + " must begin with a section header ")
+ − 122
+ − 123 self.setup_env( config )
+ − 124
+ − 125 def setVerbose(self, verbose):
+ − 126 self._verbosity = verbose
+ − 127
+ − 128 def setup_env(self, config):
+ − 129 os.environ["REPET_HOST"] = config.get("repet_env", "repet_host")
+ − 130 os.environ["REPET_USER"] = config.get("repet_env", "repet_user")
+ − 131 os.environ["REPET_PW"] = config.get("repet_env", "repet_pw")
+ − 132 os.environ["REPET_DB"] = config.get("repet_env", "repet_db")
+ − 133 os.environ["REPET_PORT"] = config.get("repet_env", "repet_port")
+ − 134 os.environ["REPET_JOB_MANAGER"] = config.get("repet_env", "repet_job_manager")
+ − 135
+ − 136 def checkOptions(self):
+ − 137 if self._inputFastaFileName != "":
+ − 138 if not FileUtils.isRessourceExists(self._inputFastaFileName):
+ − 139 self._logAndRaise("Input fasta file does not exist!")
+ − 140 else:
+ − 141 self._logAndRaise("No specified -i option! It is mandatory")
+ − 142
+ − 143 if self._outputFileName =="":
+ − 144 self._outputFileName = os.path.basename(self._inputFastaFileName)+'.splice'
+ − 145
+ − 146 if self._copyType!=1 or self._copyType!=2:
+ − 147 self._logAndRaise("Copy type must be only 1 or 2!")
+ − 148 if self._configFileName != "":
+ − 149 iDb = DbMySql(cfgFileName = self._configFileName)
+ − 150 iDb.close()
+ − 151 else:
+ − 152 self._logAndRaise("No specified config file name!")
+ − 153
+ − 154
+ − 155 def run(self):
+ − 156 LoggerFactory.setLevel(self._log, self._verbosity)
+ − 157 self.checkOptions()
+ − 158
+ − 159 msg = "START SplicerFromAnnotation"
+ − 160 msg += "\n input info file: %s" % self._inputFastaFileName
+ − 161 msg += "\n Copy type is: %s" % self._copyType
+ − 162 msg += "\n identity is: %s" % self._identity
+ − 163 msg += "\n host is: %s" % os.environ["REPET_HOST"]
+ − 164 msg += "\n user is: %s" % os.environ["REPET_USER"]
+ − 165 msg += "\n DB is: %s" % os.environ["REPET_DB"]
+ − 166 msg += "\n port is: %s" % os.environ["REPET_PORT"]
+ − 167 self._log.debug("%s\n" % msg)
+ − 168
+ − 169 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)
+ − 170 os.system(cmd)
+ − 171
+ − 172 cmd="GetSpecificTELibAccordingToAnnotation.py -i %s_chr_allTEs_nr_noSSR_join_path.annotStatsPerTE.tab -t %s_refTEs_seq -v 2" % (self._projectName,self._projectName)
+ − 173 os.system(cmd)
+ − 174
+ − 175 if self._copyType == 1 :
+ − 176 f = open("Splicer_inputFile_chr_allTEs_nr_noSSR_join_path.annotStatsPerTE_FullLengthCopy.txt", "r")
+ − 177 else :
+ − 178 f = open("Splicer_inputFile_chr_allTEs_nr_noSSR_join_path.annotStatsPerTE_FullLengthFrag.txt", "r")
+ − 179
+ − 180 lines=f.readlines()[1:]
+ − 181 if len(lines)>0:
+ − 182 lConsensusHeader_copyType=[i.split('\t',1)[0] for i in lines]
+ − 183 db = DbFactory.createInstance()
+ − 184
+ − 185 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)
+ − 186 db.execute( sql_cmd )
+ − 187
+ − 188 iTPA = TablePathAdaptator(db, "%s_annotationIdentitySup%d_path" % (self._projectName, int(self._identity)))
+ − 189 lAllDistinctPath=[]
+ − 190 for consensusName in lConsensusHeader_copyType:
+ − 191 lDistinctPath = iTPA.getIdListFromSubject(consensusName)
+ − 192 lAllDistinctPath=lAllDistinctPath+lDistinctPath
+ − 193
+ − 194 iTPA = TablePathAdaptator(db,"%s_chr_allTEs_nr_noSSR_join_path" % self._projectName)
+ − 195 sql_cmd = "CREATE TABLE %s_annotationToSplice_path LIKE %s_chr_allTEs_nr_noSSR_join_path" % ( self._projectName, self._projectName )
+ − 196 db.execute( sql_cmd )
+ − 197
+ − 198 for pathId in lAllDistinctPath:
+ − 199 sql_cmd = "INSERT INTO %s_annotationToSplice_path SELECT * FROM %s_chr_allTEs_nr_noSSR_join_path where path =%d" % ( self._projectName, self._projectName, pathId )
+ − 200 db.execute( sql_cmd )
+ − 201 db.close()
+ − 202
+ − 203 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)
+ − 204 os.system(cmd)
+ − 205
+ − 206 else :
+ − 207 msg = "There is no consensus in this copy type.\n"
+ − 208 self._log.info(msg)
+ − 209 f.close()
+ − 210
+ − 211 self._log.info("END SplicerFromAnnotation")
+ − 212 return 0
+ − 213
+ − 214 if __name__ == '__main__':
+ − 215 iGetTELib = SplicerFromAnnotation()
+ − 216 iGetTELib.setAttributesFromCmdLine()
+ − 217 iGetTELib.run()
+ − 218