--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/tools/SplicerFromAnnotation.py	Mon Apr 29 03:20:15 2013 -0400
@@ -0,0 +1,218 @@
+#!/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() 
+    
\ No newline at end of file