annotate commons/tools/GetSpecificTELibAccordingToAnnotation.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
from commons.core.sql.DbMySql import DbMySql
from commons.core.utils.RepetOptionParser import RepetOptionParser
from commons.core.utils.FileUtils import FileUtils
from commons.core.sql.TableSeqAdaptator import TableSeqAdaptator
from commons.core.LoggerFactory import LoggerFactory

LOG_DEPTH = "repet.tools"  
LOG_FORMAT = "%(message)s"
#TODO: use configuration file

## 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 GetSpecificTELibAccordingToAnnotation(object):
    
    def __init__(self, inInfoFileName = "", tableName = "", verbose = 0):
        self._inInfoFileName = inInfoFileName
        self._tableName = tableName
        self._verbose = verbose
        self._log = LoggerFactory.createLogger("%s.%s" % (LOG_DEPTH, self.__class__.__name__), self._verbose, LOG_FORMAT)
    
    def setAttributesFromCmdLine(self):
        desc = "Splits a GiveInfoTEannot \"statsPerTE.txt\" file in 3 subfiles containing consensus which have at least one copy, one full length fragment or one full length copy. "
        desc += "A TEs library is built according to each category. Connection to the database parameters are retrieved from the environment"
        
        examples = "\nExample : with a project called \"MyTEannotAnalysis\":\n"
        examples += "\t$ python GetSpecificTELibAccordingToAnnotation.py -i MyTEannotAnalysis_chr_allTEs_nr_noSSR_join_path_statsPerTE.txt -t MyTEannotAnalysis_refTEs_seq"
        examples += "\n\t"
        examples += "\n\n"
        
        parser = RepetOptionParser(description = desc, epilog = examples)
        parser.add_option("-i", "--file",     dest = "inInfoFileName",  action = "store", type = "string", help = "input file (mandatory) = output file from GiveInfoTEannot.py (e.g. <project_name>_chr_allTEs_nr_noSSR_join_path_statsPerTE.txt)",  default = "")
        parser.add_option("-t", "--table",    dest = "tableName",       action = "store", type = "string", help = "table name of TEs sequences (mandatory, seq format, e.g. <project_name>_refTEs_seq)", default = "")
        parser.add_option("-v", "--verbose",  dest = "verbose",         action = "store", type = "int",    help = "verbosity level (default=0, else 1)", default = 0)
        (options, args) = parser.parse_args()
        self._setAttributesFromOptions(options)
        
    def _setAttributesFromOptions(self, options):
        self.setInInfoFileName(options.inInfoFileName)
        self.setTableName(options.tableName)
        self.setVerbose(options.verbose)
        
    def setTableName(self, tableName):
        self._tableName = tableName
        
    def setInInfoFileName(self, inInfoFileName):
        self._inInfoFileName = inInfoFileName
        
    def setVerbose(self, verbose):
        self._verbose = verbose
   
    def checkOptions(self):
        if self._inInfoFileName != "":
            if not FileUtils.isRessourceExists(self._inClassifFileName):
                self._logAndRaise("ERROR: Input GiveInfoTEannot.txt output file does not exist!")
        else:
            self._logAndRaise("ERROR: No specified -i option!")
        
        if self._tableName != "":
            iDb = DbMySql()
            if not iDb.doesTableExist(self._tableName):
                self._logAndRaise("ERROR: table does not exist!")
            iDb.close()
        else:
            self._logAndRaise("ERROR: No specified -t option!")

    def _logAndRaise(self, errorMsg):
        self._log.error(errorMsg)
        raise Exception(errorMsg)

    def writeFastaFileFromGiveInfoTEAnnot(self, fileName):
        fFileHandler = open(fileName,"r")
        lineHeader = fFileHandler.readline()
        line = fFileHandler.readline()
        lConsensusName = []
        while line:         
            lConsensusName.append(line.split()[0])
            line = fFileHandler.readline()

        fFileHandler.close()
        iDb = DbMySql()
        iTSA = TableSeqAdaptator(iDb, self._tableName)
        outPutFileName = "%s.fa" % os.path.splitext(fileName)[0]
        iTSA.saveAccessionsListInFastaFile(lConsensusName, outPutFileName)
        iDb.close()
                      
    def run(self):
        LoggerFactory.setLevel(self._log, self._verbose)

        outInfoFileNameFullCopy = "%s_FullLengthCopy.txt" % os.path.splitext(os.path.basename(self._inInfoFileName))[0]
        outInfoFileNameCopy = "%s_OneCopyAndMore.txt" % os.path.splitext(os.path.basename(self._inInfoFileName))[0]
        outInfoFileNameFullFrag = "%s_FullLengthFrag.txt" % os.path.splitext(os.path.basename(self._inInfoFileName))[0]
        
        outInfoFileFullCopy = open(outInfoFileNameFullCopy, "w")
        outInfoFileCopy = open(outInfoFileNameCopy, "w")
        outInfoFileFullFrag = open(outInfoFileNameFullFrag, "w")
            
        self._log.info("START GetSpecificTELibAccordingToAnnotation\n input info file: %s" % self._inInfoFileName)
        
        inFileFh = open(self._inInfoFileName, "r")
        line = inFileFh.readline()
        lHeaders = line.split()
        if "fullLgthCopies" not in lHeaders:
            self._logAndRaise("ERROR: No headers in %s!" % self._inInfoFileName )
        
        outInfoFileFullCopy.write(line)
        outInfoFileCopy.write(line)
        outInfoFileFullFrag.write(line)
            
        line = inFileFh.readline()
        while line:
            dTokens = {}
            for index, token in enumerate(line.split()):
                dTokens[lHeaders[index]] = token
                    
            if int(dTokens["fullLgthCopies"]) > 0:
                outInfoFileFullCopy.write(line)
            if int(dTokens["copies"]) > 0:
                outInfoFileCopy.write(line)
            if int(dTokens["fullLgthFrags"]) > 0:
                outInfoFileFullFrag.write(line)
            line = inFileFh.readline()
                
        inFileFh.close()
        outInfoFileFullCopy.close()
        outInfoFileCopy.close()
        outInfoFileFullFrag.close()
        
        self.writeFastaFileFromGiveInfoTEAnnot(outInfoFileNameFullCopy)
        self.writeFastaFileFromGiveInfoTEAnnot(outInfoFileNameCopy)
        self.writeFastaFileFromGiveInfoTEAnnot(outInfoFileNameFullFrag)
        
        self._log.info("END GetSpecificTELibAccordingToAnnotation\n" )
            
        return 0

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