view commons/tools/GetSpecificTELibAccordingToAnnotation.py @ 31:0ab839023fe4

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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
#
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# modify and/ or redistribute the software under the terms of the CeCILL
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#
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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()