annotate commons/tools/GameXmlMaker.py @ 18:94ab73e8a190

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#!/usr/bin/env python

##@file GameXmlMaker.py

# 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 glob
import sys
import xml.dom.minidom
from commons.core.utils.RepetOptionParser import RepetOptionParser
from commons.core.utils.FileUtils import FileUtils
from commons.core.seq.BioseqDB import BioseqDB
from commons.core.sql.DbFactory import DbFactory
from commons.core.sql.TablePathAdaptator import TablePathAdaptator
from commons.core.sql.TableSetAdaptator import TableSetAdaptator
from commons.core.sql.TableMapAdaptator import TableMapAdaptator

## GameXmlMaker exports .
#
class GameXmlMaker(object):

    def __init__(self, inFastaName = "", tablesFileName = "", configFileName = "", verbose = 0):
        self._inFastaName = inFastaName
        self._tablesFileName = tablesFileName
        self._configFileName = configFileName
        self._verbose = verbose
        self._gameXMLFileName = ""
    
    def setAttributesFromCmdLine(self):
        description = "GameXmlMaker with -f option <=> step 1 : create gff files (write only the sequence and not the annotation. Only one sequence in each file)\n"
        description += "GameXmlMaker with -t option <=> step 2 : add annotations in each file\n"
        parser = RepetOptionParser(description = description)
        parser.add_option("-f", "--inseq",       dest = "inFastaName",      action = "store",       type = "string", help = "'fasta' file or 'seq' table recording the input sequences (required to generate new '.gamexml' files)", default = "")
        parser.add_option("-t", "--tablesfile",  dest = "tablesFileName",   action = "store",       type = "string", help = "tabulated file of table name to use to update the GameXML files (fields: tier name, format, table name)", default = "")
        parser.add_option("-g", "--gameXML",     dest = "gameXML",          action = "store",       type = "string", help = "gameXML file to update (if not specified, update all gameXML files in directory", default = "")
        parser.add_option("-C", "--config",      dest = "configFileName",   action = "store",       type = "string", help = "configuration file for database connection", default = "")
        parser.add_option("-v", "--verbose",     dest = "verbose",          action = "store",       type = "int",    help = "verbosity level (default=0, else 1 or 2)", default = 0)
        (options, args) = parser.parse_args()
        self._setAttributesFromOptions(options)
        
    def _setAttributesFromOptions(self, options):
        self.setInFastaName(options.inFastaName)
        self.setTablesFileName(options.tablesFileName)
        self.setGameXMLFileName(options.gameXML)
        self.setConfigFileName(options.configFileName)
        self.setVerbose(options.verbose)
        
    def setInFastaName(self, inFastaName):
        self._inFastaName = inFastaName
        
    def setTablesFileName(self, tablesFileName):
        self._tablesFileName = tablesFileName
        
    def setGameXMLFileName(self, gamexmlFileName):   
        self._gameXMLFileName = gamexmlFileName
        
    def setConfigFileName(self, configFileName):
        self._configFileName = configFileName
        
    def setVerbose(self, verbose):
        self._verbose = verbose

    def checkOptions(self):       
        if self._inFastaName == "" and self._tablesFileName == "":
            raise Exception("ERROR: options -f or -t required")
    
        if self._configFileName != "":
            if not FileUtils.isRessourceExists(self._configFileName):
                raise Exception("ERROR: configuration file does not exist!")
            
    def run(self):
        self.checkOptions()
        if self._verbose > 0:
            print "START GameXmlMaker"
            sys.stdout.flush()
        
        if self._inFastaName != "":
            self._createGameXMLFiles()
        
        if self._tablesFileName != "":
            lXMLNewFile = []    
            if self._gameXMLFileName == "":
                lXMLNewFile = glob.glob("*.gamexml")
            else:
                lXMLNewFile.append(self._gameXMLFileName)  
                
            for newGamexmlFile in lXMLNewFile:
                self._updateGameXMLFileFromlTablesFile(newGamexmlFile)
            
        if self._verbose > 0:
            print "END GFF3Maker"
            sys.stdout.flush()
            
    ## Create as many XML files as sequences given in fasta file.
    #
    def _createGameXMLFiles(self):
        if self._verbose > 0:
            print "reading file %s" % self._inFastaName
            sys.stdout.flush()
            
        iBioseqDB = BioseqDB(self._inFastaName)
        
        if self._verbose > 0:
            print "nb of sequences = %i" % iBioseqDB.getSize()
            sys.stdout.flush()
            
        for iBioseq in iBioseqDB.db:
            self._writeGameXMLFileFromBioseq(iBioseq)

    def _writeGameXMLFileFromBioseq(self, iBioseq):
        """
        write new '.gamexml' file with <game> and <seq> tags
        """
        docXML = xml.dom.minidom.getDOMImplementation().createDocument(None, 'game', None)
        root = docXML.documentElement

        seq = docXML.createElement('seq')
        seq.setAttribute('id', iBioseq.getHeader())
        seq.setAttribute('focus', 'true')
        root.appendChild(seq)
        
        seqNameTag = docXML.createElement('name')
        seqNameTag.appendChild(docXML.createTextNode(iBioseq.getHeader()))
        seq.appendChild(seqNameTag)
        
        residuesTag = docXML.createElement('residues')
        residuesTag.appendChild(docXML.createTextNode(iBioseq.getSequence()))
        seq.appendChild(residuesTag)

        mapPos = docXML.createElement('map_position')
        root.appendChild(mapPos)
        
        arm = docXML.createElement('arm')
        arm.appendChild(docXML.createTextNode(iBioseq.getHeader()))
        mapPos.appendChild(arm)
        
        span = docXML.createElement('span')
        mapPos.appendChild(span)
        
        start = docXML.createElement('start')
        start.appendChild(docXML.createTextNode('1'))
        span.appendChild(start)
        
        end = docXML.createElement('end')
        end.appendChild(docXML.createTextNode(str(iBioseq.getLength())))
        span.appendChild(end)
        
        fileName = "%s.gamexml" % iBioseq.getHeader()
        docXML.writexml(open(fileName, "w"))
        
        if self._verbose > 0:
            print "file '%s' written" % fileName
            sys.stdout.flush()


    def _parseResultSpanInfo(self, element, type):
        Qstart = -1
        Qend = -1
        Sstart = -1
        Send = -1
        query = ""
        subject = ""
        identity = 0
        id = ""
        
        if type == "path":
            Qstart = element.getQueryStart()
            Qend = element.getQueryEnd()
            Sstart = element.getSubjectStart()
            Send = element.getSubjectEnd()
            query = element.getQueryName()
            subject = element.getSubjectName()
            identity = element.getIdentity()
            id = element.getIdentifier()
        
        elif type == "set":
            Qstart = element.getStart()
            Qend = element.getEnd()
            query = element.getName()
            subject = element.getName()
            id = element.getId()

        elif type == "map":
            Qstart = element.getStart()
            Qend = element.getEnd()
            query = element.getSeqname()
            subject = element.getName()
            id  = "-1"
            
        return (Qstart,Qend,Sstart,Send,query,subject,identity,id)

    def _addPathSpan(self, docXML, spanInfo, parent):
        Qstart,Qend,Sstart,Send,query,subject,identity,id = spanInfo
        Qstart = str(Qstart)
        Qend = str(Qend)
        Sstart = str(Sstart)
        Send = str(Send)
        identity = str(identity)
        id = str(id)
        
        resultSpan = docXML.createElement('result_span')
        parent.appendChild(resultSpan)
        
        relship1 = docXML.createElement('seq_relationship')
        relship1.setAttribute('type', 'query')
        relship1.setAttribute('seq', query)
        relship2 = docXML.createElement('seq_relationship')
        relship2.setAttribute('type', 'subject')
        relship2.setAttribute('seq', '%s::%s' % (subject, id))
        score = docXML.createElement('score')
        resultSpan.appendChild(relship1)
        resultSpan.appendChild(relship2)
        score.appendChild(docXML.createTextNode(identity))
        resultSpan.appendChild(score)
        sp1 = docXML.createElement('span')
        sp2 = docXML.createElement('span')
        start1 = docXML.createElement('start')
        start1.appendChild(docXML.createTextNode(Qstart))
        start2 = docXML.createElement('start')
        start2.appendChild(docXML.createTextNode(Sstart))
        end1 = docXML.createElement('end')
        end1.appendChild(docXML.createTextNode(Qend))
        end2 = docXML.createElement('end')
        end2.appendChild(docXML.createTextNode(Send))
        relship1.appendChild(sp1)
        sp1.appendChild(start1)
        sp1.appendChild(end1)
        relship2.appendChild(sp2)
        sp2.appendChild(start2)
        sp2.appendChild(end2)

    def _addComputationalAnalysisTags(self, docXML, programName):
        computationalAnalysis = None
        
        lComputationalAnalysis = docXML.getElementsByTagName('computational_analysis')
        for computationalAnalysisTag in lComputationalAnalysis:
            if computationalAnalysisTag.getElementsByTagName("program")[0].nodeValue == programName:
                computationalAnalysis = computationalAnalysisTag
                break
            
        if computationalAnalysis == None :
            computationalAnalysis = docXML.createElement('computational_analysis')
            root = docXML.documentElement
            root.appendChild(computationalAnalysis)
            
            program = docXML.createElement('program')
            program.appendChild(docXML.createTextNode(programName))
            computationalAnalysis.appendChild(program)
            
            db = docXML.createElement('database')
            db.appendChild(docXML.createTextNode('db'))
            computationalAnalysis.appendChild(db)
            
        return computationalAnalysis
        
    def _addResultSetFromPath(self, docXML, iPath, parent):
        computationalAnalysis = parent
        resultSet = docXML.createElement('result_set')
        resultSet.setAttribute('id', str(iPath.getIdentifier())) 
        computationalAnalysis.appendChild(resultSet)
        resultSetName = docXML.createElement('name')
        resultSetName.appendChild(docXML.createTextNode("%s::%s" %(iPath.getSubjectName(),str(iPath.getIdentifier()))))
        resultSet.appendChild(resultSetName)
        return resultSet
    
    def _addResultSetFromSet(self, docXML, iSet, parent):
        computationalAnalysis = parent
        resultSet = docXML.createElement('result_set')
        resultSet.setAttribute('id', str(iSet.getId())) 
        computationalAnalysis.appendChild(resultSet)
        resultSetName = docXML.createElement('name')
        resultSetName.appendChild(docXML.createTextNode("%s::%s" %(iSet.getName(),str(iSet.getId()))))
        resultSet.appendChild(resultSetName)
        return resultSet
    
    def _addResultSetFromMap(self, docXML, iMap, parent):
        computationalAnalysis = parent
        resultSet = docXML.createElement('result_set')
        resultSet.setAttribute('id', "-1") 
        computationalAnalysis.appendChild(resultSet)
        resultSetName = docXML.createElement('name')
        resultSetName.appendChild(docXML.createTextNode("%s::%s" %(iMap.getName(), "-1")))
        resultSet.appendChild(resultSetName)
        return resultSet

    def _updateGameXMLFileFromlTablesFile(self, gameXMLFile):
        docXML = xml.dom.minidom.parse(gameXMLFile) 
        
        f = open(self._tablesFileName, "r")
        line = f.readline()
            
        while line: 
            if not line.startswith("#"):
                list = line.split()
                programName = list[0]
                format = list[1]
                table = list[2]

                gameXMLFileName = os.path.splitext(gameXMLFile)[0]
                computationalAnalysis = self._addComputationalAnalysisTags(docXML,programName)
                if format == "path":    
                    iDB = DbFactory.createInstance(self._configFileName)
                    iTpa = TablePathAdaptator(iDB, table)
                    
                    lPaths = iTpa.getPathListFromQuery(gameXMLFileName)
                    dResultSets = {}

                    for iPath in lPaths:
                        if dResultSets.get(iPath.getIdentifier()) is None:
                            resultSet = self._addResultSetFromPath(docXML, iPath,computationalAnalysis)
                            dResultSets[iPath.getIdentifier()] = resultSet
                        else:
                            resultSet = dResultSets[iPath.getIdentifier()]
                        spanInfo = self._parseResultSpanInfo(iPath, "path")
                        self._addPathSpan(docXML, spanInfo, resultSet)
                        
                if format == "set":
                    iDB = DbFactory.createInstance(self._configFileName)
                    iTsa = TableSetAdaptator(iDB, table)
                    lSet = iTsa.getSetListFromSeqName(gameXMLFileName)
                    
                    dResultSets = {}

                    for iSet in lSet:
                        if dResultSets.get(iSet.getId()) is None:
                            resultSet = self._addResultSetFromSet(docXML, iSet,computationalAnalysis)
                            dResultSets[iSet.getId()] = resultSet
                        else:
                            resultSet = dResultSets[iSet.getId()]
                            
                        spanInfo = self._parseResultSpanInfo(iSet, "set")
                        self._addPathSpan(docXML, spanInfo, resultSet)
                        
                if format == "map":
                    iDB = DbFactory.createInstance(self._configFileName)
                    iTma = TableMapAdaptator(iDB, table)
                    lMap = iTma.getMapListFromChr(gameXMLFileName)
                    dResultSets = {}
                    for iMap in lMap:
                        resultSet = self._addResultSetFromMap(docXML, iMap,computationalAnalysis)
                        spanInfo = self._parseResultSpanInfo(iMap, "map")
                        self._addPathSpan(docXML, spanInfo, resultSet)
                        
            line = f.readline()
            
        outputGameXMLFile = open(gameXMLFile, "w")            
        xmlstr = docXML.toxml()
        outputGameXMLFile.write(xmlstr)
        outputGameXMLFile.close()
            
if __name__ == "__main__":
    iGameXmlMaker = GameXmlMaker()
    iGameXmlMaker.setAttributesFromCmdLine()
    iGameXmlMaker.run()