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

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#!/usr/bin/env python

# Copyright INRA (Institut National de la Recherche Agronomique)
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# http://urgi.versailles.inra.fr
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import re
import os
from commons.core.LoggerFactory import LoggerFactory
from commons.core.utils.RepetOptionParser import RepetOptionParser
from commons.core.checker.ConfigChecker import ConfigRules, ConfigChecker
import subprocess
from commons.core.seq.AlignedBioseqDB import AlignedBioseqDB
from commons.core.sql.TableSeqAdaptator import TableSeqAdaptator
from commons.core.coord.PathUtils import PathUtils
from commons.core.coord.SetUtils import SetUtils
from commons.core.sql.TablePathAdaptator import TablePathAdaptator
from commons.core.coord.Set import Set
from commons.core.sql.DbFactory import DbFactory

## Align a TE on genome according to annotation

LOG_DEPTH = "repet.tools"

class AlignTEOnGenomeAccordingToAnnotation(object):
    
    def __init__(self, pathTableName = "", queryTableName = "", subjectTableName = "", mergeSamePathId = False, outTableName = "", matchPenality=10, mism=8, gapo=16, gape=4, gapl=20, configFileName = "", doClean = False, verbosity = 0):
        self._pathTableName = pathTableName
        self._queryTableName = queryTableName
        self._subjectTableName = subjectTableName
        self._mergeSamePathId = mergeSamePathId
        self.setOutTableName(outTableName)
        self._matchPenality = matchPenality
        self._mismatch = mism
        self._gapOpening = gapo
        self._gapExtend = gape
        self._gapLength = gapl
        self._configFileName = configFileName
        self._doClean = doClean
        self._verbosity = verbosity
        self._iDb = None
        self._log = LoggerFactory.createLogger("%s.%s" % (LOG_DEPTH, self.__class__.__name__), self._verbosity)
        
    def setAttributesFromCmdLine(self):
        description = "Align a TE on genome according to annotation."
        epilog = "\nExample 1: launch without verbosity and keep temporary files.\n"
        epilog += "\t$ python AlignTEOnGenomeAccordingToAnnotation.py -p DmelChr4_chr_allTEs_nr_noSSR_join_path -q DmelChr4_chr_seq -s DmelChr4_refTEs_seq -v 0"
        epilog += "\n"
        parser = RepetOptionParser(description = description, epilog = epilog)
        parser.add_option("-p", "--path",       dest = "pathTableName",     action = "store",       type = "string", help = "path table name [compulsory] [format: path]", default = "")
        parser.add_option("-q", "--query",      dest = "queryTableName",    action = "store",       type = "string", help = "query table name [compulsory] [format: seq]", default = "")
        parser.add_option("-s", "--subject",    dest = "subjectTableName",  action = "store",       type = "string", help = "subject table name [compulsory] [format: seq]", default = "")
        parser.add_option("-m", "--merge",      dest = "mergeSamePathId",   action = "store_true",                   help = "merge joined matchs [optional] [default: False]", default = False)
        parser.add_option("-o", "--out",        dest = "outTableName",      action = "store",       type = "string", help = "output table name [default: <pathTableName>_align]", default = "")
        #TODO: add options for : matchPenality=10, mism=8, gapo=16, gape=4, gapl=20
        parser.add_option("-C", "--config",     dest = "configFileName",    action = "store",       type = "string", help = "configuration file name (e.g. TEannot.cfg)", default = "")
        #NOTE: doClean unused
#        parser.add_option("-c", "--clean",      dest = "doClean",           action = "store_true",                   help = "clean temporary files [optional] [default: False]", default = False)
        parser.add_option("-v", "--verbosity",  dest = "verbosity",         action = "store",       type = "int",    help = "verbosity [optional] [default: 1]", default = 1)
        options = parser.parse_args()[0]
        self._setAttributesFromOptions(options)
        
    def _setAttributesFromOptions(self, options):
        self.setPathTableName(options.pathTableName)
        self.setQueryTableName(options.queryTableName)
        self.setSubjectTableName(options.subjectTableName)
        self.setMergeSamePathId(options.mergeSamePathId)
        self.setOutTableName(options.outTableName)
        self.setConfigFileName(options.configFileName)
#        self.setDoClean(options.doClean)
        self.setVerbosity(options.verbosity)

    def _checkConfig(self):       
        iConfigRules = ConfigRules()
        iConfigRules.addRuleSection(section="", mandatory=True)
        iConfigRules.addRuleOption(section="", option ="fasta_name", mandatory=True, type="string")
        iConfigRules.addRuleOption(section="", option ="clean", mandatory=True, type="bool")
        iConfigChecker = ConfigChecker(self._configFileName, iConfigRules)
        iConfig = iConfigChecker.getConfig()
        self._setAttributesFromConfig(iConfig)
        
    def _setAttributesFromConfig(self, iConfig):
        self.setOutTableName(self._outTableName)
        self.setDoClean(iConfig.get("", "clean"))
        
    def setPathTableName(self, pathTableName):
        self._pathTableName = pathTableName
        
    def setQueryTableName(self, queryTableName):
        self._queryTableName = queryTableName
        
    def setSubjectTableName(self, subjectTableName):
        self._subjectTableName = subjectTableName
        
    def setMergeSamePathId(self, mergeSamePathId):
        self._mergeSamePathId = mergeSamePathId
        
    def setOutTableName(self, outTableName):
        if outTableName == "":
            self._outTableName = "%s_align" % self._pathTableName
        else:
            self._outTableName = outTableName
        
    def setConfigFileName(self, configFileName):
        self._configFileName = configFileName
        
    def setDoClean(self, doClean):
        self._doClean = doClean
        
    def setVerbosity(self, verbosity):
        self._verbosity = verbosity
        
    def setDbInstance(self, iDb):
        self._iDb = iDb
        
    def _checkOptions(self):
        if self._pathTableName == "" or not self._iDb.doesTableExist(self._pathTableName):
            self._logAndRaise("ERROR: Missing path table")
        if self._queryTableName == "" or not self._iDb.doesTableExist(self._queryTableName):
            self._logAndRaise("ERROR: Missing query table")
        if self._subjectTableName == "" or not self._iDb.doesTableExist(self._subjectTableName):
            self._logAndRaise("ERROR: Missing subject table")
            
    def _logAndRaise(self, errorMsg):
        self._log.error(errorMsg)
        raise Exception(errorMsg)

    def alignBioseqWithNWalign(self, iBioseq1, iBioseq2):
        fastaFileName1 = "seqtoalign1.tmp"
        iBioseq1.save(fastaFileName1)
        fastaFileName2 = "seqtoalign2.tmp"
        iBioseq2.save(fastaFileName2)
        alignBioseqDBFileName = "aligned.tmp"
        cmd = "NWalign"
        cmd += " %s" % fastaFileName1
        cmd += " %s" % fastaFileName2
        cmd += " -m %s" % self._matchPenality
        cmd += " -d %s" % self._mismatch
        cmd += " -g %s" % self._gapOpening
        cmd += " -e %s" % self._gapExtend
        cmd += " -l %s" % self._gapLength
        cmd += " -D"
        cmd += " -o %s" % alignBioseqDBFileName
        process = subprocess.Popen(cmd, shell = True)
        self._log.debug("Running : %s" % cmd)
        process.communicate()
        if process.returncode != 0:
            self._logAndRaise("ERROR when launching '%s'" % cmd)
        iAlignedBioseqDB = AlignedBioseqDB()
        iAlignedBioseqDB.load(alignBioseqDBFileName)
        os.remove(fastaFileName1)
        os.remove(fastaFileName2)
        os.remove(alignBioseqDBFileName)
        return iAlignedBioseqDB
    
    def alignSeqAccordingToPathAndBuildAlignedSeqTable(self):
        if self._iDb.doesTableExist(self._outTableName):
            self._logAndRaise("ERROR: out table %s already exists" % self._outTableName)
            
        #TODO: create alignedSeq table in DbMySql...
        sqlCmd="CREATE TABLE %s (path int unsigned, query_aligned_seq longtext, subject_aligned_seq longtext, score int unsigned, identity float unsigned)" % self._outTableName
        self._iDb.execute(sqlCmd)

        iQueryTSA = TableSeqAdaptator(self._iDb, self._queryTableName)
        iSubjectTSA = TableSeqAdaptator(self._iDb, self._subjectTableName)
        iTPA = TablePathAdaptator(self._iDb, self._pathTableName)
        
        if self._mergeSamePathId:
            lPathId = iTPA.getIdList()
            pathNb = len(lPathId)
            count = 0
            for pathNum in lPathId:
                self._log.debug(count,"/",pathNb,"=>path",pathNum,"...")
                lPaths = iTPA.getPathListFromId(pathNum)
                #TODO: getSetListFromQueries() call getSubjectAsSetOfQuery() => "reverse complement" the query (coordinates are inversed, so getBioseq() will take the reverse-comp.) : is it correct ?
                lQuerySets = PathUtils.getSetListFromQueries(lPaths)
                #NOTE: merge sets if overlap
                lQueryMergedSets = SetUtils.mergeSetsInList(lQuerySets)
                #TODO: getBioseqFromSetList() build a sequence that does not exist : is it correct ?
                iQueryBioseq = iQueryTSA.getBioseqFromSetList(lQueryMergedSets)
                lSubjectSets = PathUtils.getSetListFromSubjects(lPaths)
                #TODO: no merge for subjects : is it correct ? matcher allow overlap on query and not on subject ?
                iSubjectBioseq = iSubjectTSA.getBioseqFromSetList(lSubjectSets)
                iAlignedBioseqDB = self.alignBioseqWithNWalign(iQueryBioseq, iSubjectBioseq)
                self._insertAlignedBioseqDBWithScoreAndIdentityInTable(pathNum, iAlignedBioseqDB)
        else:
            lPathId = iTPA.getIdList()
            pathNb = len(lPathId)
            count = 0
            for pathNum in lPathId:
                self._log.debug(count,"/",pathNb,"=>path",pathNum,"...")
                lPaths = iTPA.getPathListFromId(pathNum)
                queryName = lPaths[0].getQueryName()
                subjectName = lPaths[0].getSubjectName()
                lQueryStart = []
                lQueryEnd = []
                lSubjectStart = []
                lSubjectEnd = []
                isReversed = not lPaths[0].isSubjectOnDirectStrand()
                for iPath in lPaths:
                    lQueryStart.append(iPath.getQueryStart())
                    lQueryEnd.append(iPath.getQueryEnd())
                    lSubjectStart.append(iPath.getSubjectStart())
                    lSubjectEnd.append(iPath.getSubjectEnd())
                queryStart = min(lQueryStart)
                queryEnd = max(lQueryEnd)
                if isReversed:
                    subjectStart = max(lSubjectStart)
                    subjectEnd = min(lSubjectEnd)
                else:
                    subjectStart = min(lSubjectStart)
                    subjectEnd = max(lSubjectEnd)
                lQuerySets = [Set(pathNum,subjectName, queryName,queryStart,queryEnd)]
                lSubjectSets = [Set(pathNum,queryName, subjectName,subjectStart,subjectEnd)]
                
                iQueryBioseq = iQueryTSA.getBioseqFromSetList(lQuerySets)
                iSubjectBioseq = iSubjectTSA.getBioseqFromSetList(lSubjectSets)
                iAlignedBioseqDB = self.alignBioseqWithNWalign(iQueryBioseq, iSubjectBioseq)
                self._insertAlignedBioseqDBWithScoreAndIdentityInTable(pathNum, iAlignedBioseqDB)
                    
    def run(self):
        LoggerFactory.setLevel(self._log, self._verbosity)
        if self._configFileName:
            self._checkConfig()
        self._iDb = DbFactory.createInstance()
        self._checkOptions()
        self._log.info("START AlignTEOnGenomeAccordingToAnnotation")
        self._log.debug("path table name: %s" % self._pathTableName)
        self._log.debug("query table name: %s" % self._queryTableName)
        self._log.debug("subject table name: %s" % self._subjectTableName)
        self.alignSeqAccordingToPathAndBuildAlignedSeqTable()
        self._iDb.close()
        self._log.info("END AlignTEOnGenomeAccordingToAnnotation")

    def _insertAlignedBioseqDBWithScoreAndIdentityInTable(self, pathNum, iAlignedBioseqDB):
        scoreWithEndLine = re.split("Score=", iAlignedBioseqDB.db[0].header)[1]
        score = int(scoreWithEndLine.split()[0])
        
        identity = re.split("Identity=", scoreWithEndLine)[1]
        if identity == "nan":
            identity = "0.0"
        identity = float(identity)*100.0
        
        #TODO: create TableAlignedSeqAdaptator (to use insert...)
        sqlCmd = 'INSERT INTO %s VALUES (%d,"%s","%s", %d,%f);' % (self._outTableName, pathNum, iAlignedBioseqDB.db[0].sequence, iAlignedBioseqDB.db[1].sequence, score, identity)
        self._iDb.execute(sqlCmd)
        
        self._log.debug("header:", iAlignedBioseqDB.db[0].header)
        self._log.debug("path", pathNum, "Score=", score, "Identity=", identity, "ok")
        self._log.debug(iAlignedBioseqDB.db[0].sequence[:80])
        self._log.debug(iAlignedBioseqDB.db[1].sequence[:80])

if __name__ == "__main__":
    iLaunch = AlignTEOnGenomeAccordingToAnnotation()
    iLaunch.setAttributesFromCmdLine()
    iLaunch.run()