annotate TEisotools-1.0/commons/core/seq/SequenceModificationsCollection.py @ 6:20ec0d14798e draft

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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
#
# This software is governed by the CeCILL license under French law and
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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 time
import shutil
from commons.core.seq.BioseqDB import BioseqDB
from commons.core.seq.SequenceModifications import SequenceModifications
from commons.core.checker.RepetException import RepetException
            
class SequenceModificationsCollection(object):
    
    def __init__(self):
        self._lSeqModif = []
        
    def __str__(self):
        result = ""
        for iSeqModif in self._lSeqModif:
            result += "%s\n" % iSeqModif.__str__()
        return result
        
    def __eq__(self, o):
        if type(o) is type(self):
            self.sort()
            o.sort()
            return self._lSeqModif == o._lSeqModif
        return False
    
    def __ne__(self, o):
        return not self.__eq__(o)
    
    def clear(self):
        self._lSeqModif = []
            
    def add(self, iSeqModif, override = False):
        for seqModif in self._lSeqModif:
            if seqModif.getOriginalHeader() == iSeqModif.getOriginalHeader():
                if override:
                    self._lSeqModif.pop(self._lSeqModif.index(seqModif))
                else:
                    raise RepetException("ERROR: '%s' already in SequenceModificationsCollection" % iSeqModif.getOriginalHeader())
            
        self._lSeqModif.append(iSeqModif)
    
    def get(self, header, mutated = False):
        for iSeqModif in self._lSeqModif:
            if mutated:
                linkToGoodMethod = iSeqModif.getMutatedHeader
            else:
                linkToGoodMethod = iSeqModif.getOriginalHeader
            
            if linkToGoodMethod() == header:
                return iSeqModif
        return None
    
    def getHeadersList(self, mutated = False):
        lHeaders = []
        if mutated:
            for iSeqModif in self._lSeqModif:
                lHeaders.append(iSeqModif.getMutatedHeader())
        else:
            for iSeqModif in self._lSeqModif:
                lHeaders.append(iSeqModif.getOriginalHeader())
        lHeaders.sort(key = lambda header: header.lower())
        return lHeaders
    
    def sort(self):
        self._lSeqModif.sort(key = lambda seqMod: seqMod.getOriginalHeader().lower(), reverse = False)
        
    def writeMutations(self, fileName, outFormat = ""):
        self.sort()
        with open(fileName, "w") as fH:
            if outFormat.lower() in ["gff", "gff3"]:
                fH.write("##gff-version 3\n")
                for iSeqModif in self._lSeqModif:
                    for mutation in iSeqModif.getMutations():
                        pos = mutation[0]
                        old = mutation[1]
                        new = mutation[2]
                        fH.write("%s\tMutateSequence\tSNP\t%i\t%i\t.\t.\t.\tName=SNP_%i;REF=%s;ALT=%s\n" % (iSeqModif.getOriginalHeader(), pos, pos, pos, old, new))
            else:
                fH.write("#Mutations:\n")
                fH.write("seqName\tposition\toldNt\tnewNt\n")
                for iSeqModif in self._lSeqModif:
                    for mutation in iSeqModif.getMutations():
                        fH.write("%s\t%i\t%s\t%s\n" % (iSeqModif.getOriginalHeader(), mutation[0], mutation[1], mutation[2]))
                    
    def writeInsertions(self, fileName, outFormat = ""):
        self.sort()
        with open(fileName, "w") as fH:
            if outFormat.lower() in ["gff", "gff3"]:
                fH.write("##gff-version 3\n")
                for iSeqModif in self._lSeqModif:
                    for iRange in iSeqModif.getInsertions():
                        if iRange.getSeqname() != ".":
                            fH.write("%s\tMutateSequence\tinsertion\t%s\t%s\t.\t.\t.\tName=insertion_%s-%s;insert=%s\n" % (iSeqModif.getOriginalHeader(),  iRange.getStart(), iRange.getEnd(), iRange.getStart(), iRange.getEnd(), iRange.getSeqname()))
                        else:
                            fH.write("%s\tMutateSequence\tinsertion\t%s\t%s\t.\t.\t.\tName=insertion_%s-%s\n" % (iSeqModif.getOriginalHeader(),  iRange.getStart(), iRange.getEnd(), iRange.getStart(), iRange.getEnd()))
            else:
                fH.write("#Insertions:\n")
                fH.write("seqName\tstart\tend\tinsertedSeqName\n")
                for iSeqModif in self._lSeqModif:
                    for iRange in iSeqModif.getInsertions():
                        fH.write("%s\t%i\t%i\t%s\n" % (iSeqModif.getOriginalHeader(), iRange.getStart(), iRange.getEnd(), iRange.getSeqname()))
                          
    def writeDeletions(self, fileName, outFormat = ""):
        self.sort()
        with open(fileName, "w") as fH:
            if outFormat.lower() in ["gff", "gff3"]:
                fH.write("##gff-version 3\n")
                for iSeqModif in self._lSeqModif:
                    for iRange in iSeqModif.getDeletions():
                        fH.write("%s\tMutateSequence\tdeletion\t%s\t%s\t.\t.\t.\tName=deletion_%s-%s\n" % (iSeqModif.getOriginalHeader(),  iRange.getStart(), iRange.getEnd(), iRange.getStart(), iRange.getEnd()))
            else:
                fH.write("#Deletions:\n")
                fH.write("seqName\tstart\tend\n")
                for iSeqModif in self._lSeqModif:
                    for iRange in iSeqModif.getDeletions():
                        fH.write("%s\t%i\t%i\n" % (iSeqModif.getOriginalHeader(), iRange.getStart(), iRange.getEnd()))
                          
    def write(self, mutationsFileName = "", insertionsFileName = "", deletionsFileName = "", outFormat = ""):
        self.sort()
        self.writeMutations(mutationsFileName, outFormat)
        self.writeInsertions(insertionsFileName, outFormat)
        self.writeDeletions(deletionsFileName, outFormat)

    def writeVCF(self, VCFFileName, fastaFileName, software = "MutateSequences"):
        self.sort()
        tmpVCFFileName = "%s.tmp" % VCFFileName
        VCFFH = open(tmpVCFFileName, "w")
        VCFFH.write("##fileformat=VCFv4.1\n")
        VCFFH.write("##fileDate=%s\n" % time.strftime("%Y%m%d"))
        VCFFH.write("##reference=%s\n" % os.path.abspath(fastaFileName))
        VCFFH.write("##INFO=<ID=SVLEN,Number=.,Type=Integer,Description=\"Difference in length between REF and ALT alleles\">\n")
        VCFFH.write("##INFO=<ID=SVTYPE,Number=1,Type=String,Description=\"Type of structural variant\">\n")
        VCFFH.write("##INFO=<ID=ALTSTART,Number=1,Type=Integer,Description=\"ALT start position on query sequence\">\n")
        VCFFH.write("##INFO=<ID=SOFTWARE,Number=1,Type=String,Description=\"Software used to generate this VCF\">\n")
        VCFFH.write("##INFO=<ID=INSERTED,Number=1,Type=String,Description=\"Inserted sequence name\">\n")
        VCFFH.write("#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\n")
        
        iBSDB = BioseqDB(fastaFileName)
        
        for iSeqModif in self._lSeqModif:
            for mutation in iSeqModif.getMutations():
                pos = mutation[0]
                old = mutation[1]
                new = mutation[2]
                VCFFH.write("%s\t%s\t.\t%s\t%s\t.\t.\tAN=2;REF=%s;ALT=%s;SOFTWARE=%s\n" % (iSeqModif.getOriginalHeader(), pos, old, new, old, new, software))
                
            for insRange in iSeqModif.getInsertions():
                if insRange.getStart() != 1:
                    refSeq = iBSDB.fetch(iSeqModif.getOriginalHeader()).getNtFromPosition(insRange.getStart() - 1)
                    altSeq = "."
                    
                    INFO = "SVTYPE=INS;AN=2;SVLEN=%d;SOFTWARE=%s" % (insRange.getEnd() - insRange.getStart() + 1, software)
                    if insRange.getSeqname() != ".":
                        INFO += ";INSERTED=%s" % insRange.getSeqname()
                    VCFLine = "%s\t%d\t.\t%s\t%s\t%s\t%s\t%s\n" % (iSeqModif.getOriginalHeader(), insRange.getStart() - 1, refSeq, altSeq, ".", ".", INFO)
                    
                else:
                    refSeq = iBSDB.fetch(iSeqModif.getOriginalHeader()).getNtFromPosition(insRange.getStart())
                    refSeq = "."
                    altSeq = "."
                    
                    INFO = "SVTYPE=INS;AN=2;SVLEN=%d;SOFTWARE=%s" % (insRange.getEnd() - insRange.getStart() + 1, software)
                    if insRange.getSeqname() != ".":
                        INFO += ";INSERTED=%s" % insRange.getSeqname()
                    VCFLine = "%s\t%d\t.\t%s\t%s\t%s\t%s\t%s\n" % (iSeqModif.getOriginalHeader(), insRange.getStart(), refSeq, altSeq, ".", ".", INFO)
                    
                VCFFH.write(VCFLine)
                
            for delRange in iSeqModif.getDeletions():
                if delRange.getStart() != 1:
                    refSeq = iBSDB.fetch(iSeqModif.getOriginalHeader()).subseq(delRange.getStart() - 1, delRange.getEnd()).getSequence()
                    altSeq = refSeq[0]
                    
                    INFO = "SVTYPE=DEL;AN=2;SVLEN=-%d;SOFTWARE=%s" % (len(refSeq)-1, software)
                    VCFLine = "%s\t%d\t.\t%s\t%s\t%s\t%s\t%s\n" % (iSeqModif.getOriginalHeader(), delRange.getStart() - 1, refSeq, altSeq, ".", ".", INFO)
                    
                else:
                    refSeq = iBSDB.fetch(iSeqModif.getOriginalHeader()).subseq(delRange.getStart(), delRange.getEnd() + 1).getSequence()
                    altSeq = refSeq[-1]
                    altSeq = "."
                    
                    INFO = "SVTYPE=DEL;AN=2;SVLEN=-%d;SOFTWARE=%s" % (len(refSeq)-1, software)
                    VCFLine = "%s\t%d\t.\t%s\t%s\t%s\t%s\t%s\n" % (iSeqModif.getOriginalHeader(), delRange.getStart(), refSeq, altSeq, ".", ".", INFO)
                
                VCFFH.write(VCFLine)
        
        #This command line can sort this VCF file properly. But can't manage to launch it properly through os.system or subprocess...
#        cmd = "(head -n 9 %s && tail -n +10 %s | head -n -1 | sort -f -k1,1 -k2,2n) > %s" % (tmpVCFFileName, tmpVCFFileName, VCFFileName)
        shutil.move(tmpVCFFileName, VCFFileName)
                
    def getCollectionBasedOnMutatedSequence(self):
        transformedSeqModifCollec = SequenceModificationsCollection()
        
        for header in self.getHeadersList():
            currentSeqModif = self.get(header)

            lModifsTuples = [("insertion", iRange) for iRange in currentSeqModif.getInsertions()]
            for iRange in currentSeqModif.getDeletions():
                lModifsTuples.append(("deletion", iRange))
            lModifsTuples.sort(key = lambda modifTuple: modifTuple[1].getStart(), reverse = False)
            
            sumIns = 0
            sumDel = 0
            
            iseqModif = SequenceModifications(currentSeqModif.getMutatedHeader(), currentSeqModif.getOriginalHeader())
            for modifTuple in lModifsTuples:
                varType = modifTuple[0]
                varRange = modifTuple[1]
                
                if varType == "insertion":
                    iseqModif.addDeletion(varRange.getStart() + sumIns - sumDel, varRange.getEnd() + sumIns - sumDel)
                    sumIns += varRange.getLength()
                
                if varType == "deletion":
                    iseqModif.addInsertion(varRange.getStart() + sumIns - sumDel, varRange.getEnd() + sumIns - sumDel)
                    sumDel += varRange.getLength()
                    
            for tSnp in currentSeqModif.getMutations():
                iseqModif.addMutation((tSnp[0], tSnp[2], tSnp[1]))
                
            iseqModif.sort()
            transformedSeqModifCollec.add(iseqModif)
        
        transformedSeqModifCollec.sort()
        
        return transformedSeqModifCollec
    
    def loadSeqModifCollectionFromFiles(self, inInsertionsFileName, inDeletionsFileName, inSNPsFileName, SNPsrate = "0.020000"):
        self.clear()
        
        with open(inInsertionsFileName, "r") as f:
            line = f.readline()
            while line:
                if "seqName" not in line and "#" not in line:
                    splittedLine = line.split()
                    seqname = splittedLine[0]
                    start = int(splittedLine[1])
                    end = int(splittedLine[2])
                    insertedSeqName = splittedLine[3]
                    
                    if self.get(seqname) is None:
                        self.add(SequenceModifications(seqname))
                        self.get(seqname).setMutatedHeader("%s_mutated_%s" % (seqname, SNPsrate))
                    self.get(seqname).addInsertion(start, end, insertedSeqName)
                line = f.readline()
        
        with open(inDeletionsFileName, "r") as f:
            line = f.readline()
            while line:
                if "seqName" not in line and "#" not in line:
                    splittedLine = line.split()
                    seqname = splittedLine[0]
                    start = int(splittedLine[1])
                    end = int(splittedLine[2])
                    
                    if self.get(seqname) is None:
                        self.add(SequenceModifications(seqname))
                        self.get(seqname).setMutatedHeader("%s_mutated_%s" % (seqname, SNPsrate))
                    self.get(seqname).addDeletion(start, end)
                line = f.readline()
        
        with open(inSNPsFileName, "r") as f:
            line = f.readline()
            while line:
                if "seqName" not in line and "#" not in line:
                    splittedLine = line.split()
                    seqname = splittedLine[0]
                    position = int(splittedLine[1])
                    oldNt = splittedLine[2]
                    newNt = splittedLine[3]
                    
                    if self.get(seqname) is None:
                        self.add(SequenceModifications(seqname))
                        self.get(seqname).setMutatedHeader("%s_mutated_%s" % (seqname, SNPsrate))
                    self.get(seqname).addMutation((position, oldNt, newNt))
                line = f.readline()
        
        for header in self.getHeadersList():
            self.get(header).sort()
        self.sort()