view 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
# 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
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# same conditions as regards security. 
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# knowledge of the CeCILL license and that you accept its terms.

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()