--- a/TEisotools-1.1.a/commons/core/seq/SequenceModificationsCollection.py	Thu Jul 21 07:36:44 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,312 +0,0 @@
-#!/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
-# 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 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()
\ No newline at end of file