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GenomeElement.cpp
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GenomeElement.cpp
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/*************************************************************************
Copyright (c) 2014-2016, Valentina BOEVA.
>>> SOURCE LICENSE >>>
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation (www.fsf.org); either version 3 of the
License, or (at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
A copy of the GNU General Public License is available at
http://www.fsf.org/licensing/licenses
>>> END OF LICENSE >>>
*************************************************************************/
#include "GenomeElement.h"
using namespace std ;
GenomeElement::GenomeElement(std::string const& chrName) {
chromosome_ = chrName;
leftRefPos_=0;
rightRefPos_=0;
isInverted_=0;
windowSize_=0;
std::string dnaSeq_="";
InsertedSVs_="";
notNpercentage_=0;
}
GenomeElement::GenomeElement(std::string const& chrName, float notNpercentage, int left, int right, int windowSize, std::string const& dnaSeq) {
chromosome_ = chrName;
leftRefPos_=left;
rightRefPos_=right;
isInverted_=0;
windowSize_=windowSize;
dnaSeq_=dnaSeq;
//gains_.resize(windowSize,0);
//dels_.resize(windowSize,0);
InsertedSVs_="";
notNpercentage_=notNpercentage;
}
GenomeElement::GenomeElement(std::string const& chrName, float notNpercentage, int left, int right, int windowSize, std::string const& dnaSeq, std::vector <int> delPos,std::vector <int> delSizes, std::vector <int> gainPos,std::vector <int> gainSizes) {
chromosome_ = chrName;
leftRefPos_=left;
rightRefPos_=right;
windowSize_=windowSize;
dnaSeq_=dnaSeq;
//gains_.resize(windowSize,0);
//dels_.resize(windowSize,0);
notNpercentage_=notNpercentage;
//for(int i=0;i<delPos.size();i++) {
// dels_[delPos[i]-leftRefPos_]=delSizes[i];
//}
//for(int i=0;i<gainPos.size();i++) {
// dels_[gainPos[i]-leftRefPos_]=gainSizes[i];
//}
InsertedSVs_="";
}
std::string GenomeElement::getChromosome() {
return chromosome_;
}
GenomeElement::~GenomeElement(void)
{
//dels_.clear();
//gains_.clear();
dnaSeq_ = "";
}
int GenomeElement::getWindowSize() {
return windowSize_;
}
bool GenomeElement::isUntouchible() {
if (InsertedSVs_.length()>0 || notNpercentage_ <= 0.5) {
return 1;
}
else return 0;
}
float GenomeElement::getNotNpercentage() {
return notNpercentage_;
}
void GenomeElement::makeSmallInsertion(int insLength) {
int startingPos = rand() % (windowSize_ - FLANKSEQ*2-1)+FLANKSEQ;
ostringstream convert;
convert << "Insertion\t" << insLength<< "\t" << (leftRefPos_+startingPos)<< "\t"<< (leftRefPos_+startingPos+insLength)<< "\t"
<< dnaSeq_.substr(startingPos-FLANKSEQ,FLANKSEQ) << "\t"<< dnaSeq_.substr(startingPos,FLANKSEQ);
InsertedSVs_= convert.str();
string insertedRegion = randomSeq(insLength);
dnaSeq_.insert(startingPos, insertedRegion);
}
void GenomeElement::makeSmallInversion(int invLength){
int startingPos = rand() % (windowSize_ - invLength-1);
string initialRegion = dnaSeq_.substr(startingPos,invLength);
string invertedRegion = complementary(initialRegion);
dnaSeq_.erase(startingPos, invLength);
dnaSeq_.insert(startingPos, invertedRegion);
windowSize_=dnaSeq_.length();
int leftFlankLength=min(FLANKSEQ,invLength);
int rightFlankLength=leftFlankLength;
ostringstream convert;
convert << "Inversion\t" << invLength<< "\t" << (leftRefPos_+startingPos)<< "\t"<< (leftRefPos_+startingPos+invLength)<< "\t"
<< initialRegion.substr(0,leftFlankLength) << "\t"<< initialRegion.substr(invLength-rightFlankLength);
InsertedSVs_= convert.str();
}
void GenomeElement::makeSmallDuplication(int dupLength) {
int startingPos = rand() % (windowSize_ - dupLength-1);
string duplicatedRegion = dnaSeq_.substr(startingPos,dupLength);
dnaSeq_.insert(startingPos, duplicatedRegion);
windowSize_=dnaSeq_.length();
int leftFlankLength=min(FLANKSEQ,dupLength);
int rightFlankLength=leftFlankLength;
ostringstream convert;
convert << "Duplication\t" << dupLength<< "\t" << (leftRefPos_+startingPos)<< "\t"<< (leftRefPos_+startingPos+dupLength)<< "\t" << duplicatedRegion.substr(0,leftFlankLength) << "\t"<< duplicatedRegion.substr(dupLength-rightFlankLength);
InsertedSVs_= convert.str();
}
void GenomeElement::makeSmallDuplicationWithInversion(int dupLength) {
if (windowSize_ - dupLength -1 <=0 ) {
cout << "..Unable to duplicate "<< dupLength <<"bp\n";
return;
}
int startingPos = rand() % (windowSize_ - dupLength -1)+1;
string duplicatedRegion = dnaSeq_.substr(startingPos,dupLength);
string duplicatedRegionInverted = complementary(duplicatedRegion);
int coin = rand()%2;
if (coin) {
dnaSeq_.insert(startingPos, duplicatedRegionInverted);
} else {
dnaSeq_.insert(startingPos+dupLength, duplicatedRegionInverted);
}
windowSize_=dnaSeq_.length();
int leftFlankLength=min(FLANKSEQ,dupLength);
int rightFlankLength=leftFlankLength;
ostringstream convert;
convert << "Duplication\t" << dupLength<< "\t" << (leftRefPos_+startingPos)<< "\t"<< (leftRefPos_+startingPos+dupLength)<< "\t" << duplicatedRegion.substr(0,leftFlankLength) << "\t"<< duplicatedRegion.substr(dupLength-rightFlankLength);
InsertedSVs_= convert.str();
}
void GenomeElement::makeSmallSizeDeletion(int delLength) {
int startingPos = rand() % (windowSize_ - delLength-1);
dnaSeq_.erase(startingPos, delLength);
windowSize_=dnaSeq_.length();
int leftFlankLength=min(FLANKSEQ,startingPos);
int rightFlankLength=min(FLANKSEQ,windowSize_-startingPos-1);
ostringstream convert;
convert << "Del\t" << delLength<< "\t" << (leftRefPos_+startingPos)<< "\t"<< (leftRefPos_+startingPos+delLength)<< "\t" << dnaSeq_.substr(startingPos-leftFlankLength,leftFlankLength) << "\t"<< dnaSeq_.substr(startingPos,rightFlankLength);
InsertedSVs_= convert.str();
}
void GenomeElement::setInsertedSV (std::string const& message) {
InsertedSVs_=message;
}
void GenomeElement::setDNAsequence(std::string const& dnaSeq) {
dnaSeq_=dnaSeq;
windowSize_=dnaSeq.length();
}
int GenomeElement::getRightRefPos() {
if (!isInverted_) return rightRefPos_;
return leftRefPos_;
}
int GenomeElement::getLeftRefPos() {
if (!isInverted_) return leftRefPos_;
return rightRefPos_;
}
std::string GenomeElement::getDnaSeq() {
return dnaSeq_;
}
std::string GenomeElement::getLeftRefSeq(int length) {
if (!isInverted_) return dnaSeq_.substr(windowSize_-FLANKSEQ,FLANKSEQ);
return dnaSeq_.substr(0,FLANKSEQ);
}
std::string GenomeElement::getRightRefSeq(int length) {
if (!isInverted_) return dnaSeq_.substr(0,FLANKSEQ);
return dnaSeq_.substr(windowSize_-FLANKSEQ,FLANKSEQ);
}
void GenomeElement::printDonorFasta(std::ofstream & file, std::ofstream & commentsFile,int ID) {
string toPrint;
if (!isInverted_)
toPrint = dnaSeq_;
else
toPrint = complementary(dnaSeq_);
for (int i = 0; i < windowSize_; i+=FASTASTRINGLEN) {
file << toPrint.substr(i,FASTASTRINGLEN) << "\n";
}
if (InsertedSVs_.length()>0)
commentsFile << ID<< "_" << chromosome_<<"\t"<< InsertedSVs_ << "\n";
}
void GenomeElement::invert() {
isInverted_ = 1;
}
void GenomeElement::uninvert() {
isInverted_ = 0;
}
bool GenomeElement::isInverted () {
return isInverted_;
}