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#include "seqeuncesFilter.h"
#include "nucleotide.h"
seqeuncesFilter::~seqeuncesFilter()
{}
void seqeuncesFilter::removeSequencesWithStop(sequenceContainer & sc, codon & alpha)
{
//going over al seqeunces
for (int i = 0; i < sc.numberOfSeqs();++i) {
int id = sc.placeToId(i);
//going over all sequence len
for (int j = 0; j < sc.seqLen();++j) {
//remove seqeunces with stop data not in the middle
if ((j != sc.seqLen()-1) && (alpha.isStopCodon(sc[id][j])))
{
LOG(4, <<"removing sequence = "<<sc.name(id)<<" : STOP codon in the middle of the reading frame!"<<endl);
sc.remove(id);
i--;
break;
}
}
}
}
void seqeuncesFilter::removeSequencesWithMissingData(sequenceContainer & sc)
{
//going over al seqeunces
for (int i = 0; i < sc.numberOfSeqs(); ++i)
{
//going over all sequence len
for (int j = 0; j < sc.seqLen(); ++j)
{
int id = sc.placeToId(i);
//remove seqeunces with unkonwn data
if (sc[id][j] == sc.getAlphabet()->unknown())
{
sc.remove(id);
i--;
break;
}
}
}
}
void seqeuncesFilter::removeSequencesWithMissingDataAndStop(sequenceContainer & sc, codon & alpha)
{
//going over al seqeunces
for (int i = 0; i < sc.numberOfSeqs(); ++i) {
int id = sc.placeToId(i);
//going over all sequence len
for (int j = 0; j < sc.seqLen();++j) {
//remove seqeunces with stop data not in the middle or missing data
if ((j != sc.seqLen()-1) && (sc[id][j] == sc.getAlphabet()->unknown() || alpha.isStopCodon(sc[id][j])))
{
sc.remove(id);
i--;
break;
}
}
}
}
void seqeuncesFilter::removeSequencesNotStartWithATG(sequenceContainer & sc, codon & alpha)
{
amino aa;
//going over al seqeunces
for (int i = 0; i < sc.numberOfSeqs();++i) {
int id = sc.placeToId(i);
int in_first = codonUtility::aaOf(sc[id][0], alpha);
if (in_first != aa.fromChar('M'))
{
LOG(4, <<"removing sequence = "<<sc.name(id)<<" : not starting with ATG!"<<endl);
sc.remove(id);
i--;
}
}
}
void seqeuncesFilter::removeSequencesNotStartWithInitiationCodons(sequenceContainer & sc,codon & alpha)
{
for (int i = 0; i < sc.numberOfSeqs();++i) {
int id = sc.placeToId(i);
int in_first = sc[id][0];
if(!alpha.isInitiationCodon(in_first)){
LOG(4, <<"removing sequence = "<<sc.name(id)<<" : not starting with initiation codon!"<<endl);
sc.remove(id);
i--;
}
}
}
void seqeuncesFilter::removeSequencesWithGapsAccordingRef(sequenceContainer & sc,int precent,string refName)
{
int refID = sc.getId(refName);
Vint seqToRemove;
//going over all position in reference seqeunce
for (int pos = 0; pos < sc[refID].seqLen(); pos++)
{
//check if the pos is gap
if (sc[refID][pos] == sc.getAlphabet()->gap())
//going over all other seqeunces to compute the precents of gaps
{
cout<<pos<<" ";
seqToRemove.clear();
MDOUBLE numOfSeqWithOutGap = 0;
cout<<sc.numberOfSeqs()<<" ";
for (int i = 0; i < sc.numberOfSeqs(); i++)
{
int id = sc.placeToId(i);
if (sc[id][pos] != sc.getAlphabet()->gap())
{
numOfSeqWithOutGap++;
seqToRemove.push_back(id);
}
}
cout<<seqToRemove.size()<<endl;
if ((100 * ((sc.numberOfSeqs() - numOfSeqWithOutGap)/sc.numberOfSeqs())) > precent)
{
for (int j = 0; j < seqToRemove.size(); j++){
sc.remove(seqToRemove[j]);
}
}
}
}
}
//removes all sequences that are shorter than lowerBound and longer than upperBound
void seqeuncesFilter::removeShortAndLongSequences(sequenceContainer & sc, int lowerBound, int upperBound)
{
const alphabet* pAlph = sc.getAlphabet();
//going over al seqeunces
for (int seq = 0; seq < sc.numberOfSeqs(); ++seq)
{
int id = sc.placeToId(seq);
//checking sequence length
int seqLen = sc[id].seqLenSpecific();
if ((seqLen < lowerBound) || (seqLen > upperBound))
{
cerr<<"removing sequence: "<<sc.name(id)<<" sequence Length = "<<seqLen<<endl;
sc.remove(id);
--seq;
}
}
}
//removes all sequences that have inserts in which most other sequences (> percent) have gaps.
//in case refName is given: check only positions in which the reference sequence has gaps.
//The remained sequences are stored in newSc.
void seqeuncesFilter::removeSequencesWithInserts(sequenceContainer & newSc,const sequenceContainer & sc,int percent, const string& refName, string outFileName)
{
if (outFileName.empty())
outFileName = "removedSequences" + double2string(percent) + ".txt";
ofstream outF(outFileName.c_str());
int refID;
if (!refName.empty())
refID = sc.getId(refName);
Vint seqToAdd(sc.numberOfSeqs(), 1);//1== add the sequence to newSc. 0 = don't add.
//going over all position (in reference seqeunce if given)
for (int pos = 0; pos < sc.seqLen(); ++pos)
{
if (!refName.empty())
{ //don't remove this position if it isn't gap in the refSeqeunce
if (sc[refID][pos] != sc.getAlphabet()->gap())
continue;
}
Vint seqToRemove; //holds the ids of sequences without gaps in the current positions
//going over all seqeunces to compute the percent of gaps
MDOUBLE numOfSeqWithGap = 0;
for (int i = 0; i < sc.numberOfSeqs(); i++)
{
int id = sc.placeToId(i);
if (sc[id][pos] != sc.getAlphabet()->gap())
{
seqToRemove.push_back(id);
}
else
numOfSeqWithGap++;
}
//outF<<"POS "<<pos<<" seqWithGaps = "<<numOfSeqWithGap<<" seqWithoutGaps = "<<sc.numberOfSeqs() - numOfSeqWithGap<<endl;
//in case most sequences have gaps in that position: remove the sequences that have inserts at that position
MDOUBLE percentGapsinPos = 100.0 * (numOfSeqWithGap / sc.numberOfSeqs());
if (percentGapsinPos > percent)
{
//outF<<"removing sequences: ";
for (int j = 0; j < seqToRemove.size(); j++)
{
int x = seqToRemove[j];
seqToAdd[seqToRemove[j]] = 0;
outF<<sc.name(sc.placeToId(x))<<endl;
}
outF<<endl;
}
}
for (int i=0; i<seqToAdd.size(); i++)
{
if (seqToAdd[i] == 1)
{
int id = sc.placeToId(i);
newSc.add(sc[id]);
}
}
outF.close();
}
void seqeuncesFilter::removeSequencesNotDivisableBy3(sequenceContainer & sc)
{
nucleotide nucAlph;
for (int i = 0; i < sc.numberOfSeqs();++i)
{
int id = sc.placeToId(i);
int seqL = sc[id].seqLen();
if ((seqL % 3) != 0)
{
LOG(4, <<"removing sequence = "<<sc.name(id)<<" : nucleotide sequence length is not divisable by 3!"<<endl);
sc.remove(id);
--i;
}
}
}
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