#include "chimera.h"
+//***************************************************************************************************************
+//this is a vertical soft filter
+string Chimera::createFilter(vector<Sequence*> seqs, float t) {
+ try {
+ filterString = "";
+ int threshold = int (t * seqs.size());
+//cout << "threshhold = " << threshold << endl;
+
+ vector<int> gaps; gaps.resize(seqs[0]->getAligned().length(), 0);
+ vector<int> a; a.resize(seqs[0]->getAligned().length(), 0);
+ vector<int> t; t.resize(seqs[0]->getAligned().length(), 0);
+ vector<int> g; g.resize(seqs[0]->getAligned().length(), 0);
+ vector<int> c; c.resize(seqs[0]->getAligned().length(), 0);
+
+ filterString = (string(seqs[0]->getAligned().length(), '1'));
+
+ //for each sequence
+ for (int i = 0; i < seqs.size(); i++) {
+
+ if (m->control_pressed) { return filterString; }
+
+ string seqAligned = seqs[i]->getAligned();
+
+ for (int j = 0; j < seqAligned.length(); j++) {
+ //if this spot is a gap
+ if ((seqAligned[j] == '-') || (seqAligned[j] == '.')) { gaps[j]++; }
+ else if (toupper(seqAligned[j]) == 'A') { a[j]++; }
+ else if (toupper(seqAligned[j]) == 'T') { t[j]++; }
+ else if (toupper(seqAligned[j]) == 'G') { g[j]++; }
+ else if (toupper(seqAligned[j]) == 'C') { c[j]++; }
+ }
+ }
+
+ //zero out spot where all sequences have blanks
+ //zero out spot where all sequences have blanks
+ int numColRemoved = 0;
+ for(int i = 0;i < seqs[0]->getAligned().length(); i++){
+
+ if (m->control_pressed) { return filterString; }
+
+ if(gaps[i] == seqs.size()) { filterString[i] = '0'; numColRemoved++; }
+
+ else if (((a[i] < threshold) && (t[i] < threshold) && (g[i] < threshold) && (c[i] < threshold))) { filterString[i] = '0'; numColRemoved++; }
+ //cout << "a = " << a[i] << " t = " << t[i] << " g = " << g[i] << " c = " << c[i] << endl;
+ }
+
+ m->mothurOut("Filter removed " + toString(numColRemoved) + " columns."); m->mothurOutEndLine();
+ return filterString;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Chimera", "createFilter");
+ exit(1);
+ }
+}
+//***************************************************************************************************************
+map<int, int> Chimera::runFilter(Sequence* seq) {
+ try {
+ map<int, int> maskMap;
+ string seqAligned = seq->getAligned();
+ string newAligned = "";
+ int count = 0;
+
+ for (int j = 0; j < seqAligned.length(); j++) {
+ //if this spot is a gap
+ if (filterString[j] == '1') {
+ newAligned += seqAligned[j];
+ maskMap[count] = j;
+ count++;
+ }
+ }
+
+ seq->setAligned(newAligned);
+
+ return maskMap;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Chimera", "runFilter");
+ exit(1);
+ }
+}
//***************************************************************************************************************
vector<Sequence*> Chimera::readSeqs(string file) {
try {
+
+ m->mothurOut("Reading sequences... "); cout.flush();
ifstream in;
openInputFile(file, in);
+
vector<Sequence*> container;
+ int count = 0;
+ length = 0;
+ unaligned = false;
//read in seqs and store in vector
while(!in.eof()){
- Sequence* current = new Sequence(in);
- container.push_back(current);
- gobble(in);
+ if (m->control_pressed) { return container; }
+
+ Sequence* current = new Sequence(in); gobble(in);
+
+ if (count == 0) { length = current->getAligned().length(); count++; } //gets first seqs length
+ else if (length != current->getAligned().length()) { //seqs are unaligned
+ unaligned = true;
+ }
+
+ if (current->getName() != "") { container.push_back(current); }
}
in.close();
+ m->mothurOut("Done."); m->mothurOutEndLine();
+
return container;
}
catch(exception& e) {
- errorOut(e, "Chimera", "readSeqs");
+ m->errorOut(e, "Chimera", "readSeqs");
exit(1);
}
}
}
}
catch(exception& e) {
- errorOut(e, "Chimera", "setMask");
+ m->errorOut(e, "Chimera", "setMask");
exit(1);
}
}
//***************************************************************************************************************
+
+vector< vector<float> > Chimera::readQuantiles() {
+ try {
+
+ ifstream in;
+ openInputFile(quanfile, in);
+
+ vector< vector<float> > quan;
+ vector <float> temp; temp.resize(6, 0);
+
+ //to fill 0
+ quan.push_back(temp);
+
+ int num; float ten, twentyfive, fifty, seventyfive, ninetyfive, ninetynine;
+
+ while(!in.eof()){
+
+ in >> num >> ten >> twentyfive >> fifty >> seventyfive >> ninetyfive >> ninetynine;
+
+ temp.clear();
+
+ temp.push_back(ten);
+ temp.push_back(twentyfive);
+ temp.push_back(fifty);
+ temp.push_back(seventyfive);
+ temp.push_back(ninetyfive);
+ temp.push_back(ninetynine);
+
+ quan.push_back(temp);
+
+ gobble(in);
+ }
+
+ in.close();
+ return quan;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Chimera", "readQuantiles");
+ exit(1);
+ }
+}
+//***************************************************************************************************************
+Sequence* Chimera::getSequence(string name) {
+ try{
+ Sequence* temp;
+
+ //look through templateSeqs til you find it
+ int spot = -1;
+ for (int i = 0; i < templateSeqs.size(); i++) {
+ if (name == templateSeqs[i]->getName()) {
+ spot = i;
+ break;
+ }
+ }
+
+ if(spot == -1) { m->mothurOut("Error: Could not find sequence."); m->mothurOutEndLine(); return NULL; }
+
+ temp = new Sequence(templateSeqs[spot]->getName(), templateSeqs[spot]->getAligned());
+
+ return temp;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Chimera", "getSequence");
+ exit(1);
+ }
+}
+//***************************************************************************************************************
+
+
+
+
projects / mothur.git / blobdiff