*/
#include "chimeraseqscommand.h"
-#include "eachgapdist.h"
-#include "ignoregaps.h"
-#include "onegapdist.h"
+#include "bellerophon.h"
+#include "pintail.h"
//***************************************************************************************************************
else {
//valid paramters for this command
- string Array[] = {"fasta", "filter", "correction", "processors", "method", "window", "increment" };
+ string Array[] = {"fasta", "filter", "correction", "processors", "method", "window", "increment", "template" };
vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
OptionParser parser(option);
if (fastafile == "not open") { abort = true; }
else if (fastafile == "not found") { fastafile = ""; mothurOut("fasta is a required parameter for the chimera.seqs command."); mothurOutEndLine(); abort = true; }
+ templatefile = validParameter.validFile(parameters, "template", true);
+ if (templatefile == "not open") { abort = true; }
+ else if (templatefile == "not found") { templatefile = ""; }
+
+
string temp;
temp = validParameter.validFile(parameters, "filter", false); if (temp == "not found") { temp = "T"; }
filter = isTrue(temp);
temp = validParameter.validFile(parameters, "increment", false); if (temp == "not found") { temp = "10"; }
convert(temp, increment);
- method = validParameter.validFile(parameters, "method", false); if (method == "not found") { method = "bellerophon"; }
+ method = validParameter.validFile(parameters, "method", false); if (method == "not found") { method = "pintail"; }
+
+ if ((method == "pintail") && (templatefile == "")) { mothurOut("You must provide a template file with the pintail method."); mothurOutEndLine(); abort = true; }
- if (method != "bellerophon") { mothurOut(method + " is not a valid method."); mothurOutEndLine(); abort = true; }
}
}
mothurOut("The chimera.seqs command reads a fastafile and creates a sorted priority score list of potentially chimeric sequences (ideally, the sequences should already be aligned).\n");
mothurOut("The chimera.seqs command parameters are fasta, filter, correction, processors and method. fasta is required.\n");
mothurOut("The filter parameter allows you to specify if you would like to apply a 50% soft filter. The default is false. \n");
- mothurOut("The correction parameter allows you to ..... The default is true. \n");
+ mothurOut("The correction parameter allows you to put more emphasis on the distance between highly similar sequences and less emphasis on the differences between remote homologs. The default is true. \n");
mothurOut("The processors parameter allows you to specify how many processors you would like to use. The default is 1. \n");
- mothurOut("The method parameter allows you to specify the method for finding chimeric sequences. The default is bellerophon. \n");
+ mothurOut("The method parameter allows you to specify the method for finding chimeric sequences. The default is pintail. \n");
mothurOut("The chimera.seqs command should be in the following format: \n");
mothurOut("chimera.seqs(fasta=yourFastaFile, filter=yourFilter, correction=yourCorrection, processors=yourProcessors, method=bellerophon) \n");
mothurOut("Example: chimera.seqs(fasta=AD.align, filter=True, correction=true, processors=2, method=yourMethod) \n");
exit(1);
}
}
-//********************************************************************************************************************
-//sorts highest score to lowest
-inline bool comparePref(Preference left, Preference right){
- return (left.score[0] > right.score[0]);
-}
//***************************************************************************************************************
if (abort == true) { return 0; }
+ if (method == "bellerophon") { chimera = new Bellerophon(fastafile); }
+ else if (method == "pintail") { chimera = new Pintail(fastafile); }
+ else { mothurOut("Not a valid method."); mothurOutEndLine(); return 0; }
- //do soft filter
- if (filter) {
- string optionString = "fasta=" + fastafile + ", soft=50, vertical=F";
- filterSeqs = new FilterSeqsCommand(optionString);
- filterSeqs->execute();
- delete filterSeqs;
-
- //reset fastafile to filtered file
- fastafile = getRootName(fastafile) + "filter.fasta";
- }
-
- distCalculator = new eachGapDist();
-
- //read in sequences
- readSeqs();
+ //set user options
+ chimera->setFilter(filter);
+ chimera->setCorrection(correction);
+ chimera->setProcessors(processors);
+ chimera->setWindow(window);
+ chimera->setIncrement(increment);
+ chimera->setTemplate(templatefile);
- int numSeqs = seqs.size();
-
- if (numSeqs == 0) { mothurOut("Error in reading you sequences."); mothurOutEndLine(); return 0; }
-
- //set default window to 25% of sequence length
- string seq0 = seqs[0].getAligned();
- if (window == 0) { window = seq0.length() / 4; }
- else if (window > (seq0.length() / 2)) {
- mothurOut("Your sequence length is = " + toString(seq0.length()) + ". You have selected a window size greater than the length of half your aligned sequence. I will run it with a window size of " + toString((seq0.length() / 2))); mothurOutEndLine();
- window = (seq0.length() / 2);
- }
-
- if (increment > (seqs[0].getAlignLength() - (2*window))) {
- if (increment != 10) {
-
- mothurOut("You have selected a increment that is too large. I will use the default."); mothurOutEndLine();
- increment = 10;
- if (increment > (seqs[0].getAlignLength() - (2*window))) { increment = 0; }
-
- }else{ increment = 0; }
- }
-cout << "increment = " << increment << endl;
- if (increment == 0) { iters = 1; }
- else { iters = ((seqs[0].getAlignLength() - (2*window)) / increment); }
+ //find chimeras
+ chimera->getChimeras();
- //initialize pref
- pref.resize(numSeqs);
-
- for (int i = 0; i < numSeqs; i++ ) {
- pref[i].leftParent.resize(2); pref[i].rightParent.resize(2); pref[i].score.resize(2); pref[i].closestLeft.resize(2); pref[i].closestRight.resize(3);
- pref[i].name = seqs[i].getName();
- pref[i].score[0] = 0.0; pref[i].score[1] = 0.0;
- pref[i].closestLeft[0] = 100000.0; pref[i].closestLeft[1] = 100000.0;
- pref[i].closestRight[0] = 100000.0; pref[i].closestRight[1] = 100000.0;
- }
-
- int midpoint = window;
- int count = 0;
- while (count < iters) {
-
- //create 2 vectors of sequences, 1 for left side and one for right side
- vector<Sequence> left; vector<Sequence> right;
-
- for (int i = 0; i < seqs.size(); i++) {
-//cout << "whole = " << seqs[i].getAligned() << endl;
- //save left side
- string seqLeft = seqs[i].getAligned().substr(midpoint-window, window);
- Sequence tempLeft;
- tempLeft.setName(seqs[i].getName());
- tempLeft.setAligned(seqLeft);
- left.push_back(tempLeft);
-//cout << "left = " << tempLeft.getAligned() << endl;
- //save right side
- string seqRight = seqs[i].getAligned().substr(midpoint, window);
- Sequence tempRight;
- tempRight.setName(seqs[i].getName());
- tempRight.setAligned(seqRight);
- right.push_back(tempRight);
-//cout << "right = " << seqRight << endl;
- }
-
- //adjust midpoint by increment
- midpoint += increment;
-
-
- //this should be parallelized
- //perference = sum of (| distance of my left to sequence j's left - distance of my right to sequence j's right | )
- //create a matrix containing the distance from left to left and right to right
- //calculate distances
- SparseMatrix* SparseLeft = new SparseMatrix();
- SparseMatrix* SparseRight = new SparseMatrix();
-
- createSparseMatrix(0, left.size(), SparseLeft, left);
- createSparseMatrix(0, right.size(), SparseRight, right);
-
- vector<SeqMap> distMapRight;
- vector<SeqMap> distMapLeft;
-
- // Create a data structure to quickly access the distance information.
- // It consists of a vector of distance maps, where each map contains
- // all distances of a certain sequence. Vector and maps are accessed
- // via the index of a sequence in the distance matrix
- distMapRight = vector<SeqMap>(numSeqs);
- distMapLeft = vector<SeqMap>(numSeqs);
- //cout << "left" << endl << endl;
- for (MatData currentCell = SparseLeft->begin(); currentCell != SparseLeft->end(); currentCell++) {
- distMapLeft[currentCell->row][currentCell->column] = currentCell->dist;
- //cout << " i = " << currentCell->row << " j = " << currentCell->column << " dist = " << currentCell->dist << endl;
- }
- //cout << "right" << endl << endl;
- for (MatData currentCell = SparseRight->begin(); currentCell != SparseRight->end(); currentCell++) {
- distMapRight[currentCell->row][currentCell->column] = currentCell->dist;
- //cout << " i = " << currentCell->row << " j = " << currentCell->column << " dist = " << currentCell->dist << endl;
- }
-
- delete SparseLeft;
- delete SparseRight;
-
-
- //fill preference structure
- generatePreferences(distMapLeft, distMapRight, midpoint);
-
- count++;
-
- }
-
- delete distCalculator;
-
- //rank preference score to eachother
- float dme = 0.0;
- float expectedPercent = 1 / (float) (pref.size());
-
- for (int i = 0; i < pref.size(); i++) { dme += pref[i].score[0]; }
-
- for (int i = 0; i < pref.size(); i++) {
-
- //gives the actual percentage of the dme this seq adds
- pref[i].score[0] = pref[i].score[0] / dme;
-
- //how much higher or lower is this than expected
- pref[i].score[0] = pref[i].score[0] / expectedPercent;
-
- }
-
-
- //sort Preferences highest to lowest
- sort(pref.begin(), pref.end(), comparePref);
-
- string outputFileName = getRootName(fastafile) + "chimeras";
+ string outputFileName = getRootName(fastafile) + method + ".chimeras";
ofstream out;
openOutputFile(outputFileName, out);
- int above1 = 0;
- out << "Name\tScore\tLeft\tRight\t" << endl;
- //output prefenence structure to .chimeras file
- for (int i = 0; i < pref.size(); i++) {
- out << pref[i].name << '\t' << pref[i].score[0] << '\t' << pref[i].leftParent[0] << '\t' << pref[i].rightParent[0] << endl;
-
- //calc # of seqs with preference above 1.0
- if (pref[i].score[0] > 1.0) {
- above1++;
- mothurOut(pref[i].name + " is a suspected chimera at breakpoint " + toString(pref[i].midpoint)); mothurOutEndLine();
- mothurOut("It's score is " + toString(pref[i].score[0]) + " with suspected left parent " + pref[i].leftParent[0] + " and right parent " + pref[i].rightParent[0]); mothurOutEndLine();
- }
-
-
- }
+ //print results
+ chimera->print(out);
- //output results to screen
- mothurOutEndLine();
- mothurOut("Sequence with preference score above 1.0: " + toString(above1)); mothurOutEndLine();
- int spot;
- spot = pref.size()-1;
- mothurOut("Minimum:\t" + toString(pref[spot].score[0])); mothurOutEndLine();
- spot = pref.size() * 0.975;
- mothurOut("2.5%-tile:\t" + toString(pref[spot].score[0])); mothurOutEndLine();
- spot = pref.size() * 0.75;
- mothurOut("25%-tile:\t" + toString(pref[spot].score[0])); mothurOutEndLine();
- spot = pref.size() * 0.50;
- mothurOut("Median: \t" + toString(pref[spot].score[0])); mothurOutEndLine();
- spot = pref.size() * 0.25;
- mothurOut("75%-tile:\t" + toString(pref[spot].score[0])); mothurOutEndLine();
- spot = pref.size() * 0.025;
- mothurOut("97.5%-tile:\t" + toString(pref[spot].score[0])); mothurOutEndLine();
- spot = 0;
- mothurOut("Maximum:\t" + toString(pref[spot].score[0])); mothurOutEndLine();
+ out.close();
- return 0;
- }
- catch(exception& e) {
- errorOut(e, "ChimeraSeqsCommand", "execute");
- exit(1);
- }
-}
-
-//***************************************************************************************************************
-void ChimeraSeqsCommand::readSeqs(){
- try {
- ifstream inFASTA;
- openInputFile(fastafile, inFASTA);
+ delete chimera;
- //read in seqs and store in vector
- while(!inFASTA.eof()){
- Sequence current(inFASTA);
-
- if (current.getAligned() == "") { current.setAligned(current.getUnaligned()); }
-
- seqs.push_back(current);
-
- gobble(inFASTA);
- }
- inFASTA.close();
-
- }
- catch(exception& e) {
- errorOut(e, "ChimeraSeqsCommand", "readSeqs");
- exit(1);
- }
-}
-
-/***************************************************************************************************************/
-int ChimeraSeqsCommand::createSparseMatrix(int startSeq, int endSeq, SparseMatrix* sparse, vector<Sequence> s){
- try {
-
- for(int i=startSeq; i<endSeq; i++){
-
- for(int j=0;j<i;j++){
-
- distCalculator->calcDist(s[i], s[j]);
- float dist = distCalculator->getDist();
-
- PCell temp(i, j, dist);
- sparse->addCell(temp);
-
- }
- }
-
-
- return 1;
- }
- catch(exception& e) {
- errorOut(e, "ChimeraSeqsCommand", "createSparseMatrix");
- exit(1);
- }
-}
-/***************************************************************************************************************/
-void ChimeraSeqsCommand::generatePreferences(vector<SeqMap> left, vector<SeqMap> right, int mid){
- try {
-
- float dme = 0.0;
- SeqMap::iterator itR;
- SeqMap::iterator itL;
-
- //initialize pref[i]
- for (int i = 0; i < pref.size(); i++) {
- pref[i].score[1] = 0.0;
- pref[i].closestLeft[1] = 100000.0;
- pref[i].closestRight[1] = 100000.0;
- pref[i].leftParent[1] = "";
- pref[i].rightParent[1] = "";
- }
-
- for (int i = 0; i < left.size(); i++) {
-
- SeqMap currentLeft = left[i]; //example i = 3; currentLeft is a map of 0 to the distance of sequence 3 to sequence 0,
- // 1 to the distance of sequence 3 to sequence 1,
- // 2 to the distance of sequence 3 to sequence 2.
- SeqMap currentRight = right[i]; // same as left but with distances on the right side.
-
- for (int j = 0; j < i; j++) {
-
- itL = currentLeft.find(j);
- itR = currentRight.find(j);
-//cout << " i = " << i << " j = " << j << " distLeft = " << itL->second << endl;
-//cout << " i = " << i << " j = " << j << " distright = " << itR->second << endl;
-
- //if you can find this entry update the preferences
- if ((itL != currentLeft.end()) && (itR != currentRight.end())) {
-
- if (!correction) {
- pref[i].score[1] += abs((itL->second - itR->second));
- pref[j].score[1] += abs((itL->second - itR->second));
-//cout << "left " << i << " " << j << " = " << itL->second << " right " << i << " " << j << " = " << itR->second << endl;
-//cout << "abs = " << abs((itL->second - itR->second)) << endl;
-//cout << i << " score = " << pref[i].score[1] << endl;
-//cout << j << " score = " << pref[j].score[1] << endl;
- }else {
- pref[i].score[1] += abs((sqrt(itL->second) - sqrt(itR->second)));
- pref[j].score[1] += abs((sqrt(itL->second) - sqrt(itR->second)));
-//cout << "left " << i << " " << j << " = " << itL->second << " right " << i << " " << j << " = " << itR->second << endl;
-//cout << "abs = " << abs((sqrt(itL->second) - sqrt(itR->second))) << endl;
-//cout << i << " score = " << pref[i].score[1] << endl;
-//cout << j << " score = " << pref[j].score[1] << endl;
- }
-//cout << "pref[" << i << "].closestLeft[1] = " << pref[i].closestLeft[1] << " parent = " << pref[i].leftParent[1] << endl;
- //are you the closest left sequence
- if (itL->second < pref[i].closestLeft[1]) {
-
- pref[i].closestLeft[1] = itL->second;
- pref[i].leftParent[1] = seqs[j].getName();
-//cout << "updating closest left to " << pref[i].leftParent[1] << endl;
- }
-//cout << "pref[" << j << "].closestLeft[1] = " << pref[j].closestLeft[1] << " parent = " << pref[j].leftParent[1] << endl;
- if (itL->second < pref[j].closestLeft[1]) {
- pref[j].closestLeft[1] = itL->second;
- pref[j].leftParent[1] = seqs[i].getName();
-//cout << "updating closest left to " << pref[j].leftParent[1] << endl;
- }
-
- //are you the closest right sequence
- if (itR->second < pref[i].closestRight[1]) {
- pref[i].closestRight[1] = itR->second;
- pref[i].rightParent[1] = seqs[j].getName();
- }
- if (itR->second < pref[j].closestRight[1]) {
- pref[j].closestRight[1] = itR->second;
- pref[j].rightParent[1] = seqs[i].getName();
- }
-
- }
- }
-
- }
-
-
-
- //calculate the dme
-
- int count0 = 0;
- for (int i = 0; i < pref.size(); i++) { dme += pref[i].score[1]; if (pref[i].score[1] == 0.0) { count0++; } }
-
- float expectedPercent = 1 / (float) (pref.size() - count0);
-//cout << endl << "dme = " << dme << endl;
- //recalculate prefernences based on dme
- for (int i = 0; i < pref.size(); i++) {
-//cout << "unadjusted pref " << i << " = " << pref[i].score[1] << endl;
- // gives the actual percentage of the dme this seq adds
- pref[i].score[1] = pref[i].score[1] / dme;
-
- //how much higher or lower is this than expected
- pref[i].score[1] = pref[i].score[1] / expectedPercent;
-
- //pref[i].score[1] = dme / (dme - 2 * pref[i].score[1]);
-
- //so a non chimeric sequence would be around 1, and a chimeric would be signifigantly higher.
-//cout << "adjusted pref " << i << " = " << pref[i].score[1] << endl;
- }
+ return 0;
- //is this score bigger then the last score
- for (int i = 0; i < pref.size(); i++) {
-
- //update biggest score
- if (pref[i].score[1] > pref[i].score[0]) {
- pref[i].score[0] = pref[i].score[1];
- pref[i].leftParent[0] = pref[i].leftParent[1];
- pref[i].rightParent[0] = pref[i].rightParent[1];
- pref[i].closestLeft[0] = pref[i].closestLeft[1];
- pref[i].closestRight[0] = pref[i].closestRight[1];
- pref[i].midpoint = mid;
- }
-
- }
-
}
catch(exception& e) {
- errorOut(e, "ChimeraSeqsCommand", "generatePreferences");
+ errorOut(e, "ChimeraSeqsCommand", "execute");
exit(1);
}
}
-/**************************************************************************************************/
/**************************************************************************************************/
projects / mothur.git / blobdiff