X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bellerophon.cpp;h=54dfb9b67ecf5e764e3c159dffcc47d6fd7004dc;hb=17a6a53298a907c005fa93fb82af9e533adcda09;hp=a60a838f0139e741c92db8c1b5edafbdb158ca02;hpb=a5afca18544555fba2d9c3670ad1f8574916b0a0;p=mothur.git diff --git a/bellerophon.cpp b/bellerophon.cpp index a60a838..54dfb9b 100644 --- a/bellerophon.cpp +++ b/bellerophon.cpp @@ -15,55 +15,62 @@ //*************************************************************************************************************** -Bellerophon::Bellerophon(string name) { +Bellerophon::Bellerophon(string name, string o) { try { fastafile = name; + outputDir = o; } catch(exception& e) { - errorOut(e, "Bellerophon", "Bellerophon"); + m->errorOut(e, "Bellerophon", "Bellerophon"); exit(1); } } //*************************************************************************************************************** -void Bellerophon::print(ostream& out) { +int Bellerophon::print(ostream& out, ostream& outAcc) { try { int above1 = 0; out << "Name\tScore\tLeft\tRight\t" << endl; //output prefenence structure to .chimeras file for (int i = 0; i < pref.size(); i++) { + + if (m->control_pressed) { return 0; } + out << pref[i].name << '\t' << setprecision(3) << 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(); + outAcc << pref[i].name << endl; + m->mothurOut(pref[i].name + " is a suspected chimera at breakpoint " + toString(pref[i].midpoint)); m->mothurOutEndLine(); + m->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]); m->mothurOutEndLine(); } } //output results to screen - mothurOutEndLine(); - mothurOut("Sequence with preference score above 1.0: " + toString(above1)); mothurOutEndLine(); + m->mothurOutEndLine(); + m->mothurOut("Sequence with preference score above 1.0: " + toString(above1)); m->mothurOutEndLine(); int spot; spot = pref.size()-1; - mothurOut("Minimum:\t" + toString(pref[spot].score[0])); mothurOutEndLine(); + m->mothurOut("Minimum:\t" + toString(pref[spot].score[0])); m->mothurOutEndLine(); spot = pref.size() * 0.975; - mothurOut("2.5%-tile:\t" + toString(pref[spot].score[0])); mothurOutEndLine(); + m->mothurOut("2.5%-tile:\t" + toString(pref[spot].score[0])); m->mothurOutEndLine(); spot = pref.size() * 0.75; - mothurOut("25%-tile:\t" + toString(pref[spot].score[0])); mothurOutEndLine(); + m->mothurOut("25%-tile:\t" + toString(pref[spot].score[0])); m->mothurOutEndLine(); spot = pref.size() * 0.50; - mothurOut("Median: \t" + toString(pref[spot].score[0])); mothurOutEndLine(); + m->mothurOut("Median: \t" + toString(pref[spot].score[0])); m->mothurOutEndLine(); spot = pref.size() * 0.25; - mothurOut("75%-tile:\t" + toString(pref[spot].score[0])); mothurOutEndLine(); + m->mothurOut("75%-tile:\t" + toString(pref[spot].score[0])); m->mothurOutEndLine(); spot = pref.size() * 0.025; - mothurOut("97.5%-tile:\t" + toString(pref[spot].score[0])); mothurOutEndLine(); + m->mothurOut("97.5%-tile:\t" + toString(pref[spot].score[0])); m->mothurOutEndLine(); spot = 0; - mothurOut("Maximum:\t" + toString(pref[spot].score[0])); mothurOutEndLine(); + m->mothurOut("Maximum:\t" + toString(pref[spot].score[0])); m->mothurOutEndLine(); + + return 1; } catch(exception& e) { - errorOut(e, "Bellerophon", "print"); + m->errorOut(e, "Bellerophon", "print"); exit(1); } } @@ -81,12 +88,18 @@ int Bellerophon::getChimeras() { //do soft filter if (filter) { string optionString = "fasta=" + fastafile + ", soft=50"; + if (outputDir != "") { optionString += ", outputdir=" + outputDir; } + filterSeqs = new FilterSeqsCommand(optionString); filterSeqs->execute(); delete filterSeqs; + if (m->control_pressed) { return 0; } + //reset fastafile to filtered file - fastafile = getRootName(fastafile) + "filter.fasta"; + if (outputDir == "") { fastafile = getRootName(fastafile) + "filter.fasta"; } + else { fastafile = outputDir + getRootName(getSimpleName(fastafile)) + "filter.fasta"; } + } distCalculator = new eachGapDist(); @@ -94,24 +107,26 @@ int Bellerophon::getChimeras() { //read in sequences seqs = readSeqs(fastafile); - if (unaligned) { mothurOut("Your sequences need to be aligned when you use the bellerophon method."); mothurOutEndLine(); return 1; } + if (m->control_pressed) { return 0; } + + if (unaligned) { m->mothurOut("Your sequences need to be aligned when you use the bellerophon method."); m->mothurOutEndLine(); return 1; } int numSeqs = seqs.size(); - if (numSeqs == 0) { mothurOut("Error in reading you sequences."); mothurOutEndLine(); exit(1); } + if (numSeqs == 0) { m->mothurOut("Error in reading you sequences."); m->mothurOutEndLine(); exit(1); } //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(); + m->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))); m->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(); + m->mothurOut("You have selected a increment that is too large. I will use the default."); m->mothurOutEndLine(); increment = 10; if (increment > (seqs[0]->getAlignLength() - (2*window))) { increment = 0; } @@ -136,10 +151,15 @@ int Bellerophon::getChimeras() { int count = 0; while (count < iters) { + if (m->control_pressed) { return 0; } + //create 2 vectors of sequences, 1 for left side and one for right side vector left; vector right; for (int i = 0; i < seqs.size(); i++) { + + if (m->control_pressed) { return 0; } + //cout << "midpoint = " << midpoint << "\twindow = " << window << endl; //cout << "whole = " << seqs[i]->getAligned().length() << endl; //save left side @@ -170,8 +190,14 @@ int Bellerophon::getChimeras() { SparseMatrix* SparseRight = new SparseMatrix(); createSparseMatrix(0, left.size(), SparseLeft, left); + + if (m->control_pressed) { delete SparseLeft; delete SparseRight; return 0; } + createSparseMatrix(0, right.size(), SparseRight, right); + if (m->control_pressed) { delete SparseLeft; delete SparseRight; return 0; } + + left.clear(); right.clear(); vector distMapRight; vector distMapLeft; @@ -185,11 +211,13 @@ int Bellerophon::getChimeras() { //cout << "left" << endl << endl; for (MatData currentCell = SparseLeft->begin(); currentCell != SparseLeft->end(); currentCell++) { distMapLeft[currentCell->row][currentCell->column] = currentCell->dist; + if (m->control_pressed) { delete SparseLeft; delete SparseRight; return 0; } //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; + if (m->control_pressed) { delete SparseLeft; delete SparseRight; return 0; } //cout << " i = " << currentCell->row << " j = " << currentCell->column << " dist = " << currentCell->dist << endl; } @@ -224,11 +252,13 @@ int Bellerophon::getChimeras() { //sort Preferences highest to lowest sort(pref.begin(), pref.end(), comparePref); + for (int i = 0; i < seqs.size(); i++) { delete seqs[i]; } seqs.clear(); + return 0; - + } catch(exception& e) { - errorOut(e, "Bellerophon", "getChimeras"); + m->errorOut(e, "Bellerophon", "getChimeras"); exit(1); } } @@ -240,6 +270,8 @@ int Bellerophon::createSparseMatrix(int startSeq, int endSeq, SparseMatrix* spar for(int i=startSeq; icontrol_pressed) { return 0; } distCalculator->calcDist(s[i], s[j]); float dist = distCalculator->getDist(); @@ -253,12 +285,12 @@ int Bellerophon::createSparseMatrix(int startSeq, int endSeq, SparseMatrix* spar return 1; } catch(exception& e) { - errorOut(e, "Bellerophon", "createSparseMatrix"); + m->errorOut(e, "Bellerophon", "createSparseMatrix"); exit(1); } } /***************************************************************************************************************/ -void Bellerophon::generatePreferences(vector left, vector right, int mid){ +int Bellerophon::generatePreferences(vector left, vector right, int mid){ try { float dme = 0.0; @@ -282,6 +314,8 @@ void Bellerophon::generatePreferences(vector left, vector right, SeqMap currentRight = right[i]; // same as left but with distances on the right side. for (int j = 0; j < i; j++) { + + if (m->control_pressed) { return 0; } itL = currentLeft.find(j); itR = currentRight.find(j); @@ -346,6 +380,8 @@ void Bellerophon::generatePreferences(vector left, vector right, //cout << endl << "dme = " << dme << endl; //recalculate prefernences based on dme for (int i = 0; i < pref.size(); i++) { + + if (m->control_pressed) { return 0; } //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; @@ -362,6 +398,8 @@ void Bellerophon::generatePreferences(vector left, vector right, //is this score bigger then the last score for (int i = 0; i < pref.size(); i++) { + if (m->control_pressed) { return 0; } + //update biggest score if (pref[i].score[1] > pref[i].score[0]) { pref[i].score[0] = pref[i].score[1]; @@ -373,10 +411,12 @@ void Bellerophon::generatePreferences(vector left, vector right, } } + + return 1; } catch(exception& e) { - errorOut(e, "Bellerophon", "generatePreferences"); + m->errorOut(e, "Bellerophon", "generatePreferences"); exit(1); } }