5 * Created by westcott on 9/25/09.
6 * Copyright 2009 Pschloss Lab. All rights reserved.
10 #include "chimeraslayer.h"
11 #include "chimerarealigner.h"
13 #include "blastdb.hpp"
15 //***************************************************************************************************************
16 ChimeraSlayer::ChimeraSlayer(string file, string temp, bool trim, string mode, int k, int ms, int mms, int win, float div,
17 int minsim, int mincov, int minbs, int minsnp, int par, int it, int inc, int numw, bool r) : Chimera() {
20 templateFileName = temp; templateSeqs = readSeqs(temp);
38 decalc = new DeCalculator();
43 m->errorOut(e, "ChimeraSlayer", "ChimeraSlayer");
47 //***************************************************************************************************************
48 ChimeraSlayer::ChimeraSlayer(string file, string temp, bool trim, map<string, int>& prior, string mode, int k, int ms, int mms, int win, float div,
49 int minsim, int mincov, int minbs, int minsnp, int par, int it, int inc, int numw, bool r) : Chimera() {
51 fastafile = file; templateSeqs = readSeqs(fastafile);
52 templateFileName = temp;
71 decalc = new DeCalculator();
73 createFilter(templateSeqs, 0.0); //just removed columns where all seqs have a gap
75 if (searchMethod == "distance") {
76 createFilter(templateSeqs, 0.0); //just removed columns where all seqs have a gap
78 //run filter on template copying templateSeqs into filteredTemplateSeqs
79 for (int i = 0; i < templateSeqs.size(); i++) {
80 if (m->control_pressed) { break; }
82 Sequence* newSeq = new Sequence(templateSeqs[i]->getName(), templateSeqs[i]->getAligned());
84 filteredTemplateSeqs.push_back(newSeq);
89 m->errorOut(e, "ChimeraSlayer", "ChimeraSlayer");
93 //***************************************************************************************************************
94 int ChimeraSlayer::doPrep() {
96 if (searchMethod == "distance") {
97 //read in all query seqs
98 vector<Sequence*> tempQuerySeqs = readSeqs(fastafile);
100 vector<Sequence*> temp = templateSeqs;
101 for (int i = 0; i < tempQuerySeqs.size(); i++) { temp.push_back(tempQuerySeqs[i]); }
103 createFilter(temp, 0.0); //just removed columns where all seqs have a gap
105 for (int i = 0; i < tempQuerySeqs.size(); i++) { delete tempQuerySeqs[i]; }
107 if (m->control_pressed) { return 0; }
109 //run filter on template copying templateSeqs into filteredTemplateSeqs
110 for (int i = 0; i < templateSeqs.size(); i++) {
111 if (m->control_pressed) { return 0; }
113 Sequence* newSeq = new Sequence(templateSeqs[i]->getName(), templateSeqs[i]->getAligned());
115 filteredTemplateSeqs.push_back(newSeq);
118 string kmerDBNameLeft;
119 string kmerDBNameRight;
121 //generate the kmerdb to pass to maligner
122 if (searchMethod == "kmer") {
123 string templatePath = m->hasPath(templateFileName);
124 string rightTemplateFileName = templatePath + "right." + m->getRootName(m->getSimpleName(templateFileName));
125 databaseRight = new KmerDB(rightTemplateFileName, kmerSize);
127 string leftTemplateFileName = templatePath + "left." + m->getRootName(m->getSimpleName(templateFileName));
128 databaseLeft = new KmerDB(leftTemplateFileName, kmerSize);
130 for (int i = 0; i < templateSeqs.size(); i++) {
132 if (m->control_pressed) { return 0; }
134 string leftFrag = templateSeqs[i]->getUnaligned();
135 leftFrag = leftFrag.substr(0, int(leftFrag.length() * 0.33));
137 Sequence leftTemp(templateSeqs[i]->getName(), leftFrag);
138 databaseLeft->addSequence(leftTemp);
140 databaseLeft->generateDB();
141 databaseLeft->setNumSeqs(templateSeqs.size());
143 for (int i = 0; i < templateSeqs.size(); i++) {
144 if (m->control_pressed) { return 0; }
146 string rightFrag = templateSeqs[i]->getUnaligned();
147 rightFrag = rightFrag.substr(int(rightFrag.length() * 0.66));
149 Sequence rightTemp(templateSeqs[i]->getName(), rightFrag);
150 databaseRight->addSequence(rightTemp);
152 databaseRight->generateDB();
153 databaseRight->setNumSeqs(templateSeqs.size());
157 kmerDBNameLeft = leftTemplateFileName.substr(0,leftTemplateFileName.find_last_of(".")+1) + char('0'+ kmerSize) + "mer";
158 ifstream kmerFileTestLeft(kmerDBNameLeft.c_str());
159 bool needToGenerateLeft = true;
161 if(kmerFileTestLeft){
162 bool GoodFile = m->checkReleaseVersion(kmerFileTestLeft, m->getVersion());
163 if (GoodFile) { needToGenerateLeft = false; }
166 if(needToGenerateLeft){
168 for (int i = 0; i < templateSeqs.size(); i++) {
170 if (m->control_pressed) { return 0; }
172 string leftFrag = templateSeqs[i]->getUnaligned();
173 leftFrag = leftFrag.substr(0, int(leftFrag.length() * 0.33));
175 Sequence leftTemp(templateSeqs[i]->getName(), leftFrag);
176 databaseLeft->addSequence(leftTemp);
178 databaseLeft->generateDB();
181 databaseLeft->readKmerDB(kmerFileTestLeft);
183 kmerFileTestLeft.close();
185 databaseLeft->setNumSeqs(templateSeqs.size());
188 kmerDBNameRight = rightTemplateFileName.substr(0,rightTemplateFileName.find_last_of(".")+1) + char('0'+ kmerSize) + "mer";
189 ifstream kmerFileTestRight(kmerDBNameRight.c_str());
190 bool needToGenerateRight = true;
192 if(kmerFileTestRight){
193 bool GoodFile = m->checkReleaseVersion(kmerFileTestRight, m->getVersion());
194 if (GoodFile) { needToGenerateRight = false; }
197 if(needToGenerateRight){
199 for (int i = 0; i < templateSeqs.size(); i++) {
200 if (m->control_pressed) { return 0; }
202 string rightFrag = templateSeqs[i]->getUnaligned();
203 rightFrag = rightFrag.substr(int(rightFrag.length() * 0.66));
205 Sequence rightTemp(templateSeqs[i]->getName(), rightFrag);
206 databaseRight->addSequence(rightTemp);
208 databaseRight->generateDB();
211 databaseRight->readKmerDB(kmerFileTestRight);
213 kmerFileTestRight.close();
215 databaseRight->setNumSeqs(templateSeqs.size());
217 }else if (searchMethod == "blast") {
220 databaseLeft = new BlastDB(m->getRootName(m->getSimpleName(fastafile)), -1.0, -1.0, 1, -3);
222 for (int i = 0; i < templateSeqs.size(); i++) { databaseLeft->addSequence(*templateSeqs[i]); }
223 databaseLeft->generateDB();
224 databaseLeft->setNumSeqs(templateSeqs.size());
230 catch(exception& e) {
231 m->errorOut(e, "ChimeraSlayer", "doprep");
235 //***************************************************************************************************************
236 vector<Sequence*> ChimeraSlayer::getTemplate(Sequence* q, vector<Sequence*>& userTemplateFiltered) {
239 //when template=self, the query file is sorted from most abundance to least abundant
240 //userTemplate grows as the query file is processed by adding sequences that are not chimeric and more abundant
241 vector<Sequence*> userTemplate;
243 int myAbund = priority[q->getName()];
245 for (int i = 0; i < templateSeqs.size(); i++) {
247 if (m->control_pressed) { return userTemplate; }
249 //have I reached a sequence with the same abundance as myself?
250 if (!(priority[templateSeqs[i]->getName()] > myAbund)) { break; }
252 //if its am not chimeric add it
253 if (chimericSeqs.count(templateSeqs[i]->getName()) == 0) {
254 userTemplate.push_back(templateSeqs[i]);
255 if (searchMethod == "distance") { userTemplateFiltered.push_back(filteredTemplateSeqs[i]); }
259 string kmerDBNameLeft;
260 string kmerDBNameRight;
262 //generate the kmerdb to pass to maligner
263 if (searchMethod == "kmer") {
264 string templatePath = m->hasPath(templateFileName);
265 string rightTemplateFileName = templatePath + "right." + m->getRootName(m->getSimpleName(templateFileName));
266 databaseRight = new KmerDB(rightTemplateFileName, kmerSize);
268 string leftTemplateFileName = templatePath + "left." + m->getRootName(m->getSimpleName(templateFileName));
269 databaseLeft = new KmerDB(leftTemplateFileName, kmerSize);
271 for (int i = 0; i < userTemplate.size(); i++) {
273 if (m->control_pressed) { return userTemplate; }
275 string leftFrag = userTemplate[i]->getUnaligned();
276 leftFrag = leftFrag.substr(0, int(leftFrag.length() * 0.33));
278 Sequence leftTemp(userTemplate[i]->getName(), leftFrag);
279 databaseLeft->addSequence(leftTemp);
281 databaseLeft->generateDB();
282 databaseLeft->setNumSeqs(userTemplate.size());
284 for (int i = 0; i < userTemplate.size(); i++) {
285 if (m->control_pressed) { return userTemplate; }
287 string rightFrag = userTemplate[i]->getUnaligned();
288 rightFrag = rightFrag.substr(int(rightFrag.length() * 0.66));
290 Sequence rightTemp(userTemplate[i]->getName(), rightFrag);
291 databaseRight->addSequence(rightTemp);
293 databaseRight->generateDB();
294 databaseRight->setNumSeqs(userTemplate.size());
299 for (int i = 0; i < userTemplate.size(); i++) {
301 if (m->control_pressed) { return userTemplate; }
303 string leftFrag = userTemplate[i]->getUnaligned();
304 leftFrag = leftFrag.substr(0, int(leftFrag.length() * 0.33));
306 Sequence leftTemp(userTemplate[i]->getName(), leftFrag);
307 databaseLeft->addSequence(leftTemp);
309 databaseLeft->generateDB();
310 databaseLeft->setNumSeqs(userTemplate.size());
312 for (int i = 0; i < userTemplate.size(); i++) {
313 if (m->control_pressed) { return userTemplate; }
315 string rightFrag = userTemplate[i]->getUnaligned();
316 rightFrag = rightFrag.substr(int(rightFrag.length() * 0.66));
318 Sequence rightTemp(userTemplate[i]->getName(), rightFrag);
319 databaseRight->addSequence(rightTemp);
321 databaseRight->generateDB();
322 databaseRight->setNumSeqs(userTemplate.size());
324 }else if (searchMethod == "blast") {
327 databaseLeft = new BlastDB(m->getRootName(m->getSimpleName(templateFileName)), -1.0, -1.0, 1, -3);
329 for (int i = 0; i < userTemplate.size(); i++) { if (m->control_pressed) { return userTemplate; } databaseLeft->addSequence(*userTemplate[i]); }
330 databaseLeft->generateDB();
331 databaseLeft->setNumSeqs(userTemplate.size());
337 catch(exception& e) {
338 m->errorOut(e, "ChimeraSlayer", "getTemplate");
343 //***************************************************************************************************************
344 ChimeraSlayer::~ChimeraSlayer() {
346 if (templateFileName != "self") {
347 if (searchMethod == "kmer") { delete databaseRight; delete databaseLeft; }
348 else if (searchMethod == "blast") { delete databaseLeft; }
351 //***************************************************************************************************************
352 void ChimeraSlayer::printHeader(ostream& out) {
353 m->mothurOutEndLine();
354 m->mothurOut("Only reporting sequence supported by " + toString(minBS) + "% of bootstrapped results.");
355 m->mothurOutEndLine();
357 out << "Name\tLeftParent\tRightParent\tDivQLAQRB\tPerIDQLAQRB\tBootStrapA\tDivQLBQRA\tPerIDQLBQRA\tBootStrapB\tFlag\tLeftWindow\tRightWindow\n";
359 //***************************************************************************************************************
360 Sequence* ChimeraSlayer::print(ostream& out, ostream& outAcc) {
362 Sequence* trim = NULL;
363 if (trimChimera) { trim = new Sequence(trimQuery.getName(), trimQuery.getAligned()); }
365 if (chimeraFlags == "yes") {
366 string chimeraFlag = "no";
367 if( (chimeraResults[0].bsa >= minBS && chimeraResults[0].divr_qla_qrb >= divR)
369 (chimeraResults[0].bsb >= minBS && chimeraResults[0].divr_qlb_qra >= divR) ) { chimeraFlag = "yes"; }
372 if (chimeraFlag == "yes") {
373 if ((chimeraResults[0].bsa >= minBS) || (chimeraResults[0].bsb >= minBS)) {
374 m->mothurOut(querySeq->getName() + "\tyes"); m->mothurOutEndLine();
375 outAcc << querySeq->getName() << endl;
377 if (templateFileName == "self") { chimericSeqs.insert(querySeq->getName()); }
380 int lengthLeft = chimeraResults[0].winLEnd - chimeraResults[0].winLStart;
381 int lengthRight = chimeraResults[0].winREnd - chimeraResults[0].winRStart;
383 string newAligned = trim->getAligned();
385 if (lengthLeft > lengthRight) { //trim right
386 for (int i = (chimeraResults[0].winRStart-1); i < newAligned.length(); i++) { newAligned[i] = '.'; }
388 for (int i = 0; i < chimeraResults[0].winLEnd; i++) { newAligned[i] = '.'; }
390 trim->setAligned(newAligned);
395 printBlock(chimeraResults[0], chimeraFlag, out);
398 out << querySeq->getName() << "\tno" << endl;
404 catch(exception& e) {
405 m->errorOut(e, "ChimeraSlayer", "print");
409 //***************************************************************************************************************
410 Sequence* ChimeraSlayer::print(ostream& out, ostream& outAcc, data_results leftPiece, data_results rightPiece) {
412 Sequence* trim = NULL;
415 string aligned = leftPiece.trimQuery.getAligned() + rightPiece.trimQuery.getAligned();
416 trim = new Sequence(leftPiece.trimQuery.getName(), aligned);
419 if ((leftPiece.flag == "yes") || (rightPiece.flag == "yes")) {
421 string chimeraFlag = "no";
422 if (leftPiece.flag == "yes") {
424 if( (leftPiece.results[0].bsa >= minBS && leftPiece.results[0].divr_qla_qrb >= divR)
426 (leftPiece.results[0].bsb >= minBS && leftPiece.results[0].divr_qlb_qra >= divR) ) { chimeraFlag = "yes"; }
429 if (rightPiece.flag == "yes") {
430 if ( (rightPiece.results[0].bsa >= minBS && rightPiece.results[0].divr_qla_qrb >= divR)
432 (rightPiece.results[0].bsb >= minBS && rightPiece.results[0].divr_qlb_qra >= divR) ) { chimeraFlag = "yes"; }
435 bool rightChimeric = false;
436 bool leftChimeric = false;
438 if (chimeraFlag == "yes") {
439 //which peice is chimeric or are both
440 if (rightPiece.flag == "yes") { if ((rightPiece.results[0].bsa >= minBS) || (rightPiece.results[0].bsb >= minBS)) { rightChimeric = true; } }
441 if (leftPiece.flag == "yes") { if ((leftPiece.results[0].bsa >= minBS) || (leftPiece.results[0].bsb >= minBS)) { leftChimeric = true; } }
443 if (rightChimeric || leftChimeric) {
444 m->mothurOut(querySeq->getName() + "\tyes"); m->mothurOutEndLine();
445 outAcc << querySeq->getName() << endl;
447 if (templateFileName == "self") { chimericSeqs.insert(querySeq->getName()); }
450 string newAligned = trim->getAligned();
452 //right side is fine so keep that
453 if ((leftChimeric) && (!rightChimeric)) {
454 for (int i = 0; i < leftPiece.results[0].winREnd; i++) { newAligned[i] = '.'; }
455 }else if ((!leftChimeric) && (rightChimeric)) { //leftside is fine so keep that
456 for (int i = (rightPiece.results[0].winLStart-1); i < newAligned.length(); i++) { newAligned[i] = '.'; }
457 }else { //both sides are chimeric, keep longest piece
459 int lengthLeftLeft = leftPiece.results[0].winLEnd - leftPiece.results[0].winLStart;
460 int lengthLeftRight = leftPiece.results[0].winREnd - leftPiece.results[0].winRStart;
462 int longest = 1; // leftleft = 1, leftright = 2, rightleft = 3 rightright = 4
463 int length = lengthLeftLeft;
464 if (lengthLeftLeft < lengthLeftRight) { longest = 2; length = lengthLeftRight; }
466 int lengthRightLeft = rightPiece.results[0].winLEnd - rightPiece.results[0].winLStart;
467 int lengthRightRight = rightPiece.results[0].winREnd - rightPiece.results[0].winRStart;
469 if (lengthRightLeft > length) { longest = 3; length = lengthRightLeft; }
470 if (lengthRightRight > length) { longest = 4; }
472 if (longest == 1) { //leftleft
473 for (int i = (leftPiece.results[0].winRStart-1); i < newAligned.length(); i++) { newAligned[i] = '.'; }
474 }else if (longest == 2) { //leftright
475 //get rid of leftleft
476 for (int i = (leftPiece.results[0].winLStart-1); i < (leftPiece.results[0].winLEnd-1); i++) { newAligned[i] = '.'; }
478 for (int i = (rightPiece.results[0].winLStart-1); i < newAligned.length(); i++) { newAligned[i] = '.'; }
479 }else if (longest == 3) { //rightleft
481 for (int i = 0; i < leftPiece.results[0].winREnd; i++) { newAligned[i] = '.'; }
482 //get rid of rightright
483 for (int i = (rightPiece.results[0].winRStart-1); i < newAligned.length(); i++) { newAligned[i] = '.'; }
486 for (int i = 0; i < leftPiece.results[0].winREnd; i++) { newAligned[i] = '.'; }
487 //get rid of rightleft
488 for (int i = (rightPiece.results[0].winLStart-1); i < (rightPiece.results[0].winLEnd-1); i++) { newAligned[i] = '.'; }
492 trim->setAligned(newAligned);
498 printBlock(leftPiece, rightPiece, leftChimeric, rightChimeric, chimeraFlag, out);
501 out << querySeq->getName() << "\tno" << endl;
507 catch(exception& e) {
508 m->errorOut(e, "ChimeraSlayer", "print");
514 //***************************************************************************************************************
515 Sequence* ChimeraSlayer::print(MPI_File& out, MPI_File& outAcc, data_results leftPiece, data_results rightPiece) {
518 bool results = false;
519 string outAccString = "";
520 string outputString = "";
522 Sequence* trim = NULL;
525 string aligned = leftPiece.trimQuery.getAligned() + rightPiece.trimQuery.getAligned();
526 trim = new Sequence(leftPiece.trimQuery.getName(), aligned);
530 if ((leftPiece.flag == "yes") || (rightPiece.flag == "yes")) {
532 string chimeraFlag = "no";
533 if (leftPiece.flag == "yes") {
535 if( (leftPiece.results[0].bsa >= minBS && leftPiece.results[0].divr_qla_qrb >= divR)
537 (leftPiece.results[0].bsb >= minBS && leftPiece.results[0].divr_qlb_qra >= divR) ) { chimeraFlag = "yes"; }
540 if (rightPiece.flag == "yes") {
541 if ( (rightPiece.results[0].bsa >= minBS && rightPiece.results[0].divr_qla_qrb >= divR)
543 (rightPiece.results[0].bsb >= minBS && rightPiece.results[0].divr_qlb_qra >= divR) ) { chimeraFlag = "yes"; }
546 bool rightChimeric = false;
547 bool leftChimeric = false;
551 if (chimeraFlag == "yes") {
552 //which peice is chimeric or are both
553 if (rightPiece.flag == "yes") { if ((rightPiece.results[0].bsa >= minBS) || (rightPiece.results[0].bsb >= minBS)) { rightChimeric = true; } }
554 if (leftPiece.flag == "yes") { if ((leftPiece.results[0].bsa >= minBS) || (leftPiece.results[0].bsb >= minBS)) { leftChimeric = true; } }
556 if (rightChimeric || leftChimeric) {
557 cout << querySeq->getName() << "\tyes" << endl;
558 outAccString += querySeq->getName() + "\n";
561 if (templateFileName == "self") { chimericSeqs.insert(querySeq->getName()); }
563 //write to accnos file
564 int length = outAccString.length();
565 char* buf2 = new char[length];
566 memcpy(buf2, outAccString.c_str(), length);
568 MPI_File_write_shared(outAcc, buf2, length, MPI_CHAR, &status);
572 string newAligned = trim->getAligned();
574 //right side is fine so keep that
575 if ((leftChimeric) && (!rightChimeric)) {
576 for (int i = 0; i < leftPiece.results[0].winREnd; i++) { newAligned[i] = '.'; }
577 }else if ((!leftChimeric) && (rightChimeric)) { //leftside is fine so keep that
578 for (int i = (rightPiece.results[0].winLStart-1); i < newAligned.length(); i++) { newAligned[i] = '.'; }
579 }else { //both sides are chimeric, keep longest piece
581 int lengthLeftLeft = leftPiece.results[0].winLEnd - leftPiece.results[0].winLStart;
582 int lengthLeftRight = leftPiece.results[0].winREnd - leftPiece.results[0].winRStart;
584 int longest = 1; // leftleft = 1, leftright = 2, rightleft = 3 rightright = 4
585 int length = lengthLeftLeft;
586 if (lengthLeftLeft < lengthLeftRight) { longest = 2; length = lengthLeftRight; }
588 int lengthRightLeft = rightPiece.results[0].winLEnd - rightPiece.results[0].winLStart;
589 int lengthRightRight = rightPiece.results[0].winREnd - rightPiece.results[0].winRStart;
591 if (lengthRightLeft > length) { longest = 3; length = lengthRightLeft; }
592 if (lengthRightRight > length) { longest = 4; }
594 if (longest == 1) { //leftleft
595 for (int i = (leftPiece.results[0].winRStart-1); i < newAligned.length(); i++) { newAligned[i] = '.'; }
596 }else if (longest == 2) { //leftright
597 //get rid of leftleft
598 for (int i = (leftPiece.results[0].winLStart-1); i < (leftPiece.results[0].winLEnd-1); i++) { newAligned[i] = '.'; }
600 for (int i = (rightPiece.results[0].winLStart-1); i < newAligned.length(); i++) { newAligned[i] = '.'; }
601 }else if (longest == 3) { //rightleft
603 for (int i = 0; i < leftPiece.results[0].winREnd; i++) { newAligned[i] = '.'; }
604 //get rid of rightright
605 for (int i = (rightPiece.results[0].winRStart-1); i < newAligned.length(); i++) { newAligned[i] = '.'; }
608 for (int i = 0; i < leftPiece.results[0].winREnd; i++) { newAligned[i] = '.'; }
609 //get rid of rightleft
610 for (int i = (rightPiece.results[0].winLStart-1); i < (rightPiece.results[0].winLEnd-1); i++) { newAligned[i] = '.'; }
614 trim->setAligned(newAligned);
620 outputString = getBlock(leftPiece, rightPiece, leftChimeric, rightChimeric, chimeraFlag);
621 outputString += "\n";
623 //write to output file
624 int length = outputString.length();
625 char* buf = new char[length];
626 memcpy(buf, outputString.c_str(), length);
628 MPI_File_write_shared(out, buf, length, MPI_CHAR, &status);
632 outputString += querySeq->getName() + "\tno\n";
634 //write to output file
635 int length = outputString.length();
636 char* buf = new char[length];
637 memcpy(buf, outputString.c_str(), length);
639 MPI_File_write_shared(out, buf, length, MPI_CHAR, &status);
646 catch(exception& e) {
647 m->errorOut(e, "ChimeraSlayer", "print");
651 //***************************************************************************************************************
652 Sequence* ChimeraSlayer::print(MPI_File& out, MPI_File& outAcc) {
655 bool results = false;
656 string outAccString = "";
657 string outputString = "";
659 Sequence* trim = NULL;
660 if (trimChimera) { trim = new Sequence(trimQuery.getName(), trimQuery.getAligned()); }
662 if (chimeraFlags == "yes") {
663 string chimeraFlag = "no";
664 if( (chimeraResults[0].bsa >= minBS && chimeraResults[0].divr_qla_qrb >= divR)
666 (chimeraResults[0].bsb >= minBS && chimeraResults[0].divr_qlb_qra >= divR) ) { chimeraFlag = "yes"; }
669 if (chimeraFlag == "yes") {
670 if ((chimeraResults[0].bsa >= minBS) || (chimeraResults[0].bsb >= minBS)) {
671 cout << querySeq->getName() << "\tyes" << endl;
672 outAccString += querySeq->getName() + "\n";
675 if (templateFileName == "self") { chimericSeqs.insert(querySeq->getName()); }
677 //write to accnos file
678 int length = outAccString.length();
679 char* buf2 = new char[length];
680 memcpy(buf2, outAccString.c_str(), length);
682 MPI_File_write_shared(outAcc, buf2, length, MPI_CHAR, &status);
686 int lengthLeft = chimeraResults[0].winLEnd - chimeraResults[0].winLStart;
687 int lengthRight = chimeraResults[0].winREnd - chimeraResults[0].winRStart;
689 string newAligned = trim->getAligned();
690 if (lengthLeft > lengthRight) { //trim right
691 for (int i = (chimeraResults[0].winRStart-1); i < newAligned.length(); i++) { newAligned[i] = '.'; }
693 for (int i = 0; i < (chimeraResults[0].winLEnd-1); i++) { newAligned[i] = '.'; }
695 trim->setAligned(newAligned);
700 outputString = getBlock(chimeraResults[0], chimeraFlag);
701 outputString += "\n";
703 //write to output file
704 int length = outputString.length();
705 char* buf = new char[length];
706 memcpy(buf, outputString.c_str(), length);
708 MPI_File_write_shared(out, buf, length, MPI_CHAR, &status);
712 outputString += querySeq->getName() + "\tno\n";
714 //write to output file
715 int length = outputString.length();
716 char* buf = new char[length];
717 memcpy(buf, outputString.c_str(), length);
719 MPI_File_write_shared(out, buf, length, MPI_CHAR, &status);
725 catch(exception& e) {
726 m->errorOut(e, "ChimeraSlayer", "print");
732 //***************************************************************************************************************
733 int ChimeraSlayer::getChimeras(Sequence* query) {
736 trimQuery.setName(query->getName()); trimQuery.setAligned(query->getAligned());
737 printResults.trimQuery = trimQuery;
740 printResults.flag = "no";
744 //you must create a template
745 vector<Sequence*> thisTemplate;
746 vector<Sequence*> thisFilteredTemplate;
747 if (templateFileName != "self") { thisTemplate = templateSeqs; thisFilteredTemplate = filteredTemplateSeqs; }
748 else { thisTemplate = getTemplate(query, thisFilteredTemplate); } //fills this template and creates the databases
750 if (m->control_pressed) { return 0; }
752 if (thisTemplate.size() == 0) { return 0; } //not chimeric
754 //moved this out of maligner - 4/29/11
755 vector<Sequence*> refSeqs = getRefSeqs(query, thisTemplate, thisFilteredTemplate);
757 Maligner maligner(refSeqs, match, misMatch, divR, minSim, minCov);
758 Slayer slayer(window, increment, minSim, divR, iters, minSNP, minBS);
760 if (templateFileName == "self") {
761 if (searchMethod == "kmer") { delete databaseRight; delete databaseLeft; }
762 else if (searchMethod == "blast") { delete databaseLeft; }
765 if (m->control_pressed) { return 0; }
767 string chimeraFlag = maligner.getResults(query, decalc);
769 if (m->control_pressed) { return 0; }
771 vector<results> Results = maligner.getOutput();
773 for (int i = 0; i < refSeqs.size(); i++) { delete refSeqs[i]; }
775 if (chimeraFlag == "yes") {
778 vector<string> parents;
779 for (int i = 0; i < Results.size(); i++) {
780 parents.push_back(Results[i].parentAligned);
783 ChimeraReAligner realigner;
784 realigner.reAlign(query, parents);
788 //get sequence that were given from maligner results
789 vector<SeqDist> seqs;
790 map<string, float> removeDups;
791 map<string, float>::iterator itDup;
792 map<string, string> parentNameSeq;
793 map<string, string>::iterator itSeq;
794 for (int j = 0; j < Results.size(); j++) {
795 float dist = (Results[j].regionEnd - Results[j].regionStart + 1) * Results[j].queryToParentLocal;
796 //only add if you are not a duplicate
798 if(Results[j].queryToParentLocal >= 90){ //local match has to be over 90% similarity
800 itDup = removeDups.find(Results[j].parent);
801 if (itDup == removeDups.end()) { //this is not duplicate
802 removeDups[Results[j].parent] = dist;
803 parentNameSeq[Results[j].parent] = Results[j].parentAligned;
804 }else if (dist > itDup->second) { //is this a stronger number for this parent
805 removeDups[Results[j].parent] = dist;
806 parentNameSeq[Results[j].parent] = Results[j].parentAligned;
813 for (itDup = removeDups.begin(); itDup != removeDups.end(); itDup++) {
814 itSeq = parentNameSeq.find(itDup->first);
815 Sequence* seq = new Sequence(itDup->first, itSeq->second);
819 member.dist = itDup->second;
820 seqs.push_back(member);
823 //limit number of parents to explore - default 3
824 if (Results.size() > parents) {
826 sort(seqs.begin(), seqs.end(), compareSeqDist);
827 //prioritize larger more similiar sequence fragments
828 reverse(seqs.begin(), seqs.end());
830 for (int k = seqs.size()-1; k > (parents-1); k--) {
836 //put seqs into vector to send to slayer
838 // cout << query->getAligned() << endl;
839 vector<Sequence*> seqsForSlayer;
840 for (int k = 0; k < seqs.size(); k++) {
841 // cout << seqs[k].seq->getAligned() << endl;
842 seqsForSlayer.push_back(seqs[k].seq);
846 if (m->control_pressed) { for (int k = 0; k < seqs.size(); k++) { delete seqs[k].seq; } return 0; }
849 chimeraFlags = slayer.getResults(query, seqsForSlayer);
850 if (m->control_pressed) { return 0; }
851 chimeraResults = slayer.getOutput();
853 printResults.flag = chimeraFlags;
854 printResults.results = chimeraResults;
857 for (int k = 0; k < seqs.size(); k++) { delete seqs[k].seq; }
859 //cout << endl << endl;
862 catch(exception& e) {
863 m->errorOut(e, "ChimeraSlayer", "getChimeras");
867 //***************************************************************************************************************
868 void ChimeraSlayer::printBlock(data_struct data, string flag, ostream& out){
870 out << querySeq->getName() << '\t';
871 out << data.parentA.getName() << "\t" << data.parentB.getName() << '\t';
873 out << data.divr_qla_qrb << '\t' << data.qla_qrb << '\t' << data.bsa << '\t';
874 out << data.divr_qlb_qra << '\t' << data.qlb_qra << '\t' << data.bsb << '\t';
876 out << flag << '\t' << data.winLStart << "-" << data.winLEnd << '\t' << data.winRStart << "-" << data.winREnd << '\t';
879 catch(exception& e) {
880 m->errorOut(e, "ChimeraSlayer", "printBlock");
884 //***************************************************************************************************************
885 void ChimeraSlayer::printBlock(data_results leftdata, data_results rightdata, bool leftChimeric, bool rightChimeric, string flag, ostream& out){
888 if ((leftChimeric) && (!rightChimeric)) { //print left
889 out << querySeq->getName() << '\t';
890 out << leftdata.results[0].parentA.getName() << "\t" << leftdata.results[0].parentB.getName() << '\t';
892 out << leftdata.results[0].divr_qla_qrb << '\t' << leftdata.results[0].qla_qrb << '\t' << leftdata.results[0].bsa << '\t';
893 out << leftdata.results[0].divr_qlb_qra << '\t' << leftdata.results[0].qlb_qra << '\t' << leftdata.results[0].bsb << '\t';
895 out << flag << '\t' << leftdata.results[0].winLStart << "-" << leftdata.results[0].winLEnd << '\t' << leftdata.results[0].winRStart << "-" << leftdata.results[0].winREnd << '\t';
897 }else if ((!leftChimeric) && (rightChimeric)) { //print right
898 out << querySeq->getName() << '\t';
899 out << rightdata.results[0].parentA.getName() << "\t" << rightdata.results[0].parentB.getName() << '\t';
901 out << rightdata.results[0].divr_qla_qrb << '\t' << rightdata.results[0].qla_qrb << '\t' << rightdata.results[0].bsa << '\t';
902 out << rightdata.results[0].divr_qlb_qra << '\t' << rightdata.results[0].qlb_qra << '\t' << rightdata.results[0].bsb << '\t';
904 out << flag << '\t' << rightdata.results[0].winLStart << "-" << rightdata.results[0].winLEnd << '\t' << rightdata.results[0].winRStart << "-" << rightdata.results[0].winREnd << '\t';
906 }else { //print both results
907 if (leftdata.flag == "yes") {
908 out << querySeq->getName() + "_LEFT" << '\t';
909 out << leftdata.results[0].parentA.getName() << "\t" << leftdata.results[0].parentB.getName() << '\t';
911 out << leftdata.results[0].divr_qla_qrb << '\t' << leftdata.results[0].qla_qrb << '\t' << leftdata.results[0].bsa << '\t';
912 out << leftdata.results[0].divr_qlb_qra << '\t' << leftdata.results[0].qlb_qra << '\t' << leftdata.results[0].bsb << '\t';
914 out << flag << '\t' << leftdata.results[0].winLStart << "-" << leftdata.results[0].winLEnd << '\t' << leftdata.results[0].winRStart << "-" << leftdata.results[0].winREnd << '\t';
917 if (rightdata.flag == "yes") {
918 if (leftdata.flag == "yes") { out << endl; }
920 out << querySeq->getName() + "_RIGHT"<< '\t';
921 out << rightdata.results[0].parentA.getName() << "\t" << rightdata.results[0].parentB.getName() << '\t';
923 out << rightdata.results[0].divr_qla_qrb << '\t' << rightdata.results[0].qla_qrb << '\t' << rightdata.results[0].bsa << '\t';
924 out << rightdata.results[0].divr_qlb_qra << '\t' << rightdata.results[0].qlb_qra << '\t' << rightdata.results[0].bsb << '\t';
926 out << flag << '\t' << rightdata.results[0].winLStart << "-" << rightdata.results[0].winLEnd << '\t' << rightdata.results[0].winRStart << "-" << rightdata.results[0].winREnd << '\t';
931 catch(exception& e) {
932 m->errorOut(e, "ChimeraSlayer", "printBlock");
936 //***************************************************************************************************************
937 string ChimeraSlayer::getBlock(data_results leftdata, data_results rightdata, bool leftChimeric, bool rightChimeric, string flag){
942 if ((leftChimeric) && (!rightChimeric)) { //get left
943 out += querySeq->getName() + "\t";
944 out += leftdata.results[0].parentA.getName() + "\t" + leftdata.results[0].parentB.getName() + "\t";
946 out += toString(leftdata.results[0].divr_qla_qrb) + "\t" + toString(leftdata.results[0].qla_qrb) + "\t" + toString(leftdata.results[0].bsa) + "\t";
947 out += toString(leftdata.results[0].divr_qlb_qra) + "\t" + toString(leftdata.results[0].qlb_qra) + "\t" + toString(leftdata.results[0].bsb) + "\t";
949 out += flag + "\t" + toString(leftdata.results[0].winLStart) + "-" + toString(leftdata.results[0].winLEnd) + "\t" + toString(leftdata.results[0].winRStart) + "-" + toString(leftdata.results[0].winREnd) + "\t";
951 }else if ((!leftChimeric) && (rightChimeric)) { //print right
952 out += querySeq->getName() + "\t";
953 out += rightdata.results[0].parentA.getName() + "\t" + rightdata.results[0].parentB.getName() + "\t";
955 out += toString(rightdata.results[0].divr_qla_qrb) + "\t" + toString(rightdata.results[0].qla_qrb) + "\t" + toString(rightdata.results[0].bsa) + "\t";
956 out += toString(rightdata.results[0].divr_qlb_qra) + "\t" + toString(rightdata.results[0].qlb_qra) + "\t" + toString(rightdata.results[0].bsb) + "\t";
958 out += flag + "\t" + toString(rightdata.results[0].winLStart) + "-" + toString(rightdata.results[0].winLEnd) + "\t" + toString(rightdata.results[0].winRStart) + "-" + toString(rightdata.results[0].winREnd) + "\t";
960 }else { //print both results
962 if (leftdata.flag == "yes") {
963 out += querySeq->getName() + "_LEFT\t";
964 out += leftdata.results[0].parentA.getName() + "\t" + leftdata.results[0].parentB.getName() + "\t";
966 out += toString(leftdata.results[0].divr_qla_qrb) + "\t" + toString(leftdata.results[0].qla_qrb) + "\t" + toString(leftdata.results[0].bsa) + "\t";
967 out += toString(leftdata.results[0].divr_qlb_qra) + "\t" + toString(leftdata.results[0].qlb_qra) + "\t" + toString(leftdata.results[0].bsb) + "\t";
969 out += flag + "\t" + toString(leftdata.results[0].winLStart) + "-" + toString(leftdata.results[0].winLEnd) + "\t" + toString(leftdata.results[0].winRStart) + "-" + toString(leftdata.results[0].winREnd) + "\t";
972 if (rightdata.flag == "yes") {
973 if (leftdata.flag == "yes") { out += "\n"; }
974 out += querySeq->getName() + "_RIGHT\t";
975 out += rightdata.results[0].parentA.getName() + "\t" + rightdata.results[0].parentB.getName() + "\t";
977 out += toString(rightdata.results[0].divr_qla_qrb) + "\t" + toString(rightdata.results[0].qla_qrb) + "\t" + toString(rightdata.results[0].bsa) + "\t";
978 out += toString(rightdata.results[0].divr_qlb_qra) + "\t" + toString(rightdata.results[0].qlb_qra) + "\t" + toString(rightdata.results[0].bsb) + "\t";
980 out += flag + "\t" + toString(rightdata.results[0].winLStart) + "-" + toString(rightdata.results[0].winLEnd) + "\t" + toString(rightdata.results[0].winRStart) + "-" + toString(rightdata.results[0].winREnd) + "\t";
987 catch(exception& e) {
988 m->errorOut(e, "ChimeraSlayer", "getBlock");
992 //***************************************************************************************************************
993 string ChimeraSlayer::getBlock(data_struct data, string flag){
996 string outputString = "";
998 outputString += querySeq->getName() + "\t";
999 outputString += data.parentA.getName() + "\t" + data.parentB.getName() + "\t";
1001 outputString += toString(data.divr_qla_qrb) + "\t" + toString(data.qla_qrb) + "\t" + toString(data.bsa) + "\t";
1002 outputString += toString(data.divr_qlb_qra) + "\t" + toString(data.qlb_qra) + "\t" + toString(data.bsb) + "\t";
1004 outputString += flag + "\t" + toString(data.winLStart) + "-" + toString(data.winLEnd) + "\t" + toString(data.winRStart) + "-" + toString(data.winREnd) + "\t";
1006 return outputString;
1008 catch(exception& e) {
1009 m->errorOut(e, "ChimeraSlayer", "getBlock");
1013 //***************************************************************************************************************
1014 vector<Sequence*> ChimeraSlayer::getRefSeqs(Sequence* q, vector<Sequence*>& thisTemplate, vector<Sequence*>& thisFilteredTemplate){
1017 vector<Sequence*> refSeqs;
1019 if (searchMethod == "distance") {
1020 //find closest seqs to query in template - returns copies of seqs so trim does not destroy - remember to deallocate
1021 Sequence* newSeq = new Sequence(q->getName(), q->getAligned());
1023 refSeqs = decalc->findClosest(newSeq, thisTemplate, thisFilteredTemplate, numWanted, minSim);
1025 }else if (searchMethod == "blast") {
1026 refSeqs = getBlastSeqs(q, thisTemplate, numWanted); //fills indexes
1027 }else if (searchMethod == "kmer") {
1028 refSeqs = getKmerSeqs(q, thisTemplate, numWanted); //fills indexes
1029 }else { m->mothurOut("not valid search."); exit(1); } //should never get here
1033 catch(exception& e) {
1034 m->errorOut(e, "ChimeraSlayer", "getRefSeqs");
1038 //***************************************************************************************************************/
1039 vector<Sequence*> ChimeraSlayer::getBlastSeqs(Sequence* q, vector<Sequence*>& db, int num) {
1042 vector<Sequence*> refResults;
1044 //get parts of query
1045 string queryUnAligned = q->getUnaligned();
1046 string leftQuery = queryUnAligned.substr(0, int(queryUnAligned.length() * 0.33)); //first 1/3 of the sequence
1047 string rightQuery = queryUnAligned.substr(int(queryUnAligned.length() * 0.66)); //last 1/3 of the sequence
1048 //cout << "whole length = " << queryUnAligned.length() << '\t' << "left length = " << leftQuery.length() << '\t' << "right length = "<< rightQuery.length() << endl;
1049 Sequence* queryLeft = new Sequence(q->getName(), leftQuery);
1050 Sequence* queryRight = new Sequence(q->getName(), rightQuery);
1052 vector<int> tempIndexesLeft = databaseLeft->findClosestMegaBlast(queryLeft, num+1, minSim);
1053 vector<int> tempIndexesRight = databaseLeft->findClosestMegaBlast(queryRight, num+1, minSim);
1056 //cout << q->getName() << '\t' << leftQuery << '\t' << "leftMatches = " << tempIndexesLeft.size() << '\t' << rightQuery << " rightMatches = " << tempIndexesRight.size() << endl;
1057 // vector<int> smaller;
1058 // vector<int> larger;
1060 // if (tempIndexesRight.size() < tempIndexesLeft.size()) { smaller = tempIndexesRight; larger = tempIndexesLeft; }
1061 // else { smaller = tempIndexesLeft; larger = tempIndexesRight; }
1065 map<int, int>::iterator it;
1066 vector<int> mergedResults;
1069 // for (int i = 0; i < smaller.size(); i++) {
1070 while(index < tempIndexesLeft.size() && index < tempIndexesRight.size()){
1072 if (m->control_pressed) { delete queryRight; delete queryLeft; return refResults; }
1074 //add left if you havent already
1075 it = seen.find(tempIndexesLeft[index]);
1076 if (it == seen.end()) {
1077 mergedResults.push_back(tempIndexesLeft[index]);
1078 seen[tempIndexesLeft[index]] = tempIndexesLeft[index];
1081 //add right if you havent already
1082 it = seen.find(tempIndexesRight[index]);
1083 if (it == seen.end()) {
1084 mergedResults.push_back(tempIndexesRight[index]);
1085 seen[tempIndexesRight[index]] = tempIndexesRight[index];
1091 for (int i = index; i < tempIndexesLeft.size(); i++) {
1092 if (m->control_pressed) { delete queryRight; delete queryLeft; return refResults; }
1094 //add right if you havent already
1095 it = seen.find(tempIndexesLeft[i]);
1096 if (it == seen.end()) {
1097 mergedResults.push_back(tempIndexesLeft[i]);
1098 seen[tempIndexesLeft[i]] = tempIndexesLeft[i];
1102 for (int i = index; i < tempIndexesRight.size(); i++) {
1103 if (m->control_pressed) { delete queryRight; delete queryLeft; return refResults; }
1105 //add right if you havent already
1106 it = seen.find(tempIndexesRight[i]);
1107 if (it == seen.end()) {
1108 mergedResults.push_back(tempIndexesRight[i]);
1109 seen[tempIndexesRight[i]] = tempIndexesRight[i];
1114 for (int i = 0; i < mergedResults.size(); i++) {
1115 //cout << mergedResults[i] << '\t' << db[mergedResults[i]]->getName() << endl;
1116 if (db[mergedResults[i]]->getName() != q->getName()) {
1117 Sequence* temp = new Sequence(db[mergedResults[i]]->getName(), db[mergedResults[i]]->getAligned());
1118 refResults.push_back(temp);
1129 catch(exception& e) {
1130 m->errorOut(e, "ChimeraSlayer", "getBlastSeqs");
1134 //***************************************************************************************************************
1135 vector<Sequence*> ChimeraSlayer::getKmerSeqs(Sequence* q, vector<Sequence*>& db, int num) {
1137 vector<Sequence*> refResults;
1139 //get parts of query
1140 string queryUnAligned = q->getUnaligned();
1141 string leftQuery = queryUnAligned.substr(0, int(queryUnAligned.length() * 0.33)); //first 1/3 of the sequence
1142 string rightQuery = queryUnAligned.substr(int(queryUnAligned.length() * 0.66)); //last 1/3 of the sequence
1144 Sequence* queryLeft = new Sequence(q->getName(), leftQuery);
1145 Sequence* queryRight = new Sequence(q->getName(), rightQuery);
1147 vector<int> tempIndexesLeft = databaseLeft->findClosestSequences(queryLeft, num);
1148 vector<int> tempIndexesRight = databaseRight->findClosestSequences(queryRight, num);
1152 map<int, int>::iterator it;
1153 vector<int> mergedResults;
1154 for (int i = 0; i < tempIndexesLeft.size(); i++) {
1156 if (m->control_pressed) { delete queryRight; delete queryLeft; return refResults; }
1158 //add left if you havent already
1159 it = seen.find(tempIndexesLeft[i]);
1160 if (it == seen.end()) {
1161 mergedResults.push_back(tempIndexesLeft[i]);
1162 seen[tempIndexesLeft[i]] = tempIndexesLeft[i];
1165 //add right if you havent already
1166 it = seen.find(tempIndexesRight[i]);
1167 if (it == seen.end()) {
1168 mergedResults.push_back(tempIndexesRight[i]);
1169 seen[tempIndexesRight[i]] = tempIndexesRight[i];
1173 //numWanted = mergedResults.size();
1175 //cout << q->getName() << endl;
1177 for (int i = 0; i < mergedResults.size(); i++) {
1178 //cout << db[mergedResults[i]]->getName() << endl;
1179 if (db[mergedResults[i]]->getName() != q->getName()) {
1180 Sequence* temp = new Sequence(db[mergedResults[i]]->getName(), db[mergedResults[i]]->getAligned());
1181 refResults.push_back(temp);
1190 catch(exception& e) {
1191 m->errorOut(e, "ChimeraSlayer", "getKmerSeqs");
1195 //***************************************************************************************************************