--- /dev/null
+/*
+ * nast.cpp
+ *
+ *
+ * Created by Pat Schloss on 12/17/08.
+ * Copyright 2008 Patrick D. Schloss. All rights reserved.
+ *
+ * This is my implementation of the NAST (nearest alignment space termination) algorithm as described in:
+ *
+ * DeSantis TZ, Hugenholtz P, Keller K, Brodie EL, Larsen N, Piceno YM, Phan R, & Anderson GL. 2006. NAST: a multiple
+ * sequence alignment server for comparative analysis of 16S rRNA genes. Nucleic Acids Research. 34:W394-9.
+ *
+ * To construct an object one needs to provide a method of getting a pairwise alignment (alignment) and the template
+ * and candidate sequence that are to be aligned to each other.
+ *
+ */
+
+#include "sequence.hpp"
+#include "alignment.hpp"
+#include "nast.hpp"
+
+/**************************************************************************************************/
+
+Nast::Nast(Alignment* method, Sequence* cand, Sequence* temp) : alignment(method), candidateSeq(cand), templateSeq(temp) {
+ try {
+ m = MothurOut::getInstance();
+ maxInsertLength = 0;
+
+ pairwiseAlignSeqs(); // This is part A in Fig. 2 of DeSantis et al.
+ regapSequences(); // This is parts B-F in Fig. 2 of DeSantis et al.
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Nast", "Nast");
+ exit(1);
+ }
+}
+
+/**************************************************************************************************/
+
+void Nast::pairwiseAlignSeqs(){ // Here we call one of the pairwise alignment methods to align our unaligned candidate
+ // and template sequences
+ try {
+ alignment->align(candidateSeq->getUnaligned(), templateSeq->getUnaligned());
+
+ string candAln = alignment->getSeqAAln();
+ string tempAln = alignment->getSeqBAln();
+
+ if(candAln == ""){
+
+ candidateSeq->setPairwise("");
+ templateSeq->setPairwise(templateSeq->getUnaligned());
+
+ }
+ else{
+ if(tempAln[0] == '-'){
+ int pairwiseAlignmentLength = tempAln.length(); // we need to make sure that the candidate sequence alignment
+ for(int i=0;i<pairwiseAlignmentLength;i++){ // starts where the template sequence alignment starts, if it
+ if(isalpha(tempAln[i])){ // starts early, we nuke the beginning of the candidate
+ candAln = candAln.substr(i); // sequence
+ tempAln = tempAln.substr(i);
+ break;
+ }
+ }
+ }
+ int pairwiseAlignmentLength = tempAln.length();
+ if(tempAln[pairwiseAlignmentLength-1] == '-'){ // we need to make sure that the candidate sequence alignment
+ for(int i=pairwiseAlignmentLength-1; i>=0; i--){// ends where the template sequence alignment ends, if it runs
+ if(isalpha(tempAln[i])){ // long, we nuke the end of the candidate sequence
+ candAln = candAln.substr(0,i+1);
+ tempAln = tempAln.substr(0,i+1);
+ break;
+ }
+ }
+ }
+
+ }
+
+ candidateSeq->setPairwise(candAln); // set the pairwise sequences in the Sequence objects for
+ templateSeq->setPairwise(tempAln); // the candidate and template sequences
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Nast", "pairwiseAlignSeqs");
+ exit(1);
+ }
+}
+
+/**************************************************************************************************/
+
+void Nast::removeExtraGaps(string& candAln, string tempAln, string newTemplateAlign){
+
+// here we do steps C-F of Fig. 2 from DeSantis et al.
+ try {
+
+ int longAlignmentLength = newTemplateAlign.length();
+
+ for(int i=0; i<longAlignmentLength; i++){ // use the long alignment as the standard
+ int rightIndex, rightRoom, leftIndex, leftRoom;
+
+ // Part C of Fig. 2 from DeSantis et al.
+ if((isalpha(newTemplateAlign[i]) != isalpha(tempAln[i]))){ //if there is a discrepancy between the regapped
+
+ rightRoom = 0; leftRoom = 0;
+
+ // Part D of Fig. 2 from DeSantis et al. // template sequence and the official template sequence
+ for(leftIndex=i-1;leftIndex>0;leftIndex--){ // then we've got problems...
+ if(!isalpha(candAln[leftIndex])){
+ leftRoom = 1; //count how far it is to the nearest gap on the LEFT side of the anomaly
+ while(leftIndex-leftRoom>=0 && !isalpha(candAln[leftIndex-leftRoom])) { leftRoom++; }
+ break;
+ }
+ }
+
+ for(rightIndex=i+1;rightIndex<longAlignmentLength-1;rightIndex++){
+ if(!isalpha(candAln[rightIndex])){
+ rightRoom = 1; //count how far it is to the nearest gap on the RIGHT side of the anomaly
+ while(rightIndex+rightRoom<longAlignmentLength && !isalpha(candAln[rightIndex+rightRoom])) { rightRoom++; }
+ break;
+ }
+ }
+
+ int insertLength = 0; // figure out how long the anomaly is
+ while(!isalpha(newTemplateAlign[i + insertLength])) { insertLength++; }
+ if(insertLength > maxInsertLength){ maxInsertLength = insertLength; }
+
+ if((leftRoom + rightRoom) >= insertLength){
+
+ // Parts D & E from Fig. 2 of DeSantis et al.
+ if((i-leftIndex) <= (rightIndex-i)){ // the left gap is closer - > move stuff left there's
+
+ if(leftRoom >= insertLength){ // enough room to the left to move
+ //cout << "lr newTemplateAlign = " << newTemplateAlign.length() << '\t' << i << '\t' << insertLength << endl;
+ string leftTemplateString = newTemplateAlign.substr(0,i);
+ string rightTemplateString = newTemplateAlign.substr((i+insertLength));
+ newTemplateAlign = leftTemplateString + rightTemplateString;
+ longAlignmentLength = newTemplateAlign.length();
+ //cout << "lr candAln = " << candAln.length() << '\t' << leftIndex << '\t' << endl;
+ string leftCandidateString = candAln.substr(0,(leftIndex-insertLength+1));
+ string rightCandidateString = candAln.substr((leftIndex+1));
+ candAln = leftCandidateString + rightCandidateString;
+
+ }else{ // not enough room to the left, have to steal some space to the right
+
+ //cout << "in else lr newTemplateAlign = " << newTemplateAlign.length() << '\t' << i << '\t' << insertLength << endl;
+ string leftTemplateString = newTemplateAlign.substr(0,i);
+ string rightTemplateString = newTemplateAlign.substr((i+insertLength));
+ newTemplateAlign = leftTemplateString + rightTemplateString;
+ longAlignmentLength = newTemplateAlign.length();
+ //cout << " in else lr candAln = " << candAln.length() << '\t' << " leftIndex = " << leftIndex << " leftroom = " << leftRoom << " rightIndex = " << rightIndex << '\t' << " rightroom = " << rightRoom << '\t' << endl;
+ string leftCandidateString = candAln.substr(0,(leftIndex-leftRoom+1));
+ string insertString = candAln.substr((leftIndex+1),(rightIndex-leftIndex-1));
+ string rightCandidateString = candAln.substr((rightIndex+(insertLength-leftRoom)));
+ candAln = leftCandidateString + insertString + rightCandidateString;
+
+ }
+ }else{ // the right gap is closer - > move stuff right there's
+ if(rightRoom >= insertLength){ // enough room to the right to move
+ //cout << "rr newTemplateAlign = " << newTemplateAlign.length() << '\t' << i << '\t' << i+insertLength << endl;
+ string leftTemplateString = newTemplateAlign.substr(0,i);
+ string rightTemplateString = newTemplateAlign.substr((i+insertLength));
+ newTemplateAlign = leftTemplateString + rightTemplateString;
+ longAlignmentLength = newTemplateAlign.length();
+ //cout << "rr candAln = " << candAln.length() << '\t' << i << '\t' << rightIndex << '\t' << rightIndex+insertLength << endl;
+ string leftCandidateString = candAln.substr(0,rightIndex);
+ string rightCandidateString = candAln.substr((rightIndex+insertLength));
+ candAln = leftCandidateString + rightCandidateString;
+
+ }
+ else{ // not enough room to the right, have to steal some
+ // space to the left lets move left and then right...
+ //cout << "in else rr newTemplateAlign = " << newTemplateAlign.length() << '\t' << i << '\t' << i+insertLength << endl;
+ string leftTemplateString = newTemplateAlign.substr(0,i);
+ string rightTemplateString = newTemplateAlign.substr((i+insertLength));
+ newTemplateAlign = leftTemplateString + rightTemplateString;
+ longAlignmentLength = newTemplateAlign.length();
+ //cout << "in else rr candAln = " << candAln.length() << '\t' << '\t' << (leftIndex-(insertLength-rightRoom)+1) << '\t' << (leftIndex+1,rightIndex-leftIndex-1) << '\t' << (rightIndex+rightRoom) << endl;
+ string leftCandidateString = candAln.substr(0,(leftIndex-(insertLength-rightRoom)+1));
+ string insertString = candAln.substr((leftIndex+1),(rightIndex-leftIndex-1));
+ string rightCandidateString = candAln.substr((rightIndex+rightRoom));
+ candAln = leftCandidateString + insertString + rightCandidateString;
+
+ }
+ }
+
+ if ((i - insertLength) < 0) { i = 0; }
+ else { i -= insertLength; }
+
+ }
+ else{
+ // there could be a case where there isn't enough room in either direction to move stuff
+//cout << "in else else newTemplateAlign = " << newTemplateAlign.length() << '\t' << i << '\t' << (i+leftRoom+rightRoom) << endl;
+ string leftTemplateString = newTemplateAlign.substr(0,i);
+ string rightTemplateString = newTemplateAlign.substr((i+leftRoom+rightRoom));
+ newTemplateAlign = leftTemplateString + rightTemplateString;
+ longAlignmentLength = newTemplateAlign.length();
+
+ //cout << "in else else newTemplateAlign = " << candAln.length() << '\t' << (leftIndex-leftRoom+1) << '\t' << (leftIndex+1) << '\t' << (rightIndex-leftIndex-1) << '\t' << (rightIndex+rightRoom) << endl;
+ string leftCandidateString = candAln.substr(0,(leftIndex-leftRoom+1));
+ string insertString = candAln.substr((leftIndex+1),(rightIndex-leftIndex-1));
+ string rightCandidateString = candAln.substr((rightIndex+rightRoom));
+ candAln = leftCandidateString + insertString + rightCandidateString;
+
+ i -= (leftRoom + rightRoom);
+ }
+
+// i -= insertLength;
+
+ //if i is negative, we want to remove the extra gaps to the right
+ if (i < 0) { m->mothurOut("i is negative"); m->mothurOutEndLine(); }
+ }
+ }
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Nast", "removeExtraGaps");
+ exit(1);
+ }
+}
+
+/**************************************************************************************************/
+
+void Nast::regapSequences(){ //This is essentially part B in Fig 2. of DeSantis et al.
+ try {
+ //cout << candidateSeq->getName() << endl;
+ string candPair = candidateSeq->getPairwise();
+ string candAln = "";
+
+ string tempPair = templateSeq->getPairwise();
+ string tempAln = templateSeq->getAligned(); // we use the template aligned sequence as our guide
+
+ int pairwiseLength = candPair.length();
+ int fullAlignLength = tempAln.length();
+
+ if(candPair == ""){
+ for(int i=0;i<fullAlignLength;i++) { candAln += '.'; }
+ candidateSeq->setAligned(candAln);
+ return;
+ }
+
+ int fullAlignIndex = 0;
+ int pairwiseAlignIndex = 0;
+ string newTemplateAlign = ""; // this is going to be messy so we want a temporary template
+ // alignment string
+ while(tempAln[fullAlignIndex] == '.' || tempAln[fullAlignIndex] == '-'){
+ candAln += '.'; // add the initial '-' and '.' to the candidate and template
+ newTemplateAlign += tempAln[fullAlignIndex];// pairwise sequences
+ fullAlignIndex++;
+ }
+
+ string lastLoop = "";
+
+ while(pairwiseAlignIndex<pairwiseLength){
+ //cout << pairwiseAlignIndex << '\t' << fullAlignIndex << '\t' << pairwiseLength << endl;
+ if(isalpha(tempPair[pairwiseAlignIndex]) && isalpha(tempAln[fullAlignIndex])
+ && isalpha(candPair[pairwiseAlignIndex])){
+ // the template and candidate pairwise and template aligned have characters
+ // need to add character onto the candidatSeq.aligned sequence
+
+ candAln += candPair[pairwiseAlignIndex];
+ newTemplateAlign += tempPair[pairwiseAlignIndex];//
+
+ pairwiseAlignIndex++;
+ fullAlignIndex++;
+ }
+ else if(isalpha(tempPair[pairwiseAlignIndex]) && !isalpha(tempAln[fullAlignIndex])
+ && isalpha(candPair[pairwiseAlignIndex])){
+ // the template pairwise and candidate pairwise are characters and the template aligned is a gap
+ // need to insert gaps into the candidateSeq.aligned sequence
+
+ candAln += '-';
+ newTemplateAlign += '-';//
+ fullAlignIndex++;
+ }
+ else if(!isalpha(tempPair[pairwiseAlignIndex]) && isalpha(tempAln[fullAlignIndex])
+ && isalpha(candPair[pairwiseAlignIndex])){
+ // the template pairwise is a gap and the template aligned and pairwise sequences have characters
+ // this is the alpha scenario. add character to the candidateSeq.aligned sequence without progressing
+ // further through the tempAln sequence.
+
+ candAln += candPair[pairwiseAlignIndex];
+ newTemplateAlign += '-';//
+ pairwiseAlignIndex++;
+ }
+ else if(isalpha(tempPair[pairwiseAlignIndex]) && isalpha(tempAln[fullAlignIndex])
+ && !isalpha(candPair[pairwiseAlignIndex])){
+ // the template pairwise and full alignment are characters and the candidate sequence has a gap
+ // should not be a big deal, just add the gap position to the candidateSeq.aligned sequence;
+
+ candAln += candPair[pairwiseAlignIndex];
+ newTemplateAlign += tempAln[fullAlignIndex];//
+ fullAlignIndex++;
+ pairwiseAlignIndex++;
+ }
+ else if(!isalpha(tempPair[pairwiseAlignIndex]) && !isalpha(tempAln[fullAlignIndex])
+ && isalpha(candPair[pairwiseAlignIndex])){
+ // the template pairwise and aligned are gaps while the candidate pairwise has a character
+ // this would be an insertion, go ahead and add the character->seems to be the opposite of the alpha scenario
+
+ candAln += candPair[pairwiseAlignIndex];
+ newTemplateAlign += tempAln[fullAlignIndex];//
+ pairwiseAlignIndex++;
+ fullAlignIndex++;
+ }
+ else if(isalpha(tempPair[pairwiseAlignIndex]) && !isalpha(tempAln[fullAlignIndex])
+ && !isalpha(candPair[pairwiseAlignIndex])){
+ // template pairwise has a character, but its full aligned sequence and candidate sequence have gaps
+ // this would happen like we need to add a gap. basically the opposite of the alpha situation
+
+ newTemplateAlign += tempAln[fullAlignIndex];//
+ candAln += "-";
+ fullAlignIndex++;
+ }
+ else if(!isalpha(tempPair[pairwiseAlignIndex]) && isalpha(tempAln[fullAlignIndex])
+ && !isalpha(candPair[pairwiseAlignIndex])){
+ // template and candidate pairwise are gaps and the template aligned is not a gap this should not be possible
+ // would skip the gaps and not progress through full alignment sequence
+ // not tested yet
+
+ m->mothurOut("We're into D " + toString(fullAlignIndex) + " " + toString(pairwiseAlignIndex)); m->mothurOutEndLine();
+ pairwiseAlignIndex++;
+ }
+ else{
+ // everything has a gap - not possible
+ // not tested yet
+
+ m->mothurOut("We're into F " + toString(fullAlignIndex) + " " + toString(pairwiseAlignIndex)); m->mothurOutEndLine();
+ pairwiseAlignIndex++;
+ fullAlignIndex++;
+ }
+ }
+
+ for(int i=fullAlignIndex;i<fullAlignLength;i++){
+ candAln += '.';
+ newTemplateAlign += tempAln[i];//
+ }
+
+ int start = 0;
+ int end = candAln.length()-1;
+
+ for(int i=0;i<candAln.length();i++){
+ if(candAln[i] == 'Z' || !isalnum(candAln[i])) { candAln[i] = '.'; } // if we padded the alignemnt from
+ else{ start = i; break; } // blast with Z's, change them to
+ } // '.' characters
+
+ for(int i=candAln.length()-1;i>=0;i--){ // ditto.
+ if(candAln[i] == 'Z' || !isalnum(candAln[i])) { candAln[i] = '.'; }
+ else{ end = i; break; }
+ }
+
+ for(int i=start;i<=end;i++){ // go through the candidate alignment sequence and make sure that
+ candAln[i] = toupper(candAln[i]); // everything is upper case
+ }
+
+
+ if(candAln.length() != tempAln.length()){ // if the regapped candidate sequence is longer than the official
+ removeExtraGaps(candAln, tempAln, newTemplateAlign);// template alignment then we need to do steps C-F in Fig.
+ } // 2 of Desantis et al.
+
+ candidateSeq->setAligned(candAln);
+ //cout << "here" << endl;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Nast", "regapSequences");
+ exit(1);
+ }
+}
+
+/**************************************************************************************************/
+
+float Nast::getSimilarityScore(){
+ try {
+
+ string cand = candidateSeq->getAligned();
+ string temp = templateSeq->getAligned();
+ int alignmentLength = temp.length();
+ int mismatch = 0;
+ int denominator = 0;
+
+ for(int i=0;i<alignmentLength;i++){
+ if(cand[i] == '-' && temp[i] == '-'){
+
+ }
+ else if(cand[i] != '.' && temp[i] != '.'){
+ denominator++;
+
+ if(cand[i] != temp[i]){
+ mismatch++;
+ }
+ }
+ }
+ float similarity = 100 * (1. - mismatch / (float)denominator);
+ if(denominator == 0){ similarity = 0.0000; }
+
+ return similarity;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Nast", "getSimilarityScore");
+ exit(1);
+ }
+}
+
+/**************************************************************************************************/
+
+int Nast::getMaxInsertLength(){
+
+ return maxInsertLength;
+
+}
+
+/**************************************************************************************************/
projects / mothur.git / blobdiff