+++ /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;
-
-}
-
-/**************************************************************************************************/
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