working on trim.seqs

diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index d72ada4cff4fb44cd557eede88d63f44a43c1cd6..537992584660b29696b602f09285aff6279aea73 100644 (file)
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -9,7 +9,6 @@
 
 #include "trimseqscommand.h"
 #include "needlemanoverlap.hpp"
-#include "nast.hpp"
 
 //***************************************************************************************************************
 
@@ -613,33 +612,43 @@ bool TrimSeqsCommand::stripBarcode(Sequence& seq, int& group){
                if ((diffs == 0) || (success == 1)) { return success;  }
                
                else { //try aligning and see if you can find it
+                       
+                       Alignment* alignment;
+                       if (barcodes.size() > 0) { //assumes barcodes are all the same length
+                               map<string,int>::iterator it=barcodes.begin();
+                               string temp = it->first;
+                               
+                               alignment = new NeedlemanOverlap(-2.0, 1.0, -1.0, (temp.length()+diffs+1));  
+                       }else{ alignment = NULL; } 
+                       
+
                        //can you find the barcode
                        for(map<string,int>::iterator it=barcodes.begin();it!=barcodes.end();it++){
                                string oligo = it->first;
+                               int length = oligo.length();
+                               
                                if(rawSequence.length() < oligo.length()){      //let's just assume that the barcodes are the same length
                                        success = 0;
                                        break;
                                }
                                
                                //use needleman to align first barcode.length()+numdiffs of sequence to each barcode
-                               Alignment* alignment = new NeedlemanOverlap(-2.0, 1.0, -1.0, (oligo.length()+diffs+1));
-                               Sequence* templateSeq = new Sequence("temp", rawSequence.substr(0,(oligo.length()+diffs)));
-                               Sequence* candidateSeq = new Sequence("temp2", oligo);
-                               Nast nast(alignment, candidateSeq, templateSeq);
-                               
-                               oligo = candidateSeq->getAligned();
-       cout << "barcode = " << oligo << " raw = " << rawSequence.substr(0,(oligo.length())) << endl;                   
-                               delete alignment;
-                               delete templateSeq;
-                               delete candidateSeq;
+                               alignment->align(oligo, rawSequence.substr(0,length+diffs));
+                               oligo = alignment->getSeqAAln();
+                               string temp = alignment->getSeqBAln();
+               cout << "barcode = " << oligo << " raw = " << rawSequence.substr(0,oligo.length()) << " raw aligned = " << temp << endl;                        
                                
-                               if(compareDNASeq(oligo, rawSequence.substr(0,oligo.length()))){
+                               int newStart=0;
+                               if(compareDNASeq(oligo, rawSequence.substr(0,oligo.length()), length, newStart)){
+               cout << "found match" << endl;
                                        group = it->second;
-                                       seq.setUnaligned(rawSequence.substr(0,oligo.length()));
+                                       seq.setUnaligned(rawSequence.substr(newStart));
                                        success = 1;
                                        break;
                                }
                        }
+                       
+                       if (alignment != NULL) {  delete alignment;  }
                }
                return success;
                
@@ -677,32 +686,35 @@ bool TrimSeqsCommand::stripForward(Sequence& seq){
                if ((diffs == 0) || (success == 1)) { return success;  }
                
                else { //try aligning and see if you can find it
+                       
+                       
+                       Alignment* alignment;
+                       if (numFPrimers > 0) { alignment = new NeedlemanOverlap(-2.0, 1.0, -1.0, (forPrimer[0].length()+diffs+1));  } //assumes primers are all the same length
+                       else{ alignment = NULL; } 
+                       
                        //can you find the primer
                        for(int i=0;i<numFPrimers;i++){
                                string oligo = forPrimer[i];
+                               int length = oligo.length();
+                               
                                if(rawSequence.length() < oligo.length()){      
                                        success = 0;
                                        break;
                                }
                                
                                //use needleman to align first primer.length()+numdiffs of sequence to each primer
-                               Alignment* alignment = new NeedlemanOverlap(-2.0, 1.0, -1.0, (oligo.length()+diffs+1));
-                               Sequence* templateSeq = new Sequence("temp", rawSequence.substr(0,(oligo.length()+diffs)));
-                               Sequence* candidateSeq = new Sequence("temp2", oligo);
-                               Nast nast(alignment, candidateSeq, templateSeq);
+                               alignment->align(oligo, rawSequence.substr(0,length+diffs));
+                               oligo = alignment->getSeqAAln();
                                
-                               oligo = candidateSeq->getAligned();
-                               
-                               delete alignment;
-                               delete templateSeq;
-                               delete candidateSeq;
-                               
-                               if(compareDNASeq(oligo, rawSequence.substr(0,oligo.length()))){
-                                       seq.setUnaligned(rawSequence.substr(0,oligo.length()));
+                               int newStart = 0;
+                               if(compareDNASeq(oligo, rawSequence.substr(0,oligo.length()), length, newStart)){
+                                       seq.setUnaligned(rawSequence.substr(newStart));
                                        success = 1;
                                        break;
                                }
                        }
+                       
+                       if (alignment != NULL) {  delete alignment;  }
                }
                
                return success;
@@ -842,7 +854,57 @@ bool TrimSeqsCommand::compareDNASeq(string oligo, string seq){
        }
 
 }
+//***************************************************************************************************************
+
+bool TrimSeqsCommand::compareDNASeq(string oligo, string seq, int numBases, int& end){
+       try {
+               bool success = 1;
+               int length = oligo.length();
+               end = length;
+               int countBases = 0;
+               int countDiffs = 0;
+               
+               if (length != 0) {
+                       if ((oligo[0] == '-') || (oligo[0] == '.')) {  success = 0; return success;  } //no gaps allowed at beginning
+               }
+               
+               for(int i=0;i<length;i++){
+                       
+                       if ((oligo[i] != '-') && (oligo[i] != '.'))  { countBases++; } 
+                       
+       //cout << oligo[i] << " " << seq[i] << " diffs = " << countDiffs << " countBases = " << countBases << endl;     
+               
+                       if(oligo[i] != seq[i]){
+                               if(oligo[i] == 'A' || oligo[i] == 'T' || oligo[i] == 'G' || oligo[i] == 'C' || oligo[i] == '-' || oligo[i] == '.')      {       countDiffs++;   }
+                               else if((oligo[i] == 'N' || oligo[i] == 'I') && (seq[i] == 'N'))                                {       countDiffs++;   }
+                               else if(oligo[i] == 'R' && (seq[i] != 'A' && seq[i] != 'G'))                                    {       countDiffs++;   }
+                               else if(oligo[i] == 'Y' && (seq[i] != 'C' && seq[i] != 'T'))                                    {       countDiffs++;   }
+                               else if(oligo[i] == 'M' && (seq[i] != 'C' && seq[i] != 'A'))                                    {       countDiffs++;   }
+                               else if(oligo[i] == 'K' && (seq[i] != 'T' && seq[i] != 'G'))                                    {       countDiffs++;   }
+                               else if(oligo[i] == 'W' && (seq[i] != 'T' && seq[i] != 'A'))                                    {       countDiffs++;   }
+                               else if(oligo[i] == 'S' && (seq[i] != 'C' && seq[i] != 'G'))                                    {       countDiffs++;   }
+                               else if(oligo[i] == 'B' && (seq[i] != 'C' && seq[i] != 'T' && seq[i] != 'G'))   {       countDiffs++;   }
+                               else if(oligo[i] == 'D' && (seq[i] != 'A' && seq[i] != 'T' && seq[i] != 'G'))   {       countDiffs++;   }
+                               else if(oligo[i] == 'H' && (seq[i] != 'A' && seq[i] != 'T' && seq[i] != 'C'))   {       countDiffs++;   }
+                               else if(oligo[i] == 'V' && (seq[i] != 'A' && seq[i] != 'C' && seq[i] != 'G'))   {       countDiffs++;   }                       
+                               
+                               if(countDiffs > diffs)  {       success = 0; break;      }
+                       }
+                       else{
+                               success = 1;
+                       }
+                       
+                       if (countBases >= numBases) { end = i; break; } //stop checking after end of barcode or primer
+               }
+       
+               return success;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "TrimSeqsCommand", "compareDNASeq");
+               exit(1);
+       }
 
+}
 //***************************************************************************************************************
 
 bool TrimSeqsCommand::stripQualThreshold(Sequence& seq, ifstream& qFile){

diff --git a/trimseqscommand.h b/trimseqscommand.h
index 601cb6129d1ba5a32e54dad125e4689d9559d5d6..4a1d3d72c4f78e7c81fc22d17d996c68ff093984 100644 (file)
--- a/trimseqscommand.h
+++ b/trimseqscommand.h
@@ -39,6 +39,7 @@ private:
        bool cullHomoP(Sequence&);
        bool cullAmbigs(Sequence&);
        bool compareDNASeq(string, string);
+       bool compareDNASeq(string, string, int, int&);
 
        bool abort;
        string fastaFile, oligoFile, qFileName, outputDir;