X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=trimseqscommand.cpp;h=ae9c436440950cca6cd33eb99e85c5b9b4db1062;hb=4a2d841cb97fb02351022efe9d7068b1dc212bf9;hp=537992584660b29696b602f09285aff6279aea73;hpb=c7f1abdd8b8d24f186320880515a848039ce051a;p=mothur.git

diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index 5379925..ae9c436 100644
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -23,7 +23,7 @@ TrimSeqsCommand::TrimSeqsCommand(string option)  {
 		else {
 			//valid paramters for this command
 			string AlignArray[] =  {"fasta", "flip", "oligos", "maxambig", "maxhomop", "minlength", "maxlength", "qfile", 
-									"qthreshold", "qaverage", "allfiles", "qtrim","diffs", "processors", "outputdir","inputdir"};
+									"qthreshold", "qaverage", "allfiles", "qtrim","tdiffs", "pdiffs", "bdiffs", "processors", "outputdir","inputdir"};
 			
 			vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
 			
@@ -104,8 +104,17 @@ TrimSeqsCommand::TrimSeqsCommand(string option)  {
 			temp = validParameter.validFile(parameters, "maxlength", false);	if (temp == "not found") { temp = "0"; }
 			convert(temp, maxLength);
 			
-			temp = validParameter.validFile(parameters, "diffs", false);		if (temp == "not found") { temp = "0"; }
-			convert(temp, diffs);
+			
+			temp = validParameter.validFile(parameters, "bdiffs", false);		if (temp == "not found") { temp = "0"; }
+			convert(temp, bdiffs);
+			
+			temp = validParameter.validFile(parameters, "pdiffs", false);		if (temp == "not found") { temp = "0"; }
+			convert(temp, pdiffs);
+			
+			temp = validParameter.validFile(parameters, "tdiffs", false);		if (temp == "not found") { int tempTotal = pdiffs + bdiffs;  temp = toString(tempTotal); }
+			convert(temp, tdiffs);
+			
+			if(tdiffs == 0){	tdiffs = bdiffs + pdiffs;	}
 			
 			temp = validParameter.validFile(parameters, "qfile", true);	
 			if (temp == "not found")	{	qFileName = "";		}
@@ -160,7 +169,9 @@ void TrimSeqsCommand::help(){
 		m->mothurOut("The maxhomop parameter .... The default is 0.\n");
 		m->mothurOut("The minlength parameter .... The default is 0.\n");
 		m->mothurOut("The maxlength parameter .... The default is 0.\n");
-		m->mothurOut("The diffs parameter .... The default is 0.\n");
+		m->mothurOut("The tdiffs parameter is used to specify the total number of differences allowed in the sequence. The default is pdiffs + bdiffs.\n");
+		m->mothurOut("The bdiffs parameter is used to specify the number of differences allowed in the barcode. The default is 0.\n");
+		m->mothurOut("The pdiffs parameter is used to specify the number of differences allowed in the primer. The default is 0.\n");
 		m->mothurOut("The qfile parameter .....\n");
 		m->mothurOut("The qthreshold parameter .... The default is 0.\n");
 		m->mothurOut("The qaverage parameter .... The default is 0.\n");
@@ -255,13 +266,13 @@ int TrimSeqsCommand::execute(){
 				if (m->control_pressed) {  return 0; }
 		#else
 				ifstream inFASTA;
-				openInputFile(fastafileNames[s], inFASTA);
-				numSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
+				openInputFile(fastaFile, inFASTA);
+				int numSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
 				inFASTA.close();
 				
 				lines.push_back(new linePair(0, numSeqs));
 				
-				driverCreateSummary(fastafile, qFileName, trimSeqFile, scrapSeqFile, groupFile, fastaFileNames, lines[0], lines[0]);
+				driverCreateTrim(fastaFile, qFileName, trimSeqFile, scrapSeqFile, groupFile, fastaFileNames, lines[0], lines[0]);
 				
 				if (m->control_pressed) {  return 0; }
 		#endif
@@ -320,7 +331,11 @@ int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string
 		if (oligoFile != "") {		
 			openOutputFile(groupFile, outGroups);   
 			for (int i = 0; i < fastaNames.size(); i++) {
+			#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 				fastaFileNames.push_back(new ofstream((fastaNames[i] + toString(getpid()) + ".temp").c_str(), ios::ate)); 
+			#else
+				fastaFileNames.push_back(new ofstream((fastaNames[i] + toString(i) + ".temp").c_str(), ios::ate)); 			
+			#endif
 			}
 		}
 		
@@ -357,6 +372,7 @@ int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string
 			if (origSeq != "") {
 				int group;
 				string trashCode = "";
+				int currentSeqsDiffs = 0;
 				
 				if(qFileName != ""){
 					if(qThreshold != 0)		{	success = stripQualThreshold(currSeq, qFile);	}
@@ -369,14 +385,19 @@ int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string
 			
 				if(barcodes.size() != 0){
 					success = stripBarcode(currSeq, group);
-					if(!success){	trashCode += 'b';	}
+//					cout << "here: " << success << endl;
+					if(success > bdiffs){	trashCode += 'b';	}
+					else{ currentSeqsDiffs += success;  }
 				}
-			
+
 				if(numFPrimers != 0){
 					success = stripForward(currSeq);
-					if(!success){	trashCode += 'f';	}
+					if(success > pdiffs){	trashCode += 'f';	}
+					else{ currentSeqsDiffs += success;  }
 				}
-					
+				
+				if (currentSeqsDiffs > tdiffs) { trashCode += 't';   }
+
 				if(numRPrimers != 0){
 					success = stripReverse(currSeq);
 					if(!success){	trashCode += 'r';	}
@@ -587,68 +608,106 @@ void TrimSeqsCommand::getOligos(vector<string>& outFASTAVec){ //vector<ofstream*
 }
 //***************************************************************************************************************
 
-bool TrimSeqsCommand::stripBarcode(Sequence& seq, int& group){
+int TrimSeqsCommand::stripBarcode(Sequence& seq, int& group){
 	try {
 		string rawSequence = seq.getUnaligned();
-		bool success = 0;	//guilty until proven innocent
+		bool success = bdiffs + 1;	//guilty until proven innocent
 		
 		//can you find the barcode
 		for(map<string,int>::iterator it=barcodes.begin();it!=barcodes.end();it++){
 			string oligo = it->first;
 			if(rawSequence.length() < oligo.length()){	//let's just assume that the barcodes are the same length
-				success = 0;
+				success = bdiffs + 1;
 				break;
 			}
 			
 			if(compareDNASeq(oligo, rawSequence.substr(0,oligo.length()))){
 				group = it->second;
 				seq.setUnaligned(rawSequence.substr(oligo.length()));
-				success = 1;
+				success = 0;
 				break;
 			}
 		}
 		
 		//if you found the barcode or if you don't want to allow for diffs
-		if ((diffs == 0) || (success == 1)) { return success;  }
+//		cout << success;
+		if ((bdiffs == 0) || (success == 0)) { return success;  }
 		
 		else { //try aligning and see if you can find it
-			
+//			cout << endl;
+
+			int maxLength = 0;
+
 			Alignment* alignment;
-			if (barcodes.size() > 0) { //assumes barcodes are all the same length
+			if (barcodes.size() > 0) {
 				map<string,int>::iterator it=barcodes.begin();
-				string temp = it->first;
-				
-				alignment = new NeedlemanOverlap(-2.0, 1.0, -1.0, (temp.length()+diffs+1));  
+
+				for(it;it!=barcodes.end();it++){
+					if(it->first.length() > maxLength){
+						maxLength = it->first.length();
+					}
+				}
+				alignment = new NeedlemanOverlap(-2.0, 1.0, -1.0, (maxLength+bdiffs+1));  
+
 			}else{ alignment = NULL; } 
 			
-
 			//can you find the barcode
+			int minDiff = 1e6;
+			int minCount = 1;
+			int minGroup = -1;
+			int minPos = 0;
+			
 			for(map<string,int>::iterator it=barcodes.begin();it!=barcodes.end();it++){
 				string oligo = it->first;
-				int length = oligo.length();
+//				int length = oligo.length();
 				
-				if(rawSequence.length() < oligo.length()){	//let's just assume that the barcodes are the same length
-					success = 0;
+				if(rawSequence.length() < maxLength){	//let's just assume that the barcodes are the same length
+					success = bdiffs + 1;
 					break;
 				}
 				
 				//use needleman to align first barcode.length()+numdiffs of sequence to each barcode
-				alignment->align(oligo, rawSequence.substr(0,length+diffs));
+				alignment->align(oligo, rawSequence.substr(0,oligo.length()+bdiffs));
 				oligo = alignment->getSeqAAln();
 				string temp = alignment->getSeqBAln();
-		cout << "barcode = " << oligo << " raw = " << rawSequence.substr(0,oligo.length()) << " raw aligned = " << temp << endl;			
+		
+				int alnLength = oligo.length();
+				
+				for(int i=oligo.length()-1;i>=0;i--){
+					if(oligo[i] != '-'){	alnLength = i+1;	break;	}
+				}
+				oligo = oligo.substr(0,alnLength);
+				temp = temp.substr(0,alnLength);
+//				
 				
 				int newStart=0;
-				if(compareDNASeq(oligo, rawSequence.substr(0,oligo.length()), length, newStart)){
-		cout << "found match" << endl;
-					group = it->second;
-					seq.setUnaligned(rawSequence.substr(newStart));
-					success = 1;
-					break;
+				int numDiff = countDiffs(oligo, temp);
+				if(numDiff < minDiff){
+					minDiff = numDiff;
+					minCount = 1;
+					minGroup = it->second;
+					minPos = 0;
+					for(int i=0;i<alnLength;i++){
+						if(temp[i] != '-'){
+							minPos++;
+						}
+					}
+				}
+				else if(numDiff == minDiff){
+					minCount++;
 				}
+
+			}
+			if(minDiff > bdiffs){	success =  bdiffs + 1;	}
+			else if(minCount > 1)	{	success =  bdiffs + 1;	}
+			else{
+				group = minGroup;
+				seq.setUnaligned("*" + rawSequence.substr(minPos));
+				success = minDiff;
 			}
 			
 			if (alignment != NULL) {  delete alignment;  }
+			
 		}
 		return success;
 		
@@ -662,63 +721,103 @@ bool TrimSeqsCommand::stripBarcode(Sequence& seq, int& group){
 
 //***************************************************************************************************************
 
-bool TrimSeqsCommand::stripForward(Sequence& seq){
+int TrimSeqsCommand::stripForward(Sequence& seq){
 	try {
 		string rawSequence = seq.getUnaligned();
-		bool success = 0;	//guilty until proven innocent
+		bool success = pdiffs + 1;	//guilty until proven innocent
 		
+		//can you find the primer
 		for(int i=0;i<numFPrimers;i++){
 			string oligo = forPrimer[i];
-			
-			if(rawSequence.length() < oligo.length()){
-				success = 0;
+
+			if(rawSequence.length() < oligo.length()){	
+				success = pdiffs + 1;
 				break;
 			}
 			
 			if(compareDNASeq(oligo, rawSequence.substr(0,oligo.length()))){
 				seq.setUnaligned(rawSequence.substr(oligo.length()));
-				success = 1;
+				success = 0;
 				break;
 			}
 		}
 		
-		//if you found the primer or if you don't want to allow for diffs
-		if ((diffs == 0) || (success == 1)) { return success;  }
+		//if you found the barcode or if you don't want to allow for diffs
+//		cout << success;
+		if ((pdiffs == 0) || (success == 0)) { return success;  }
 		
 		else { //try aligning and see if you can find it
-			
-			
+//			cout << endl;
+
+			int maxLength = 0;
+
 			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; } 
+			if (numFPrimers > 0) {
+
+				for(int i=0;i<numFPrimers;i++){
+					if(forPrimer[i].length() > maxLength){
+						maxLength = forPrimer[i].length();
+					}
+				}
+				alignment = new NeedlemanOverlap(-2.0, 1.0, -1.0, (maxLength+pdiffs+1));  
+
+			}else{ alignment = NULL; } 
+			
+			//can you find the barcode
+			int minDiff = 1e6;
+			int minCount = 1;
+			int minPos = 0;
 			
-			//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;
+				if(rawSequence.length() < maxLength){	
+					success = pdiffs + 1;
 					break;
 				}
 				
-				//use needleman to align first primer.length()+numdiffs of sequence to each primer
-				alignment->align(oligo, rawSequence.substr(0,length+diffs));
+				//use needleman to align first barcode.length()+numdiffs of sequence to each barcode
+				alignment->align(oligo, rawSequence.substr(0,oligo.length()+pdiffs));
 				oligo = alignment->getSeqAAln();
+				string temp = alignment->getSeqBAln();
+		
+				int alnLength = oligo.length();
 				
-				int newStart = 0;
-				if(compareDNASeq(oligo, rawSequence.substr(0,oligo.length()), length, newStart)){
-					seq.setUnaligned(rawSequence.substr(newStart));
-					success = 1;
-					break;
+				for(int i=oligo.length()-1;i>=0;i--){
+					if(oligo[i] != '-'){	alnLength = i+1;	break;	}
+				}
+				oligo = oligo.substr(0,alnLength);
+				temp = temp.substr(0,alnLength);
+//								
+				int newStart=0;
+				int numDiff = countDiffs(oligo, temp);
+				if(numDiff < minDiff){
+					minDiff = numDiff;
+					minCount = 1;
+					minPos = 0;
+					for(int i=0;i<alnLength;i++){
+						if(temp[i] != '-'){
+							minPos++;
+						}
+					}
+				}
+				else if(numDiff == minDiff){
+					minCount++;
 				}
+
+			}
+			if(minDiff > pdiffs){	success =  pdiffs + 1;	}
+			else if(minCount > 1)	{	success =  pdiffs + 1;	}
+			else{
+				seq.setUnaligned("*" + rawSequence.substr(minPos));
+				success = minDiff;
 			}
 			
 			if (alignment != NULL) {  delete alignment;  }
+			
 		}
-		
 		return success;
-		
+
 	}
 	catch(exception& e) {
 		m->errorOut(e, "TrimSeqsCommand", "stripForward");
@@ -856,24 +955,14 @@ bool TrimSeqsCommand::compareDNASeq(string oligo, string seq){
 }
 //***************************************************************************************************************
 
-bool TrimSeqsCommand::compareDNASeq(string oligo, string seq, int numBases, int& end){
+int TrimSeqsCommand::countDiffs(string oligo, string seq){
 	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++;	}
@@ -888,19 +977,13 @@ bool TrimSeqsCommand::compareDNASeq(string oligo, string seq, int numBases, int&
 				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;
+		
+		return countDiffs;
 	}
 	catch(exception& e) {
-		m->errorOut(e, "TrimSeqsCommand", "compareDNASeq");
+		m->errorOut(e, "TrimSeqsCommand", "countDiffs");
 		exit(1);
 	}