From: westcott <westcott>
Date: Tue, 15 Jun 2010 13:50:04 +0000 (+0000)
Subject: changed how we count sequences in a fastafile to allow for '>' in sequence names
X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=commitdiff_plain;h=cd985cf388dcc4c7de8251339206aec5f7e12f1e

changed how we count sequences in a fastafile to allow for '>' in sequence names
---

diff --git a/aligncommand.cpp b/aligncommand.cpp
index c5407ca..1f93068 100644
--- a/aligncommand.cpp
+++ b/aligncommand.cpp
@@ -373,7 +373,7 @@ int AlignCommand::execute(){
 			if(processors == 1){
 				ifstream inFASTA;
 				openInputFile(candidateFileNames[s], inFASTA);
-				numFastaSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
+				getNumSeqs(inFASTA, numFastaSeqs);
 				inFASTA.close();
 				
 				lines.push_back(new linePair(0, numFastaSeqs));
@@ -472,7 +472,7 @@ int AlignCommand::execute(){
 	#else
 			ifstream inFASTA;
 			openInputFile(candidateFileNames[s], inFASTA);
-			numFastaSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
+			getNumSeqs(inFASTA, numFastaSeqs);
 			inFASTA.close();
 			
 			lines.push_back(new linePair(0, numFastaSeqs));
diff --git a/chimeraccodecommand.cpp b/chimeraccodecommand.cpp
index 45f7f54..280fd8f 100644
--- a/chimeraccodecommand.cpp
+++ b/chimeraccodecommand.cpp
@@ -304,7 +304,7 @@ int ChimeraCcodeCommand::execute(){
 			if(processors == 1){
 				ifstream inFASTA;
 				openInputFile(fastafile, inFASTA);
-				numSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
+				getNumSeqs(inFASTA, numSeqs);
 				inFASTA.close();
 				
 				lines.push_back(new linePair(0, numSeqs));
@@ -393,7 +393,7 @@ int ChimeraCcodeCommand::execute(){
 		#else
 			ifstream inFASTA;
 			openInputFile(fastafile, inFASTA);
-			numSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
+			getNumSeqs(inFASTA, numSeqs);
 			inFASTA.close();
 			lines.push_back(new linePair(0, numSeqs));
 			
diff --git a/chimeracheckcommand.cpp b/chimeracheckcommand.cpp
index 66cf12f..4947dc9 100644
--- a/chimeracheckcommand.cpp
+++ b/chimeracheckcommand.cpp
@@ -245,7 +245,7 @@ int ChimeraCheckCommand::execute(){
 			if(processors == 1){
 				ifstream inFASTA;
 				openInputFile(fastafile, inFASTA);
-				numSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
+				getNumSeqs(inFASTA, numSeqs);
 				inFASTA.close();
 				
 				lines.push_back(new linePair(0, numSeqs));
@@ -309,7 +309,7 @@ int ChimeraCheckCommand::execute(){
 		#else
 			ifstream inFASTA;
 			openInputFile(fastafile, inFASTA);
-			numSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
+			getNumSeqs(inFASTA, numSeqs);
 			inFASTA.close();
 			lines.push_back(new linePair(0, numSeqs));
 			
diff --git a/chimerapintailcommand.cpp b/chimerapintailcommand.cpp
index 6cef8bb..c43dd38 100644
--- a/chimerapintailcommand.cpp
+++ b/chimerapintailcommand.cpp
@@ -312,7 +312,7 @@ int ChimeraPintailCommand::execute(){
 			if(processors == 1){
 				ifstream inFASTA;
 				openInputFile(fastafile, inFASTA);
-				numSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
+				getNumSeqs(inFASTA, numSeqs);
 				inFASTA.close();
 				
 				lines.push_back(new linePair(0, numSeqs));
@@ -399,7 +399,7 @@ int ChimeraPintailCommand::execute(){
 		#else
 			ifstream inFASTA;
 			openInputFile(fastafile, inFASTA);
-			numSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
+			getNumSeqs(inFASTA, numSeqs);
 			inFASTA.close();
 			lines.push_back(new linePair(0, numSeqs));
 			
diff --git a/chimeraslayercommand.cpp b/chimeraslayercommand.cpp
index 8a0e287..004cfb0 100644
--- a/chimeraslayercommand.cpp
+++ b/chimeraslayercommand.cpp
@@ -329,7 +329,7 @@ int ChimeraSlayerCommand::execute(){
 			if(processors == 1){
 				ifstream inFASTA;
 				openInputFile(fastafile, inFASTA);
-				numSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
+				getNumSeqs(inFASTA, numSeqs);
 				inFASTA.close();
 				
 				lines.push_back(new linePair(0, numSeqs));
@@ -417,7 +417,7 @@ int ChimeraSlayerCommand::execute(){
 		#else
 			ifstream inFASTA;
 			openInputFile(fastafile, inFASTA);
-			numSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
+			getNumSeqs(inFASTA, numSeqs);
 			inFASTA.close();
 			lines.push_back(new linePair(0, numSeqs));
 			
diff --git a/classify.cpp b/classify.cpp
index 7f45126..22728eb 100644
--- a/classify.cpp
+++ b/classify.cpp
@@ -97,7 +97,7 @@ void Classify::generateDatabaseAndNames(string tfile, string tempFile, string me
 		if (method == "suffix") {
 			ifstream inFASTA;
 			openInputFile(tempFile, inFASTA);
-			numSeqs = count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
+			getNumSeqs(inFASTA, numSeqs);
 			inFASTA.close();
 		}
 
diff --git a/classifyotucommand.cpp b/classifyotucommand.cpp
index 94a60d4..aac1637 100644
--- a/classifyotucommand.cpp
+++ b/classifyotucommand.cpp
@@ -114,7 +114,7 @@ ClassifyOtuCommand::ClassifyOtuCommand(string option)  {
 
 void ClassifyOtuCommand::help(){
 	try {
-		m->mothurOut("The classify.otu command parameters are list, taxonomy, name, cutoff, and label.  The taxonomy and list parameters are required.\n");
+		m->mothurOut("The classify.otu command parameters are list, taxonomy, name, cutoff, label and probs.  The taxonomy and list parameters are required.\n");
 		m->mothurOut("The name parameter allows you add a names file with your taxonomy file.\n");
 		m->mothurOut("The label parameter allows you to select what distance levels you would like a output files created for, and is separated by dashes.\n");
 		m->mothurOut("The default value for label is all labels in your inputfile.\n");
diff --git a/classifyseqscommand.cpp b/classifyseqscommand.cpp
index e5c0494..6c5d827 100644
--- a/classifyseqscommand.cpp
+++ b/classifyseqscommand.cpp
@@ -470,7 +470,7 @@ int ClassifySeqsCommand::execute(){
 			if(processors == 1){
 				ifstream inFASTA;
 				openInputFile(fastaFileNames[s], inFASTA);
-				numFastaSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
+				getNumSeqs(inFASTA, numFastaSeqs);
 				inFASTA.close();
 				
 				lines.push_back(new linePair(0, numFastaSeqs));
@@ -520,7 +520,7 @@ int ClassifySeqsCommand::execute(){
 	#else
 			ifstream inFASTA;
 			openInputFile(fastaFileNames[s], inFASTA);
-			numFastaSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
+			getNumSeqs(inFASTA, numFastaSeqs);
 			inFASTA.close();
 			
 			lines.push_back(new linePair(0, numFastaSeqs));
diff --git a/filterseqscommand.cpp b/filterseqscommand.cpp
index 1c70b3e..a6290a6 100644
--- a/filterseqscommand.cpp
+++ b/filterseqscommand.cpp
@@ -336,8 +336,9 @@ int FilterSeqsCommand::filterSequences() {
 		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 				if(processors == 1){
 					ifstream inFASTA;
+					int numFastaSeqs;
 					openInputFile(fastafileNames[s], inFASTA);
-					int numFastaSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
+					getNumSeqs(inFASTA, numFastaSeqs);
 					inFASTA.close();
 					
 					lines.push_back(new linePair(0, numFastaSeqs));
@@ -361,8 +362,9 @@ int FilterSeqsCommand::filterSequences() {
 				if (m->control_pressed) {  return 1; }
 		#else
 				ifstream inFASTA;
+				int numFastaSeqs;
 				openInputFile(fastafileNames[s], inFASTA);
-				int numFastaSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
+				getNumSeqs(inFASTA, numFastaSeqs);
 				inFASTA.close();
 					
 				lines.push_back(new linePair(0, numFastaSeqs));
@@ -625,8 +627,9 @@ string FilterSeqsCommand::createFilter() {
 		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 				if(processors == 1){
 					ifstream inFASTA;
+					int numFastaSeqs;
 					openInputFile(fastafileNames[s], inFASTA);
-					int numFastaSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
+					getNumSeqs(inFASTA, numFastaSeqs);
 					inFASTA.close();
 					
 					numSeqs += numFastaSeqs;
@@ -642,8 +645,9 @@ string FilterSeqsCommand::createFilter() {
 				if (m->control_pressed) {  return filterString; }
 		#else
 				ifstream inFASTA;
+				int numFastaSeqs;
 				openInputFile(fastafileNames[s], inFASTA);
-				int numFastaSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
+				getNumSeqs(inFASTA, numFastaSeqs);
 				inFASTA.close();
 				
 				numSeqs += numFastaSeqs;
diff --git a/mothur.h b/mothur.h
index 5d12977..a7946fd 100644
--- a/mothur.h
+++ b/mothur.h
@@ -632,6 +632,19 @@ inline int getNumSeqs(ifstream& file){
 	return numSeqs;
 
 }
+/***********************************************************************/
+inline void getNumSeqs(ifstream& file, int& numSeqs){
+	
+	string input;
+	numSeqs = 0;
+	while(!file.eof()){
+		input = getline(file);
+		if (input.length() != 0) {
+			if(input[0] == '>'){ numSeqs++;	}
+		}
+	}
+}
+
 /***********************************************************************/
 
 inline bool inVector(string member, vector<string> group){
diff --git a/screenseqscommand.cpp b/screenseqscommand.cpp
index 878a06b..66e0cb0 100644
--- a/screenseqscommand.cpp
+++ b/screenseqscommand.cpp
@@ -295,7 +295,7 @@ int ScreenSeqsCommand::execute(){
 			if(processors == 1){
 				ifstream inFASTA;
 				openInputFile(fastafile, inFASTA);
-				numFastaSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
+				getNumSeqs(inFASTA, numFastaSeqs);
 				inFASTA.close();
 				
 				lines.push_back(new linePair(0, numFastaSeqs));
@@ -369,7 +369,7 @@ int ScreenSeqsCommand::execute(){
 	#else
 			ifstream inFASTA;
 			openInputFile(fastafile, inFASTA);
-			numFastaSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
+			getNumSeqs(inFASTA, numFastaSeqs);
 			inFASTA.close();
 			
 			lines.push_back(new linePair(0, numFastaSeqs));
diff --git a/seqsummarycommand.cpp b/seqsummarycommand.cpp
index d613391..7226f9d 100644
--- a/seqsummarycommand.cpp
+++ b/seqsummarycommand.cpp
@@ -228,9 +228,9 @@ int SeqSummaryCommand::execute(){
 				if(processors == 1){
 					ifstream inFASTA;
 					openInputFile(fastafile, inFASTA);
-					numSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
-					inFASTA.close();
-			cout << numSeqs << endl;		
+					getNumSeqs(inFASTA, numSeqs);
+					inFASTA.close();	
+						
 					lines.push_back(new linePair(0, numSeqs));
 					
 					driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, summaryFile, lines[0]);
@@ -250,7 +250,7 @@ int SeqSummaryCommand::execute(){
 		#else
 				ifstream inFASTA;
 				openInputFile(fastafile, inFASTA);
-				numSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
+				getNumSeqs(inFASTA, numSeqs);
 				inFASTA.close();
 				
 				lines.push_back(new linePair(0, numSeqs));
diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index 71e5c92..3fd3ad1 100644
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -224,8 +224,9 @@ int TrimSeqsCommand::execute(){
 		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 				if(processors == 1){
 					ifstream inFASTA;
+					int numSeqs;
 					openInputFile(fastaFile, inFASTA);
-					int numSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
+					getNumSeqs(inFASTA, numSeqs);
 					inFASTA.close();
 					
 					lines.push_back(new linePair(0, numSeqs));
@@ -266,8 +267,9 @@ int TrimSeqsCommand::execute(){
 				if (m->control_pressed) {  return 0; }
 		#else
 				ifstream inFASTA;
+				int numSeqs;
 				openInputFile(fastaFile, inFASTA);
-				int numSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
+				getNumSeqs(inFASTA, numSeqs);
 				inFASTA.close();
 				
 				lines.push_back(new linePair(0, numSeqs));