X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getseqscommand.cpp;h=83fdf73e9af36fd9826f5a8c2efcc11655ac938e;hb=541bab1dac00688b4c3a8c4a95ab464412663c50;hp=779ea912ebebbe58ec22e65723899c4ea566b85f;hpb=1a5c2356c1b955c6ec024b2baf9f46377ee7c72e;p=mothur.git

diff --git a/getseqscommand.cpp b/getseqscommand.cpp
index 779ea91..83fdf73 100644
--- a/getseqscommand.cpp
+++ b/getseqscommand.cpp
@@ -45,7 +45,7 @@ string GetSeqsCommand::getHelpString(){
 		helpString += "The get.seqs command reads an .accnos file and any of the following file types: fasta, name, group, count, list, taxonomy, quality or alignreport file.\n";
 		helpString += "It outputs a file containing only the sequences in the .accnos file.\n";
 		helpString += "The get.seqs command parameters are accnos, fasta, name, group, list, taxonomy, qfile, alignreport and dups.  You must provide accnos unless you have a valid current accnos file, and at least one of the other parameters.\n";
-		helpString += "The dups parameter allows you to add the entire line from a name file if you add any name from the line. default=false. \n";
+		helpString += "The dups parameter allows you to add the entire line from a name file if you add any name from the line. default=true. \n";
 		helpString += "The get.seqs command should be in the following format: get.seqs(accnos=yourAccnos, fasta=yourFasta).\n";
 		helpString += "Example get.seqs(accnos=amazon.accnos, fasta=amazon.fasta).\n";
 		helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n";
@@ -427,7 +427,14 @@ int GetSeqsCommand::readFasta(){
 			
 			Sequence currSeq(in);
 			name = currSeq.getName();
+            
+            if (!dups) {//adjust name if needed
+                map<string, string>::iterator it = uniqueMap.find(name);
+                if (it != uniqueMap.end()) { currSeq.setName(it->second); }
+            }
 			
+            name = currSeq.getName();
+            
 			if (name != "") {
 				//if this name is in the accnos file
 				if (names.count(name) != 0) {
@@ -485,13 +492,18 @@ int GetSeqsCommand::readQual(){
 			string name = "";
 			string scores = "";
 			
-			in >> name; 
+			in >> name;
+            
+            if (!dups) {//adjust name if needed
+                map<string, string>::iterator it = uniqueMap.find(name);
+                if (it != uniqueMap.end()) { name = it->second; }
+            }
 				
 			if (name.length() != 0) { 
 				saveName = name.substr(1);
 				while (!in.eof())	{	
 					char c = in.get(); 
-					if (c == 10 || c == 13){	break;	}
+					if (c == 10 || c == 13 || c == -1){	break;	}
 					else { name += c; }	
 				} 
 				m->gobble(in);
@@ -577,7 +589,7 @@ int GetSeqsCommand::readCount(){
         //check for groups that have been eliminated
         CountTable ct;
         if (ct.testGroups(outputFileName)) {
-            ct.readTable(outputFileName);
+            ct.readTable(outputFileName, true);
             ct.printTable(outputFileName);
         }
 		
@@ -700,7 +712,7 @@ int GetSeqsCommand::readName(){
 		
 			if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName);  return 0; }
 
-			in >> firstCol;				
+			in >> firstCol;			m->gobble(in);
 			in >> secondCol;
 			
 			string hold = "";
@@ -724,6 +736,7 @@ int GetSeqsCommand::readName(){
 				selectedCount += parsedNames.size();
                 if (m->debug) { sanity["name"].insert(firstCol); }
 			}else {
+                
 				selectedCount += validSecond.size();
 				
 				//if the name in the first column is in the set then print it and any other names in second column also in set
@@ -742,12 +755,15 @@ int GetSeqsCommand::readName(){
 				
 				//make first name in set you come to first column and then add the remaining names to second column
 				}else {
+                    
 					//you want part of this row
 					if (validSecond.size() != 0) {
 					
 						wroteSomething = true;
 						
 						out << validSecond[0] << '\t';
+                        //we are changing the unique name in the fasta file
+                        uniqueMap[firstCol] = validSecond[0];
 					
 						//you know you have at least one valid second since first column is valid
 						for (int i = 0; i < validSecond.size()-1; i++) {  out << validSecond[i] << ',';  }
@@ -805,6 +821,7 @@ int GetSeqsCommand::readGroup(){
 
 			in >> name;				//read from first column
 			in >> group;			//read from second column
+            
 			
 			//if this name is in the accnos file
 			if (names.count(name) != 0) {
@@ -862,6 +879,11 @@ int GetSeqsCommand::readTax(){
 
 			in >> name;				//read from first column
 			in >> tax;			//read from second column
+            
+            if (!dups) {//adjust name if needed
+                map<string, string>::iterator it = uniqueMap.find(name);
+                if (it != uniqueMap.end()) { name = it->second; }
+            }
 			
 			//if this name is in the accnos file
 			if (names.count(name) != 0) {
@@ -924,6 +946,11 @@ int GetSeqsCommand::readAlign(){
 
 
 			in >> name;				//read from first column
+            
+            if (!dups) {//adjust name if needed
+                map<string, string>::iterator it = uniqueMap.find(name);
+                if (it != uniqueMap.end()) { name = it->second; }
+            }
 			
 			//if this name is in the accnos file
 			if (names.count(name) != 0) {