X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=removeseqscommand.cpp;h=00b94a9dac842ceeca4a2a0362d87f14ba12ca1b;hb=006601d68abe8d0061f77e8d28323b160750e343;hp=1fb94462ac48fa13ac871c6b9d3cf4f3ae2ceff6;hpb=ea4f373c28543cd1002b0dd7dc6e55c526647d59;p=mothur.git

diff --git a/removeseqscommand.cpp b/removeseqscommand.cpp
index 1fb9446..00b94a9 100644
--- a/removeseqscommand.cpp
+++ b/removeseqscommand.cpp
@@ -10,6 +10,7 @@
 #include "removeseqscommand.h"
 #include "sequence.hpp"
 #include "listvector.hpp"
+#include "counttable.h"
 
 //**********************************************************************************************************************
 vector<string> RemoveSeqsCommand::setParameters(){	
@@ -71,7 +72,7 @@ string RemoveSeqsCommand::getOutputFileNameTag(string type, string inputName="")
             else if (type == "list")        {   outputFileName =  "pick" + m->getExtension(inputName);   }
             else if (type == "qfile")       {   outputFileName =  "pick" + m->getExtension(inputName);   }
             else if (type == "alignreport") {   outputFileName =  "pick.align.report";                   }
-            else if (type == "count")       {   outputFileName =  "pick.count.table";   }
+            else if (type == "count")       {   outputFileName =  "pick.count_table";   }
             else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
         }
         return outputFileName;
@@ -405,6 +406,12 @@ int RemoveSeqsCommand::readFasta(){
 			if (m->control_pressed) { in.close();  out.close();  m->mothurRemove(outputFileName);  return 0; }
 			
 			Sequence currSeq(in);
+            
+            if (!dups) {//adjust name if needed
+                map<string, string>::iterator it = uniqueMap.find(currSeq.getName());
+                if (it != uniqueMap.end()) { currSeq.setName(it->second); }
+            }
+
 			name = currSeq.getName();
 			
 			if (name != "") {
@@ -412,7 +419,7 @@ int RemoveSeqsCommand::readFasta(){
 				if (names.count(name) == 0) {
 					wroteSomething = true;
 					
-					currSeq.printSequence(out);
+                    currSeq.printSequence(out);
 				}else {  removedCount++;  }
 			}
 			m->gobble(in);
@@ -476,6 +483,11 @@ int RemoveSeqsCommand::readQual(){
 			
 			m->gobble(in);
 			
+            if (!dups) {//adjust name if needed
+                map<string, string>::iterator it = uniqueMap.find(saveName);
+                if (it != uniqueMap.end()) { name = ">" + it->second; saveName = it->second; }
+            }
+            
 			if (names.count(saveName) == 0) {
 				wroteSomething = true;
 				
@@ -538,6 +550,14 @@ int RemoveSeqsCommand::readCount(){
         }
         in.close();
 		out.close();
+        
+        //check for groups that have been eliminated
+        CountTable ct;
+        if (ct.testGroups(outputFileName)) {
+            ct.readTable(outputFileName);
+            ct.printTable(outputFileName);
+        }
+
 		
 		if (wroteSomething == false) {  m->mothurOut("Your file contains only sequences from the .accnos file."); m->mothurOutEndLine();  }
 		outputTypes["count"].push_back(outputFileName); outputNames.push_back(outputFileName);
@@ -686,6 +706,8 @@ int RemoveSeqsCommand::readName(){
 						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] << ',';  }
@@ -779,9 +801,15 @@ int RemoveSeqsCommand::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) {
 				wroteSomething = true;
+            
 				out << name << '\t' << tax << endl;
 			}else {  removedCount++;  }
 					
@@ -831,6 +859,11 @@ int RemoveSeqsCommand::readAlign(){
 			if (m->control_pressed) { in.close();  out.close();  m->mothurRemove(outputFileName);  return 0; }
 			
 			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) {