X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=getseqscommand.cpp;h=7f0f3ddb51da8496c292367b5dfc728b3915d53f;hp=142023e7a40881c1c6397a761ba350132490b75c;hb=499f4ac6e321f9f03d4c3aa25c3b6880892c8b83;hpb=af0a94ea8f02421b2b73e77e68753a2b4c37768e

diff --git a/getseqscommand.cpp b/getseqscommand.cpp
index 142023e..7f0f3dd 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";
@@ -88,7 +88,7 @@ string GetSeqsCommand::getOutputPattern(string type) {
         else if (type == "name")        {   pattern = "[filename],pick,[extension]";    }
         else if (type == "group")       {   pattern = "[filename],pick,[extension]";    }
         else if (type == "count")       {   pattern = "[filename],pick,[extension]";    }
-        else if (type == "list")        {   pattern = "[filename],pick,[extension]";    }
+        else if (type == "list")        {   pattern = "[filename],[distance],pick,[extension]";    }
         else if (type == "qfile")       {   pattern = "[filename],pick,[extension]";    }
         else if (type == "accnosreport")      {   pattern = "[filename],pick.accnos.report";    }
         else if (type == "alignreport")      {   pattern = "[filename],pick.align.report";    }
@@ -430,9 +430,11 @@ int GetSeqsCommand::readFasta(){
             
             if (!dups) {//adjust name if needed
                 map<string, string>::iterator it = uniqueMap.find(name);
-                if (it != uniqueMap.end()) { name = it->second; }
+                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) {
@@ -587,7 +589,7 @@ int GetSeqsCommand::readCount(){
         //check for groups that have been eliminated
         CountTable ct;
         if (ct.testGroups(outputFileName)) {
-            ct.readTable(outputFileName, true);
+            ct.readTable(outputFileName, true, false);
             ct.printTable(outputFileName);
         }
 		
@@ -612,9 +614,6 @@ int GetSeqsCommand::readList(){
         map<string, string> variables; 
 		variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(listfile));
         variables["[extension]"] = m->getExtension(listfile);
-		string outputFileName = getOutputFileName("list", variables);
-		ofstream out;
-		m->openOutputFile(outputFileName, out);
 		
 		ifstream in;
 		m->openInputFile(listfile, in);
@@ -627,8 +626,6 @@ int GetSeqsCommand::readList(){
 		while(!in.eof()){
 			
 			selectedCount = 0;
-			
-			if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName);  return 0; }
 
 			//read in list vector
 			ListVector list(in);
@@ -636,6 +633,18 @@ int GetSeqsCommand::readList(){
 			//make a new list vector
 			ListVector newList;
 			newList.setLabel(list.getLabel());
+            
+            variables["[distance]"] = list.getLabel();
+            string outputFileName = getOutputFileName("list", variables);
+			
+			ofstream out;
+			m->openOutputFile(outputFileName, out);
+			outputTypes["list"].push_back(outputFileName);  outputNames.push_back(outputFileName);
+            
+            vector<string> binLabels = list.getLabels();
+            vector<string> newBinLabels;
+            
+            if (m->control_pressed) { in.close(); out.close();  return 0; }
 			
 			//for each bin
 			for (int i = 0; i < list.getNumBins(); i++) {
@@ -655,23 +664,26 @@ int GetSeqsCommand::readList(){
 				//if there are names in this bin add to new list
 				if (newNames != "") { 
 					newNames = newNames.substr(0, newNames.length()-1); //rip off extra comma
-					newList.push_back(newNames);	
+					newList.push_back(newNames);
+                    newBinLabels.push_back(binLabels[i]);
 				}
 			}
 				
 			//print new listvector
 			if (newList.getNumBins() != 0) {
 				wroteSomething = true;
+				newList.setLabels(newBinLabels);
+                newList.printHeaders(out);
 				newList.print(out);
 			}
 			
 			m->gobble(in);
+            out.close();
 		}
 		in.close();	
-		out.close();
+		
 		
 		if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();  }
-		outputNames.push_back(outputFileName); outputTypes["list"].push_back(outputFileName);
 		
 		m->mothurOut("Selected " + toString(selectedCount) + " sequences from your list file."); m->mothurOutEndLine();
 		
@@ -710,7 +722,7 @@ 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 = "";
@@ -734,6 +746,7 @@ 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
@@ -752,6 +765,7 @@ 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) {