X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimerauchimecommand.cpp;h=e82dc1bc8dce5ffd0887025d5816b5eec8d0eab9;hb=67ea6ccd74dbd64828d31b952808255f206364ff;hp=3ed61707385f4859a4b4558bd35124fac1b2b417;hpb=2a29fceeeb8754c3fd97ba830d2fbed5c4349ee8;p=mothur.git

diff --git a/chimerauchimecommand.cpp b/chimerauchimecommand.cpp
index 3ed6170..e82dc1b 100644
--- a/chimerauchimecommand.cpp
+++ b/chimerauchimecommand.cpp
@@ -727,10 +727,8 @@ int ChimeraUchimeCommand::execute(){
 				
 				if(processors == 1)	{	totalSeqs = driverGroups(outputFileName, newFasta, accnosFileName, alnsFileName, newCountFile, 0, groups.size(), groups);
                     
-                    //read my own
-                    if (hasCount && !dups) {
-                        CountTable newCount; newCount.readTable(nameFile);
-                        
+                    if (hasCount && dups) {
+                        CountTable c; c.readTable(nameFile);
                         if (!m->isBlank(newCountFile)) {
                             ifstream in2;
                             m->openInputFile(newCountFile, in2);
@@ -738,12 +736,12 @@ int ChimeraUchimeCommand::execute(){
                             string name, group;
                             while (!in2.eof()) {
                                 in2 >> name >> group; m->gobble(in2);
-                                newCount.setAbund(name, group, 0);
+                                c.setAbund(name, group, 0);
                             }
                             in2.close();
                         }
                         m->mothurRemove(newCountFile);
-                        newCount.printTable(newCountFile);
+                        c.printTable(newCountFile);
                     }
 
                 }else				{	totalSeqs = createProcessesGroups(outputFileName, newFasta, accnosFileName, alnsFileName, newCountFile, groups, nameFile, groupFile, fastaFileNames[s]);			}
@@ -757,25 +755,27 @@ int ChimeraUchimeCommand::execute(){
                     m->mothurOutEndLine(); m->mothurOut("It took " + toString(time(NULL) - start) + " secs to check " + toString(totalSeqs) + " sequences. " + toString(totalChimeras) + " chimeras were found.");	m->mothurOutEndLine();
                     m->mothurOut("The number of sequences checked may be larger than the number of unique sequences because some sequences are found in several samples."); m->mothurOutEndLine(); 
 				}else {
-                    /*if (hasCount) {  //removed empty seqs
-                        ofstream out2;
-                        m->openOutputFile(accnosFileName, out2);
-                        
+                    
+                    if (hasCount) {
+                        set<string> doNotRemove;
                         CountTable c; c.readTable(newCountFile);
-                        vector<string> nseqs = c.getNamesOfSeqs();
-                        vector<string> ngroups = c.getNamesOfGroups();
-                        for (int l = 0; l < nseqs.size(); l++) {
-                            if (c.getNumSeqs(nseqs[l]) == 0) {
-                                c.remove(nseqs[l]);
-                                out2 << nseqs[l] << endl;
-                            }
+                        vector<string> namesInTable = c.getNamesOfSeqs();
+                        for (int i = 0; i < namesInTable.size(); i++) {
+                            int temp = c.getNumSeqs(namesInTable[i]);
+                            if (temp == 0) {  c.remove(namesInTable[i]);  }
+                            else { doNotRemove.insert((namesInTable[i])); }
                         }
-                        for (int l = 0; l < ngroups.size(); l++) {
-                            if (c.getGroupCount(ngroups[l]) == 0) {  c.removeGroup(ngroups[l]); }
+                        //remove names we want to keep from accnos file.
+                        set<string> accnosNames = m->readAccnos(accnosFileName);
+                        ofstream out2;
+                        m->openOutputFile(accnosFileName, out2);
+                        for (set<string>::iterator it = accnosNames.begin(); it != accnosNames.end(); it++) {
+                            if (doNotRemove.count(*it) == 0) {  out2 << (*it) << endl; }
                         }
                         out2.close();
                         c.printTable(newCountFile);
-                    }*/
+                        outputNames.push_back(newCountFile); outputTypes["count"].push_back(newCountFile);
+                    }
                 }
                 
                 if (hasCount) { delete cparser; }
@@ -820,6 +820,11 @@ int ChimeraUchimeCommand::execute(){
 		if (itTypes != outputTypes.end()) {
 			if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setAccnosFile(current); }
 		}
+        
+        itTypes = outputTypes.find("count");
+		if (itTypes != outputTypes.end()) {
+			if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setCountTableFile(current); }
+		}
 		
 		m->mothurOutEndLine();
 		m->mothurOut("Output File Names: "); m->mothurOutEndLine();
@@ -840,10 +845,6 @@ int ChimeraUchimeCommand::deconvoluteResults(map<string, string>& uniqueNames, s
 		map<string, string>::iterator itUnique;
 		int total = 0;
 		
-		//edit accnos file
-		ifstream in2; 
-		m->openInputFile(accnosFileName, in2);
-		
 		ofstream out2;
 		m->openOutputFile(accnosFileName+".temp", out2);
 		
@@ -853,27 +854,32 @@ int ChimeraUchimeCommand::deconvoluteResults(map<string, string>& uniqueNames, s
 		set<string> chimerasInFile;
 		set<string>::iterator itChimeras;
 
-		
-		while (!in2.eof()) {
-			if (m->control_pressed) { in2.close(); out2.close(); m->mothurRemove(outputFileName); m->mothurRemove((accnosFileName+".temp")); return 0; }
-			
-			in2 >> name; m->gobble(in2);
-			
-			//find unique name
-			itUnique = uniqueNames.find(name);
-			
-			if (itUnique == uniqueNames.end()) { m->mothurOut("[ERROR]: trouble parsing accnos results. Cannot find " + name + "."); m->mothurOutEndLine(); m->control_pressed = true; }
-			else {
-				itChimeras = chimerasInFile.find((itUnique->second));
-				
-				if (itChimeras == chimerasInFile.end()) {
-					out2 << itUnique->second << endl;
-					chimerasInFile.insert((itUnique->second));
-					total++;
-				}
-			}
-		}
-		in2.close();
+        if (!m->isBlank(accnosFileName)) {
+            //edit accnos file
+            ifstream in2;
+            m->openInputFile(accnosFileName, in2);
+            
+            while (!in2.eof()) {
+                if (m->control_pressed) { in2.close(); out2.close(); m->mothurRemove(outputFileName); m->mothurRemove((accnosFileName+".temp")); return 0; }
+                
+                in2 >> name; m->gobble(in2);
+                
+                //find unique name
+                itUnique = uniqueNames.find(name);
+                
+                if (itUnique == uniqueNames.end()) { m->mothurOut("[ERROR]: trouble parsing accnos results. Cannot find " + name + "."); m->mothurOutEndLine(); m->control_pressed = true; }
+                else {
+                    itChimeras = chimerasInFile.find((itUnique->second));
+                    
+                    if (itChimeras == chimerasInFile.end()) {
+                        out2 << itUnique->second << endl;
+                        chimerasInFile.insert((itUnique->second));
+                        total++;
+                    }
+                }
+            }
+            in2.close();
+        }
 		out2.close();
 		
 		m->mothurRemove(accnosFileName);
@@ -1182,6 +1188,7 @@ int ChimeraUchimeCommand::driverGroups(string outputFName, string filename, stri
 		int totalSeqs = 0;
 		int numChimeras = 0;
         
+        
         ofstream outCountList;
         if (hasCount && dups) { m->openOutputFile(countlist, outCountList); }
         
@@ -1893,7 +1900,7 @@ int ChimeraUchimeCommand::createProcessesGroups(string outputFName, string filen
         
         
 #endif		
-		
+      
         //read my own
         if (hasCount && dups) {
             if (!m->isBlank(accnos + ".byCount")) {
@@ -1909,7 +1916,7 @@ int ChimeraUchimeCommand::createProcessesGroups(string outputFName, string filen
             }
             m->mothurRemove(accnos + ".byCount");
         }
-				
+       
 		//append output files
 		for(int i=0;i<processIDS.size();i++){
 			m->appendFiles((outputFName + toString(processIDS[i]) + ".temp"), outputFName);
@@ -1941,8 +1948,8 @@ int ChimeraUchimeCommand::createProcessesGroups(string outputFName, string filen
 		}
         
         //print new *.pick.count_table
-        if (hasCount && dups) { newCount.printTable(newCountFile); }
-		
+        if (hasCount && dups) {  newCount.printTable(newCountFile);   }
+ 		
 		return num;	
 		
 	}