removed make count from make.contigs

diff --git a/makecontigscommand.cpp b/makecontigscommand.cpp
index 8d532871a39b6de20a8e86c85a1173e1e852b6ba..c8f20f10eed04c59df0aa27c136029e43713579e 100644 (file)
--- a/makecontigscommand.cpp
+++ b/makecontigscommand.cpp
@@ -7,7 +7,6 @@
 //
 
 #include "makecontigscommand.h"
-#include "counttable.h"
 
 //**********************************************************************************************************************
 vector<string> MakeContigsCommand::setParameters(){    
@@ -26,7 +25,6 @@ vector<string> MakeContigsCommand::setParameters(){
 
         CommandParameter palign("align", "Multiple", "needleman-gotoh", "needleman", "", "", "","",false,false); parameters.push_back(palign);
         CommandParameter pallfiles("allfiles", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pallfiles);
-        CommandParameter pmakecount("makecount", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pmakecount);
         CommandParameter ptrimoverlap("trimoverlap", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(ptrimoverlap);
                CommandParameter pmatch("match", "Number", "", "1.0", "", "", "","",false,false); parameters.push_back(pmatch);
                CommandParameter pmismatch("mismatch", "Number", "", "-1.0", "", "", "","",false,false); parameters.push_back(pmismatch);
@@ -54,7 +52,7 @@ string MakeContigsCommand::getHelpString(){
                string helpString = "";
                helpString += "The make.contigs command reads a file, forward fastq file and a reverse fastq file or forward fasta and reverse fasta files and outputs new fasta.  It will also provide new quality files if the fastq or file parameter is used.\n";
         helpString += "If an oligos file is provided barcodes and primers will be trimmed, and a group file will be created.\n";
-               helpString += "The make.contigs command parameters are file, ffastq, rfastq, ffasta, rfasta, fqfile, rqfile, oligos, format, tdiffs, bdiffs, pdiffs, align, match, mismatch, gapopen, gapextend, insert, deltaq, allfiles, makecount and processors.\n";
+               helpString += "The make.contigs command parameters are file, ffastq, rfastq, ffasta, rfasta, fqfile, rqfile, oligos, format, tdiffs, bdiffs, pdiffs, align, match, mismatch, gapopen, gapextend, insert, deltaq, allfiles and processors.\n";
                helpString += "The ffastq and rfastq, file, or ffasta and rfasta parameters are required.\n";
         helpString += "The file parameter is 2 or 3 column file containing the forward fastq files in the first column and their matching reverse fastq files in the second column, or a groupName then forward fastq file and reverse fastq file.  Mothur will process each pair and create a combined fasta and report file with all the sequences.\n";
         helpString += "The ffastq and rfastq parameters are used to provide a forward fastq and reverse fastq file to process.  If you provide one, you must provide the other.\n";
@@ -75,7 +73,6 @@ string MakeContigsCommand::getHelpString(){
         helpString += "The insert parameter allows you to set a quality scores threshold. In the case where we are trying to decide whether to keep a base or remove it because the base is compared to a gap in the other fragment, if the base has a quality score equal to or below the threshold we eliminate it. Default=20.\n";
         helpString += "The processors parameter allows you to specify how many processors you would like to use.  The default is 1. \n";
         helpString += "The allfiles parameter will create separate group and fasta file for each grouping. The default is F.\n";
-        helpString += "The makecount parameter will create a count table file instead of a group file. The default is F.\n";
 
         helpString += "The trimoverlap parameter allows you to trim the sequences to only the overlapping section. The default is F.\n";
         helpString += "The make.contigs command should be in the following format: \n";
@@ -95,7 +92,6 @@ string MakeContigsCommand::getOutputPattern(string type) {
         
         if (type == "fasta") {  pattern = "[filename],[tag],contigs.fasta"; } 
         else if (type == "group") {  pattern = "[filename],[tag],contigs.groups"; }
-        else if (type == "count") {  pattern = "[filename],[tag],contigs.count_table"; }
         else if (type == "report") {  pattern = "[filename],[tag],contigs.report"; }
         else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
         
@@ -115,8 +111,7 @@ MakeContigsCommand::MakeContigsCommand(){
                outputTypes["fasta"] = tempOutNames;
         outputTypes["group"] = tempOutNames;
         outputTypes["report"] = tempOutNames;
-        outputTypes["count"] = tempOutNames;
-       }
+    }
        catch(exception& e) {
                m->errorOut(e, "MakeContigsCommand", "MakeContigsCommand");
                exit(1);
@@ -151,7 +146,6 @@ MakeContigsCommand::MakeContigsCommand(string option)  {
                        outputTypes["fasta"] = tempOutNames;
             outputTypes["report"] = tempOutNames;
             outputTypes["group"] = tempOutNames;
-            outputTypes["count"] = tempOutNames;
                        
             
                        //if the user changes the input directory command factory will send this info to us in the output parameter 
@@ -327,8 +321,6 @@ MakeContigsCommand::MakeContigsCommand(string option)  {
             temp = validParameter.validFile(parameters, "allfiles", false);            if (temp == "not found") { temp = "F"; }
                        allFiles = m->isTrue(temp);
             
-            temp = validParameter.validFile(parameters, "makecount", false);           if (temp == "not found") { temp = "F"; }
-                       makeCount = m->isTrue(temp);
             
             temp = validParameter.validFile(parameters, "trimoverlap", false);         if (temp == "not found") { temp = "F"; }
                        trimOverlap = m->isTrue(temp);
@@ -379,7 +371,6 @@ int MakeContigsCommand::execute(){
         cvars["[filename]"] = compOutputDir + m->getRootName(m->getSimpleName(file));
         cvars["[tag]"] = "";
         string compositeGroupFile = getOutputFileName("group",cvars);
-        if (makeCount) { compositeGroupFile = getOutputFileName("count",cvars); }
         cvars["[tag]"] = "trim";
         string compositeFastaFile = getOutputFileName("fasta",cvars);
         cvars["[tag]"] = "scrap";
@@ -398,7 +389,7 @@ int MakeContigsCommand::execute(){
         }
         
         map<string, int> totalGroupCounts;
-        CountTable compositeCt;
+        
         for (int l = 0; l < filesToProcess.size(); l++) {
             
             m->mothurOut("\n>>>>>\tProcessing " + filesToProcess[l][0][0] + " (file " + toString(l+1) + " of " + toString(filesToProcess.size()) + ")\t<<<<<\n");
@@ -416,7 +407,6 @@ int MakeContigsCommand::execute(){
             if(oligosfile != ""){  createOligosGroup = getOligos(fastaFileNames, variables["[filename]"]);  }
             if (createOligosGroup || createFileGroup) {
                 outputGroupFileName = getOutputFileName("group",variables);
-                if (makeCount) { outputGroupFileName = getOutputFileName("count",variables); }
             }
             
             //give group in file file precedence
@@ -431,7 +421,7 @@ int MakeContigsCommand::execute(){
                         
             m->mothurOut("Making contigs...\n"); 
             createProcesses(filesToProcess[l], outFastaFile, outScrapFastaFile, outMisMatchFile, fastaFileNames, l);
-            m->mothurOut("Done.\n");
+             m->mothurOut("Here...\n"); 
             
             //remove temp fasta and qual files
             for (int i = 0; i < processors; i++) { for(int j = 0; j < filesToProcess[l][i].size(); j++) { m->mothurRemove(filesToProcess[l][i][j]); }  }
@@ -471,85 +461,40 @@ int MakeContigsCommand::execute(){
                     
                     ofstream out;
                     string thisGroupName = thisOutputDir + m->getRootName(m->getSimpleName(it->first));
-                    if (!makeCount) { thisGroupName += getOutputFileName("group",variables); outputNames.push_back(thisGroupName); outputTypes["group"].push_back(thisGroupName);
-                        m->openOutputFile(thisGroupName, out);
+                    thisGroupName += getOutputFileName("group",variables); outputNames.push_back(thisGroupName); outputTypes["group"].push_back(thisGroupName);
+                    m->openOutputFile(thisGroupName, out);
+                    
+                    while (!in.eof()){
+                        if (m->control_pressed) { break; }
                         
-                        while (!in.eof()){
-                            if (m->control_pressed) { break; }
-                            
-                            Sequence currSeq(in); m->gobble(in);
-                            out << currSeq.getName() << '\t' << it->second << endl;
-                        }
-                        out.close();
-                    }
-                    else {
-                        thisGroupName += getOutputFileName("count",variables); outputNames.push_back(thisGroupName); outputTypes["count"].push_back(thisGroupName);
-                        CountTable ct;
-                        ct.addGroup(it->second);
-                        while (!in.eof()){
-                            if (m->control_pressed) { break; }
-                            
-                            Sequence currSeq(in); m->gobble(in);
-                            vector<int> tempGroupCount; tempGroupCount.push_back(1);
-                            ct.push_back(currSeq.getName(), tempGroupCount);
-                        }
-                        ct.printTable(thisGroupName);
+                        Sequence currSeq(in); m->gobble(in);
+                        out << currSeq.getName() << '\t' << it->second << endl;
                     }
+                    out.close();
                     in.close();
                 }
             }
             
             if (createFileGroup || createOligosGroup) {
-                if (makeCount) {
-                    if ((allFiles) || (filesToProcess.size() == 1)) {
-                        CountTable ct;
-                        for (map<string, int>::iterator itGroups = groupCounts.begin(); itGroups != groupCounts.end(); itGroups++) {
-                            ct.addGroup(itGroups->first);
-                        }
-                        vector<string> groups = ct.getNamesOfGroups();
-                        for (map<string, string>::iterator itGroup = groupMap.begin(); itGroup != groupMap.end(); itGroup++) {
-                            vector<int> tempGroupCounts; tempGroupCounts.resize(groups.size(), 0);
-                            ct.push_back(itGroup->first, tempGroupCounts);
-                            ct.setAbund(itGroup->first, itGroup->second, 1);
-                        }
-                        ct.printTable(outputGroupFileName);
-                    }
-                }else {
-                    ofstream outGroup;
-                    m->openOutputFile(outputGroupFileName, outGroup);
-                    for (map<string, string>::iterator itGroup = groupMap.begin(); itGroup != groupMap.end(); itGroup++) {
-                        outGroup << itGroup->first << '\t' << itGroup->second << endl;
-                    }
-                    outGroup.close();
+                ofstream outGroup;
+                m->openOutputFile(outputGroupFileName, outGroup);
+                for (map<string, string>::iterator itGroup = groupMap.begin(); itGroup != groupMap.end(); itGroup++) {
+                    outGroup << itGroup->first << '\t' << itGroup->second << endl;
                 }
+                outGroup.close();
             }
             
             if (filesToProcess.size() > 1) { //merge into large combo files
                 if (createFileGroup || createOligosGroup) {
-                    if (makeCount) {
-                        for (map<string, string>::iterator itGroup = groupMap.begin(); itGroup != groupMap.end(); itGroup++) {
-                            vector<string> groups = compositeCt.getNamesOfGroups();
-                            if (m->inUsersGroups(itGroup->second, groups)) {
-                                vector<int> tempGroupCounts; tempGroupCounts.resize(groups.size(), 0);
-                                compositeCt.push_back(itGroup->first, tempGroupCounts);
-                                compositeCt.setAbund(itGroup->first, itGroup->second, 1);
-                            }else{
-                                compositeCt.addGroup(itGroup->second);
-                                vector<int> tempGroupCounts; tempGroupCounts.resize(groups.size()+1, 0);
-                                compositeCt.push_back(itGroup->first, tempGroupCounts);
-                                compositeCt.setAbund(itGroup->first, itGroup->second, 1);
-                            }
-                        }
-                    }else {
-                        if (l == 0) {
-                            ofstream outCGroup;
-                            m->openOutputFile(compositeGroupFile, outCGroup); outCGroup.close();
-                            outputNames.push_back(compositeGroupFile); outputTypes["group"].push_back(compositeGroupFile);
-                        }
-                        m->appendFiles(outputGroupFileName, compositeGroupFile);
-                        if (!allFiles) { m->mothurRemove(outputGroupFileName);  }
-                        else { outputNames.push_back(outputGroupFileName); outputTypes["group"].push_back(outputGroupFileName); }
+                    if (l == 0) {
+                        ofstream outCGroup;
+                        m->openOutputFile(compositeGroupFile, outCGroup); outCGroup.close();
+                        outputNames.push_back(compositeGroupFile); outputTypes["group"].push_back(compositeGroupFile);
                     }
+                    m->appendFiles(outputGroupFileName, compositeGroupFile);
+                    if (!allFiles) { m->mothurRemove(outputGroupFileName);  }
+                    else { outputNames.push_back(outputGroupFileName); outputTypes["group"].push_back(outputGroupFileName); }
+                    
                     for (map<string, int>::iterator itGroups = groupCounts.begin(); itGroups != groupCounts.end(); itGroups++) {
                         map<string, int>::iterator itTemp = totalGroupCounts.find(itGroups->first);
                         if (itTemp == totalGroupCounts.end()) { totalGroupCounts[itGroups->first] = itGroups->second; } //new group create it in totalGroups
@@ -575,16 +520,12 @@ int MakeContigsCommand::execute(){
                 outputNames.push_back(outScrapFastaFile); outputTypes["fasta"].push_back(outScrapFastaFile);
                 outputNames.push_back(outMisMatchFile); outputTypes["report"].push_back(outMisMatchFile);
                 if (createFileGroup || createOligosGroup) {
-                    if (makeCount) { outputNames.push_back(outputGroupFileName); outputTypes["count"].push_back(outputGroupFileName);  }
-                    else { outputNames.push_back(outputGroupFileName); outputTypes["group"].push_back(outputGroupFileName); }
+                     outputNames.push_back(outputGroupFileName); outputTypes["group"].push_back(outputGroupFileName); 
                 }
             }
+            m->mothurOut("Done.\n");
         }
         
-        if ((filesToProcess.size() > 1) && makeCount) { //merge into large combo files
-            compositeCt.printTable(compositeGroupFile);
-            outputNames.push_back(compositeGroupFile); outputTypes["count"].push_back(compositeGroupFile);
-        }
         m->mothurOut("It took " + toString(time(NULL) - start) + " secs to process " + toString(numReads) + " sequences.\n");
         
         if (m->control_pressed) {      for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]); } return 0;    }
@@ -611,12 +552,6 @@ int MakeContigsCommand::execute(){
                if (itTypes != outputTypes.end()) {
                        if ((itTypes->second).size() != 0) { currentGroup = (itTypes->second)[0]; m->setGroupFile(currentGroup); }
                }
-        
-        string currentCount = "";
-               itTypes = outputTypes.find("count");
-               if (itTypes != outputTypes.end()) {
-                       if ((itTypes->second).size() != 0) { currentCount = (itTypes->second)[0]; m->setCountTableFile(currentCount); }
-               }
                
         //output files created by command
                m->mothurOutEndLine();

diff --git a/subsamplecommand.cpp b/subsamplecommand.cpp
index 32745a25ee0ae66e6f6cbcb50cc4db4469cca21f..4128191598d22e8e7280f403dca79494e61da948 100644 (file)
--- a/subsamplecommand.cpp
+++ b/subsamplecommand.cpp
@@ -1007,7 +1007,7 @@ int SubSampleCommand::getSubSampleList() {
                ListVector* list = input->getListVector();
                string lastLabel = list->getLabel();
                
-               //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
+        //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
                set<string> processedLabels;
                set<string> userLabels = labels;
 
@@ -1265,11 +1265,18 @@ int SubSampleCommand::getSubSampleList() {
         
         if (taxonomyfile != "") {
             if (namefile == "") {
-                //fake nameMap
-                for (set<string>::iterator it = subset.begin(); it != subset.end(); it++) {
-                    vector<string> temp; temp.push_back(*it);
-                    nameMap[*it] = temp;
+                InputData input(listfile, "list");
+                ListVector* list = input.getListVector();
+                string lastLabel = list->getLabel();
+                
+                for (int i = 0; i < list->getNumBins(); i++) {
+                    vector<string> temp;
+                    string bin = list->get(i);
+                    m->splitAtComma(bin, temp);
+                    for (int j = 0; j < temp.size(); j++) { vector<string> tempFakeOut; tempFakeOut.push_back(temp[j]); nameMap[temp[j]] = tempFakeOut; }
                 }
+                delete list;
+                    
                 int tcount = getTax(subset);
                 if (tcount != subset.size()) { m->mothurOut("[ERROR]: subsampled list file contains " + toString(subset.size()) + " sequences, but I only found " + toString(tcount) + " in your taxonomy file, did you forget a name file? Please correct."); m->mothurOutEndLine(); }
             }else {

diff --git a/trimflowscommand.cpp b/trimflowscommand.cpp
index 3abc7609ac85187513f416c378225e726c8bd197..1bab57f853a200d50aa4a62545f15a4697e167a8 100644 (file)
--- a/trimflowscommand.cpp
+++ b/trimflowscommand.cpp
@@ -429,6 +429,7 @@ int TrimFlowsCommand::driverCreateTrim(string flowFileName, string trimFlowFileN
                        flowData.capFlows(maxFlows);    
                        
                        Sequence currSeq = flowData.getSequence();
+            //cout << currSeq.getName() << '\t' << currSeq.getUnaligned() << endl;
                        if(!flowData.hasMinFlows(minFlows)){    //screen to see if sequence is of a minimum number of flows
                                success = 0;
                                trashCode += 'l';
@@ -551,13 +552,16 @@ void TrimFlowsCommand::getOligos(vector<vector<string> >& outFlowFileNames){
                
                while(!oligosFile.eof()){
                
-                       oligosFile >> type; m->gobble(oligosFile);      //get the first column value of the row - is it a comment or a feature we are interested in?
-
+                       oligosFile >> type;     //get the first column value of the row - is it a comment or a feature we are interested in?
+            
+            if (m->debug) { m->mothurOut("[DEBUG]: type = " + type + ".\n"); }
+            
                        if(type[0] == '#'){     //igore the line because there's a comment
-                               while (!oligosFile.eof())       {       char c = oligosFile.get(); if (c == 10 || c == 13){     break;  }       } // get rest of line if there's any crap there
+                               while (!oligosFile.eof())       {       char c = oligosFile.get(); if (c == 10 || c == 13){     break;  }       }
+                m->gobble(oligosFile);// get rest of line if there's any crap there
                        }
                        else{                           //there's a feature we're interested in
-
+                m->gobble(oligosFile);
                                for(int i=0;i<type.length();i++){       type[i] = toupper(type[i]);  }                                  //make type case insensitive
 
                                oligosFile >> oligo;    //get the DNA sequence for the feature
@@ -566,7 +570,9 @@ void TrimFlowsCommand::getOligos(vector<vector<string> >& outFlowFileNames){
                                        oligo[i] = toupper(oligo[i]);
                                        if(oligo[i] == 'U')     {       oligo[i] = 'T'; }
                                }
-
+                
+                if (m->debug) { m->mothurOut("[DEBUG]: oligos = " + oligo + ".\n"); }
+                
                                if(type == "FORWARD"){  //if the feature is a forward primer...
                                        group = "";
 
@@ -595,7 +601,9 @@ void TrimFlowsCommand::getOligos(vector<vector<string> >& outFlowFileNames){
                                        //check for repeat barcodes
                                        map<string, int>::iterator itBar = barcodes.find(oligo);
                                        if (itBar != barcodes.end()) { m->mothurOut("barcode " + oligo + " is in your oligos file already."); m->mothurOutEndLine();  }
-
+                    
+                    if (m->debug) { m->mothurOut("[DEBUG]: group = " + group + ".\n"); }
+                    
                                        barcodes[oligo]=indexBarcode; indexBarcode++;
                                        barcodeNameVector.push_back(group);
                                }else if(type == "LINKER"){

diff --git a/unweighted.cpp b/unweighted.cpp
index e95834fb485fb6131fcacdb458e3f6c96b862693..56694e32e3a977b08df087dfc8deeabb2524564c 100644 (file)
--- a/unweighted.cpp
+++ b/unweighted.cpp
@@ -104,7 +104,7 @@ EstOutput Unweighted::createProcesses(Tree* t, vector< vector<string> > namesOfG
                                
                                if (m->control_pressed) { exit(0); }
                                
-                               m->mothurOut("Merging results."); m->mothurOutEndLine();
+                               //m->mothurOut("Merging results."); m->mothurOutEndLine();
                                
                                //pass numSeqs to parent
                                ofstream out;
@@ -156,7 +156,7 @@ EstOutput Unweighted::createProcesses(Tree* t, vector< vector<string> > namesOfG
                        m->mothurRemove(s);
                }
                
-               m->mothurOut("DONE."); m->mothurOutEndLine(); m->mothurOutEndLine();
+               //m->mothurOut("DONE."); m->mothurOutEndLine(); m->mothurOutEndLine();
                
                return results;
 #endif