consensus.seqs can now find a consensus on a whole fasta file without needing a listfile

diff --git a/consensusseqscommand.cpp b/consensusseqscommand.cpp
index 84519b8e320817c63112d19d18be2f49c43e9228..9c447c217b30247bedbddb7b3351b71952de4c55 100644 (file)
--- a/consensusseqscommand.cpp
+++ b/consensusseqscommand.cpp
@@ -135,7 +135,7 @@ ConsensusSeqsCommand::ConsensusSeqsCommand(string option)  {
                        
                        listfile = validParameter.validFile(parameters, "list", true);
                        if (listfile == "not open") { abort = true; }
-                       else if (listfile == "not found") { listfile = ""; m->mothurOut("list is a required parameter for the consensus.seqs command."); m->mothurOutEndLine(); abort = true;  }        
+                       else if (listfile == "not found") { listfile = "";  }   
                        
                        label = validParameter.validFile(parameters, "label", false);                   
                        if (label == "not found") { label = ""; }
@@ -158,7 +158,7 @@ ConsensusSeqsCommand::ConsensusSeqsCommand(string option)  {
 
 void ConsensusSeqsCommand::help(){
        try {
-               m->mothurOut("The consensus.seqs command reads a fastafile and listfile and creates a consensus sequence for each otu. Sequences must be aligned.\n");
+               m->mothurOut("The consensus.seqs command can be used in 2 ways: create a consensus sequence from a fastafile, or with a listfile create a consensus sequence for each otu. Sequences must be aligned.\n");
                m->mothurOut("The consensus.seqs command parameters are fasta, list, name and label.\n");
                m->mothurOut("The fasta parameter allows you to enter the fasta file containing your sequences, and is required. \n");
                m->mothurOut("The list parameter allows you to enter a your list file. \n");
@@ -194,85 +194,176 @@ int ConsensusSeqsCommand::execute(){
                
                if (m->control_pressed) { return 0; }
                
-               InputData* input = new InputData(listfile, "list");
-               ListVector* list = input->getListVector();
-               
-               string lastLabel = list->getLabel();
-               set<string> processedLabels;
-               set<string> userLabels = labels;
-
-               //as long as you are not at the end of the file or done wih the lines you want
-               while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
-                       
-                       if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {       remove(outputNames[i].c_str()); } delete list; delete input;  return 0;  }
-                       
-                       if(allLines == 1 || labels.count(list->getLabel()) == 1){                       
                                
-                               m->mothurOut(list->getLabel()); m->mothurOutEndLine();
+               if (listfile == "") {
+                       
+                       ofstream outSummary;
+                       string outputSummaryFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "cons.summary";
+                       m->openOutputFile(outputSummaryFile, outSummary);
+                       outSummary.setf(ios::fixed, ios::floatfield); outSummary.setf(ios::showpoint);
+                       outputNames.push_back(outputSummaryFile); outputTypes["summary"].push_back(outputSummaryFile);
+                       
+                       ofstream outFasta;
+                       string outputFastaFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "cons.fasta";
+                       m->openOutputFile(outputFastaFile, outFasta);
+                       outputNames.push_back(outputFastaFile); outputTypes["fasta"].push_back(outputFastaFile);
+                       
+                       vector<string> seqs;
+                       int seqLength = 0;
+                       for (map<string, string>::iterator it = nameMap.begin(); it != nameMap.end(); it++) {
                                
-                               processList(list);
+                               if (m->control_pressed) { outSummary.close(); outFasta.close(); for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); } return 0; }
                                
-                               processedLabels.insert(list->getLabel());
-                               userLabels.erase(list->getLabel());
+                               string seq = fastaMap[it->second];
+                               seqs.push_back(seq);
+                               
+                               if (seqLength == 0) { seqLength = seq.length(); }
+                               else if (seqLength != seq.length()) { m->mothurOut("[ERROR]: sequence are not the same length, please correct."); m->mothurOutEndLine(); m->control_pressed = true; }
+
                        }
                        
-                       if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
-                               string saveLabel = list->getLabel();
+                       vector< vector<float> > percentages; percentages.resize(5);
+                       for (int j = 0; j < percentages.size(); j++) { percentages[j].resize(seqLength, 0.0); }
+                       
+                       string consSeq = "";
+                       //get counts
+                       for (int j = 0; j < seqLength; j++) {
                                
-                               delete list; 
+                               if (m->control_pressed) { outSummary.close(); outFasta.close(); for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); } return 0; }
                                
-                               list = input->getListVector(lastLabel);
-                               m->mothurOut(list->getLabel()); m->mothurOutEndLine();
+                               vector<int> counts; counts.resize(5, 0); //A,T,G,C,Gap
+                               int numDots = 0;
                                
-                               processList(list);
+                               for (int i = 0; i < seqs.size(); i++) {
+                                       
+                                       if (seqs[i][j] == '.') { numDots++; }
+                                       
+                                       char base = toupper(seqs[i][j]);
+                                       if (base == 'A') { counts[0]++; }
+                                       else if (base == 'T') { counts[1]++; }
+                                       else if (base == 'G') { counts[2]++; }
+                                       else if (base == 'C') { counts[3]++; }
+                                       else { counts[4]++; }
+                               }
+                               
+                               char conBase = '.';
+                               if (numDots != seqs.size()) { conBase = getBase(counts); }
                                
-                               processedLabels.insert(list->getLabel());
-                               userLabels.erase(list->getLabel());
+                               consSeq += conBase;
+                               
+                               percentages[0][j] = counts[0] / (float) seqs.size();
+                               percentages[1][j] = counts[1] / (float) seqs.size();
+                               percentages[2][j] = counts[2] / (float) seqs.size();
+                               percentages[3][j] = counts[3] / (float) seqs.size();
+                               percentages[4][j] = counts[4] / (float) seqs.size();
                                
-                               //restore real lastlabel to save below
-                               list->setLabel(saveLabel);
                        }
                        
-                       lastLabel = list->getLabel();
+                       outSummary << "A" << '\t';
+                       for (int j = 0; j < seqLength; j++) { outSummary << percentages[0][j] << '\t'; }
+                       outSummary << endl;
+                       outSummary << "T" << '\t';
+                       for (int j = 0; j < seqLength; j++) { outSummary << percentages[1][j] << '\t'; }
+                       outSummary << endl;
+                       outSummary << "G" << '\t';
+                       for (int j = 0; j < seqLength; j++) { outSummary << percentages[2][j] << '\t'; }
+                       outSummary << endl;
+                       outSummary << "C" << '\t';
+                       for (int j = 0; j < seqLength; j++) { outSummary << percentages[3][j] << '\t'; }
+                       outSummary << endl;
+                       outSummary << "Gap" << '\t';
+                       for (int j = 0; j < seqLength; j++) { outSummary << percentages[4][j] << '\t'; }
+                       outSummary << endl;
                        
-                       delete list; list = NULL;
+                               
+                       outFasta << ">conseq" << endl << consSeq << endl;
+                       
+                       outSummary.close(); outFasta.close();
                        
-                       //get next line to process
-                       list = input->getListVector();                          
-               }
-               
-               
-               if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str()); } if (list != NULL) { delete list; } delete input; return 0;  }
                
-               //output error messages about any remaining user labels
-               set<string>::iterator it;
-               bool needToRun = false;
-               for (it = userLabels.begin(); it != userLabels.end(); it++) {  
-                       m->mothurOut("Your file does not include the label " + *it); 
-                       if (processedLabels.count(lastLabel) != 1) {
-                               m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
-                               needToRun = true;
-                       }else {
-                               m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
+               }else {
+                       
+                                               
+                       InputData* input = new InputData(listfile, "list");
+                       ListVector* list = input->getListVector();
+                       
+                       string lastLabel = list->getLabel();
+                       set<string> processedLabels;
+                       set<string> userLabels = labels;
+
+                       //as long as you are not at the end of the file or done wih the lines you want
+                       while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
+                               
+                               if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {       remove(outputNames[i].c_str()); } delete list; delete input;  return 0;  }
+                               
+                               if(allLines == 1 || labels.count(list->getLabel()) == 1){                       
+                                       
+                                       m->mothurOut(list->getLabel()); m->mothurOutEndLine();
+                                       
+                                       processList(list);
+                                       
+                                       processedLabels.insert(list->getLabel());
+                                       userLabels.erase(list->getLabel());
+                               }
+                               
+                               if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+                                       string saveLabel = list->getLabel();
+                                       
+                                       delete list; 
+                                       
+                                       list = input->getListVector(lastLabel);
+                                       m->mothurOut(list->getLabel()); m->mothurOutEndLine();
+                                       
+                                       processList(list);
+                                       
+                                       processedLabels.insert(list->getLabel());
+                                       userLabels.erase(list->getLabel());
+                                       
+                                       //restore real lastlabel to save below
+                                       list->setLabel(saveLabel);
+                               }
+                               
+                               lastLabel = list->getLabel();
+                               
+                               delete list; list = NULL;
+                               
+                               //get next line to process
+                               list = input->getListVector();                          
                        }
-               }
-               
-               //run last label if you need to
-               if (needToRun == true)  {
-                       if (list != NULL) { delete list; }
                        
-                       list = input->getListVector(lastLabel);
                        
-                       m->mothurOut(list->getLabel()); m->mothurOutEndLine();
+                       if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str()); } if (list != NULL) { delete list; } delete input; return 0;  }
                        
-                       processList(list);
+                       //output error messages about any remaining user labels
+                       set<string>::iterator it;
+                       bool needToRun = false;
+                       for (it = userLabels.begin(); it != userLabels.end(); it++) {  
+                               m->mothurOut("Your file does not include the label " + *it); 
+                               if (processedLabels.count(lastLabel) != 1) {
+                                       m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
+                                       needToRun = true;
+                               }else {
+                                       m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
+                               }
+                       }
                        
-                       delete list; list = NULL;
+                       //run last label if you need to
+                       if (needToRun == true)  {
+                               if (list != NULL) { delete list; }
+                               
+                               list = input->getListVector(lastLabel);
+                               
+                               m->mothurOut(list->getLabel()); m->mothurOutEndLine();
+                               
+                               processList(list);
+                               
+                               delete list; list = NULL;
+                       }
+                       
+                       if (list != NULL) { delete list; }
+                       delete input;
                }
                
-               if (list != NULL) { delete list; }
-               delete input;
-               
                m->mothurOutEndLine();
                m->mothurOut("Output File Name: "); m->mothurOutEndLine();
                for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }       

diff --git a/mothur b/mothur
index dd02cf23c1474b2e4cf0f8c6501d60b4f3ebef7c..f98378a61f3a546a8f38d45533fd788f52ae286b 100755 (executable)
Binary files a/mothur and b/mothur differ

diff --git a/removeotuscommand.cpp b/removeotuscommand.cpp
index 6828c7287f3530aa009ec9d42e12c8eaacbb724c..0e7d302ecc065c00a364dfe8e58b0b6e46750a6a 100644 (file)
--- a/removeotuscommand.cpp
+++ b/removeotuscommand.cpp
@@ -367,11 +367,17 @@ int RemoveOtusCommand::processList(ListVector*& list, GroupMap*& groupMap, ofstr
                                if (m->inUsersGroups(group, Groups)) {  removeBin = true; }
                                groupFileOutput += individual + "\t" + group + "\n";                            
                                
-                               //if there are no sequences from the groups we want to remove in this bin add to new list, output to groupfile
-                               newList.push_back(binnames);    
-                               outGroup << groupFileOutput;
+                               if (!removeBin) {
+                                       //if there are no sequences from the groups we want to remove in this bin add to new list, output to groupfile
+                                       newList.push_back(binnames);    
+                                       outGroup << groupFileOutput;
+                               }else {
+                                       numOtus++;
+                               }
+                       }else {
                                numOtus++;
                        }
+                       
                }
                
                //print new listvector

diff --git a/subsamplecommand.cpp b/subsamplecommand.cpp
index 7a857e8df70d4ab99328e3988e1f23faf9837a49..ac45d2ff562d0d4f5741901e23549b632073b97b 100644 (file)
--- a/subsamplecommand.cpp
+++ b/subsamplecommand.cpp
@@ -245,6 +245,7 @@ void SubSampleCommand::help(){
        try {
                m->mothurOut("The sub.sample command is designed to be used as a way to normalize your data, or create a smaller set from your original set.\n");
                m->mothurOut("The sub.sample command parameters are fasta, name, list, group, rabund, sabund, shared, groups, size and label.  You must provide a fasta, list, sabund, rabund or shared file as an input file.\n");
+               m->mothurOut("The namefile is only used with the fasta file, not with the listfile, because the list file should contain all sequences.\n");
                m->mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like included. The group names are separated by dashes.\n");
                m->mothurOut("The label parameter allows you to select what distance levels you would like, and are also separated by dashes.\n");
                m->mothurOut("The size parameter allows you indicate the size of your subsample.\n");

diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index 3c0d378f709042cc3e1c2ca2b87e730a62dbf359..7ee5c99dd86775124a83400a92f3ac1d9e24ad16 100644 (file)
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -337,7 +337,7 @@ int TrimSeqsCommand::execute(){
                        outputNames.push_back(groupFile); outputTypes["group"].push_back(groupFile);
                        getOligos(fastaFileNames, qualFileNames);
                }
-               cout << fastaFileNames.size() << '\t' << qualFileNames.size() << endl;
+               
                vector<unsigned long int> fastaFilePos;
                vector<unsigned long int> qFilePos;
                
@@ -362,7 +362,6 @@ int TrimSeqsCommand::execute(){
                if (m->control_pressed) {  return 0; }                  
                                                                                
                for(int i=0;i<fastaFileNames.size();i++){
-                       cout << fastaFileNames[i] << endl;
                        
                        if (m->isBlank(fastaFileNames[i])) {  remove(fastaFileNames[i].c_str());        }
                        else if (filesToRemove.count(fastaFileNames[i]) > 0) { remove(fastaFileNames[i].c_str()); }
@@ -397,7 +396,6 @@ int TrimSeqsCommand::execute(){
                
                if(qFileName != ""){
                        for(int i=0;i<qualFileNames.size();i++){
-                               cout << qualFileNames[i] << endl;
                                if (m->isBlank(qualFileNames[i])) {  remove(qualFileNames[i].c_str());  }
                                else if (filesToRemove.count(qualFileNames[i]) > 0) {  remove(qualFileNames[i].c_str()); }
                                else {
@@ -860,7 +858,7 @@ void TrimSeqsCommand::getOligos(vector<string>& outFASTAVec, vector<string>& out
                //int indexPrimer = 0;
                
                while(!inOligos.eof()){
-                       inOligos >> type;
+                       inOligos >> type; m->gobble(inOligos);
                                        
                        if(type[0] == '#'){
                                while (!inOligos.eof()) {       char c = inOligos.get(); if (c == 10 || c == 13){       break;  }       } // get rest of line if there's any crap there
@@ -891,29 +889,29 @@ void TrimSeqsCommand::getOligos(vector<string>& outFASTAVec, vector<string>& out
                                        map<string, int>::iterator itPrime = primers.find(oligo);
                                        if (itPrime != primers.end()) { m->mothurOut("primer " + oligo + " is in your oligos file already."); m->mothurOutEndLine();  }
                                        
-                                       primers[oligo]=index; index++;
-                                       groupVector.push_back(group);
+                                               primers[oligo]=index; index++;
+                                               groupVector.push_back(group);
                                        
-                                       if(allFiles){
-                                               outFASTAVec.push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
-                                               if(qFileName != ""){
-                                                       outQualVec.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
-                                               }
-                                               if (group == "") { //if there is not a group for this primer, then this file will not get written to, but we add it to keep the indexes correct
-                                                       filesToRemove.insert((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
+                                               if(allFiles){
+                                                       outFASTAVec.push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
                                                        if(qFileName != ""){
-                                                               filesToRemove.insert((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
+                                                               outQualVec.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
+                                                       }
+                                                       if (group == "") { //if there is not a group for this primer, then this file will not get written to, but we add it to keep the indexes correct
+                                                               filesToRemove.insert((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
+                                                               if(qFileName != ""){
+                                                                       filesToRemove.insert((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
+                                                               }
+                                                       }else {
+                                                               outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
+                                                               outputTypes["fasta"].push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
+                                                               if(qFileName != ""){
+                                                                       outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
+                                                                       outputTypes["qual"].push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
+                                                               }                                                       
                                                        }
-                                               }else {
-                                                       outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
-                                                       outputTypes["fasta"].push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
-                                                       if(qFileName != ""){
-                                                               outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
-                                                               outputTypes["qual"].push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
-                                                       }                                                       
                                                }
-                                       }
-
+                                       
                                }
                                else if(type == "REVERSE"){
                                        Sequence oligoRC("reverse", oligo);
@@ -927,19 +925,20 @@ void TrimSeqsCommand::getOligos(vector<string>& outFASTAVec, vector<string>& out
                                        map<string, int>::iterator itBar = barcodes.find(oligo);
                                        if (itBar != barcodes.end()) { m->mothurOut("barcode " + oligo + " is in your oligos file already."); m->mothurOutEndLine();  }
                                        
-                                       barcodes[oligo]=index; index++;
-                                       groupVector.push_back(group);
+                                               barcodes[oligo]=index; index++;
+                                               groupVector.push_back(group);
+                                               
+                                               if(allFiles){
+                                                       outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
+                                                       outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
+                                                       outFASTAVec.push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
+                                                       if(qFileName != ""){
+                                                               outQualVec.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
+                                                               outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
+                                                               outputTypes["qual"].push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
+                                                       }                                                       
+                                               }
                                        
-                                       if(allFiles){
-                                               outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
-                                               outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
-                                               outFASTAVec.push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
-                                               if(qFileName != ""){
-                                                       outQualVec.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
-                                                       outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
-                                                       outputTypes["qual"].push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
-                                               }                                                       
-                                       }
                                }else{  m->mothurOut(type + " is not recognized as a valid type. Choices are forward, reverse, and barcode. Ignoring " + oligo + "."); m->mothurOutEndLine();  }
                        }
                        m->gobble(inOligos);