--- /dev/null
+/*
+ * consensusseqscommand.cpp
+ * Mothur
+ *
+ * Created by westcott on 11/23/10.
+ * Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "consensusseqscommand.h"
+#include "sequence.hpp"
+#include "inputdata.h"
+
+//**********************************************************************************************************************
+vector<string> ConsensusSeqsCommand::setParameters(){
+ try {
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
+ CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
+ CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(plist);
+ CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
+ CommandParameter pcutoff("cutoff", "Number", "", "100", "", "", "",false,false); parameters.push_back(pcutoff);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+
+ vector<string> myArray;
+ for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ConsensusSeqsCommand", "setParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string ConsensusSeqsCommand::getHelpString(){
+ try {
+ string helpString = "";
+ helpString += "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";
+ helpString += "The consensus.seqs command parameters are fasta, list, name, cutoff and label.\n";
+ helpString += "The fasta parameter allows you to enter the fasta file containing your sequences, and is required, unless you have a valid current fasta file. \n";
+ helpString += "The list parameter allows you to enter a your list file. \n";
+ helpString += "The name parameter allows you to enter a names file associated with the fasta file. \n";
+ helpString += "The label parameter allows you to select what distance levels you would like output files for, and are separated by dashes.\n";
+ helpString += "The cutoff parameter allows you set a percentage of sequences that support the base. For example: cutoff=97 would only return a sequence that only showed ambiguities for bases that were not supported by at least 97% of sequences.\n";
+ helpString += "The consensus.seqs command should be in the following format: \n";
+ helpString += "consensus.seqs(fasta=yourFastaFile, list=yourListFile) \n";
+ helpString += "Example: consensus.seqs(fasta=abrecovery.align, list=abrecovery.fn.list) \n";
+ helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n";
+ return helpString;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ConsensusSeqsCommand", "getHelpString");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
+ConsensusSeqsCommand::ConsensusSeqsCommand(){
+ try {
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["fasta"] = tempOutNames;
+ outputTypes["name"] = tempOutNames;
+ outputTypes["summary"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ConsensusSeqsCommand", "ConsensusSeqsCommand");
+ exit(1);
+ }
+}
+//***************************************************************************************************************
+ConsensusSeqsCommand::ConsensusSeqsCommand(string option) {
+ try {
+ abort = false; calledHelp = false;
+ allLines = 1;
+
+ //allow user to run help
+ if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
+
+ else {
+
+ vector<string> myArray = setParameters();
+
+ OptionParser parser(option);
+ map<string,string> parameters = parser.getParameters();
+
+ ValidParameters validParameter;
+ map<string,string>::iterator it;
+
+ //check to make sure all parameters are valid for command
+ for (it = parameters.begin(); it != parameters.end(); it++) {
+ if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
+ }
+
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["fasta"] = tempOutNames;
+ outputTypes["name"] = tempOutNames;
+ outputTypes["summary"] = tempOutNames;
+
+
+ //if the user changes the input directory command factory will send this info to us in the output parameter
+ string inputDir = validParameter.validFile(parameters, "inputdir", false);
+ if (inputDir == "not found"){ inputDir = ""; }
+ else {
+ string path;
+ it = parameters.find("fasta");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["fasta"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("name");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["name"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("list");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["list"] = inputDir + it->second; }
+ }
+ }
+
+
+ //check for parameters
+ fastafile = validParameter.validFile(parameters, "fasta", true);
+ if (fastafile == "not open") { abort = true; }
+ else if (fastafile == "not found") {
+ fastafile = m->getFastaFile();
+ if (fastafile != "") { m->mothurOut("Using " + fastafile + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
+ else { m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
+ }else { m->setFastaFile(fastafile); }
+
+ namefile = validParameter.validFile(parameters, "name", true);
+ if (namefile == "not open") { namefile = ""; abort = true; }
+ else if (namefile == "not found") { namefile = ""; }
+ else { m->setNameFile(namefile); }
+
+ listfile = validParameter.validFile(parameters, "list", true);
+ if (listfile == "not open") { abort = true; }
+ else if (listfile == "not found") { listfile = ""; }
+ else { m->setListFile(listfile); }
+
+ label = validParameter.validFile(parameters, "label", false);
+ if (label == "not found") { label = ""; }
+ else {
+ if(label != "all") { m->splitAtDash(label, labels); allLines = 0; }
+ else { allLines = 1; }
+ }
+
+ string temp = validParameter.validFile(parameters, "cutoff", false); if (temp == "not found") { temp = "100"; }
+ m->mothurConvert(temp, cutoff);
+
+ //if the user changes the output directory command factory will send this info to us in the output parameter
+ outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = m->hasPath(fastafile); }
+
+ if (namefile == ""){
+ vector<string> files; files.push_back(fastafile);
+ parser.getNameFile(files);
+ }
+ }
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ConsensusSeqsCommand", "ConsensusSeqsCommand");
+ exit(1);
+ }
+}
+//***************************************************************************************************************
+
+int ConsensusSeqsCommand::execute(){
+ try{
+
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
+
+ readFasta();
+
+ if (m->control_pressed) { return 0; }
+
+ if (namefile != "") { readNames(); }
+
+ if (m->control_pressed) { return 0; }
+
+
+ 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);
+
+ outSummary << "PositioninAlignment\tA\tT\tG\tC\tGap\tNumberofSeqs\tConsensusBase" << endl;
+
+ 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++) {
+
+ if (m->control_pressed) { outSummary.close(); outFasta.close(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
+
+ 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; }
+
+ }
+
+ 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++) {
+
+ if (m->control_pressed) { outSummary.close(); outFasta.close(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
+
+ vector<int> counts; counts.resize(5, 0); //A,T,G,C,Gap
+ int numDots = 0;
+
+ 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, seqs.size()); }
+
+ 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();
+
+ }
+
+ for (int j = 0; j < seqLength; j++) {
+ outSummary << (j+1) << '\t' << percentages[0][j] << '\t'<< percentages[1][j] << '\t'<< percentages[2][j] << '\t' << percentages[3][j] << '\t' << percentages[4][j] << '\t' << seqs.size() << '\t' << consSeq[j] << endl;
+ }
+
+
+ outFasta << ">conseq" << endl << consSeq << endl;
+
+ outSummary.close(); outFasta.close();
+
+
+ }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++) { m->mothurRemove(outputNames[i]); } 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();
+ }
+
+
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } 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();
+ }
+ }
+
+ //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;
+ }
+
+ m->mothurOutEndLine();
+ m->mothurOut("Output File Name: "); m->mothurOutEndLine();
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
+ m->mothurOutEndLine();
+
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ConsensusSeqsCommand", "execute");
+ exit(1);
+ }
+}
+//***************************************************************************************************************
+
+int ConsensusSeqsCommand::processList(ListVector*& list){
+ try{
+
+ ofstream outSummary;
+ string outputSummaryFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + list->getLabel() + ".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 outName;
+ string outputNameFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + list->getLabel() + ".cons.names";
+ m->openOutputFile(outputNameFile, outName);
+ outputNames.push_back(outputNameFile); outputTypes["name"].push_back(outputNameFile);
+
+ ofstream outFasta;
+ string outputFastaFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + list->getLabel() + ".cons.fasta";
+ m->openOutputFile(outputFastaFile, outFasta);
+ outputNames.push_back(outputFastaFile); outputTypes["fasta"].push_back(outputFastaFile);
+
+ outSummary << "OTU#\tPositioninAlignment\tA\tT\tG\tC\tGap\tNumberofSeqs\tConsensusBase" << endl;
+
+ for (int i = 0; i < list->getNumBins(); i++) {
+
+ if (m->control_pressed) { outSummary.close(); outName.close(); outFasta.close(); return 0; }
+
+ string bin = list->get(i);
+
+ string newName = "";
+ string consSeq = getConsSeq(bin, outSummary, newName, i);
+
+ outFasta << ">seq" << (i+1) << endl << consSeq << endl;
+ outName << "seq" << (i+1) << '\t' << "seq" << (i+1) << "," << newName << endl;
+ }
+
+ outSummary.close(); outName.close(); outFasta.close();
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ConsensusSeqsCommand", "processList");
+ exit(1);
+ }
+}
+
+//***************************************************************************************************************
+//made this smart enough to owrk with unique or non unique list file
+string ConsensusSeqsCommand::getConsSeq(string bin, ofstream& outSummary, string& name, int binNumber){
+ try{
+
+ string consSeq = "";
+ bool error = false;
+
+ //the whole bin is the second column if no names file, otherwise build it
+ name = bin;
+ if (namefile != "") { name = ""; }
+
+ vector<string> binNames;
+ m->splitAtComma(bin, binNames);
+
+ //get sequence strings for each name in the bin
+ vector<string> seqs;
+
+ set<string> addedAlready;
+ int seqLength = 0;
+ for (int i = 0; i < binNames.size(); i++) {
+
+ map<string, string>::iterator it;
+
+ it = nameMap.find(binNames[i]);
+ if (it == nameMap.end()) {
+ if (namefile == "") { m->mothurOut("[ERROR]: " + binNames[i] + " is not in your fasta file, please correct."); m->mothurOutEndLine(); error = true; }
+ else { m->mothurOut("[ERROR]: " + binNames[i] + " is not in your fasta or name file, please correct."); m->mothurOutEndLine(); error = true; }
+ break;
+ }else {
+
+ //add sequence string to seqs vector to process below
+ 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(); error = true; break; }
+
+ if (namefile != "") {
+ //did we add this line from name file already?
+ if (addedAlready.count(it->second) == 0) {
+ name += "," + nameFileMap[it->second];
+ addedAlready.insert(it->second);
+ }
+ }
+
+ }
+ }
+
+ if (error) { m->control_pressed = true; return consSeq; }
+
+ if (namefile != "") { name = name.substr(1); }
+
+ vector< vector<float> > percentages; percentages.resize(5);
+ for (int j = 0; j < percentages.size(); j++) { percentages[j].resize(seqLength, 0.0); }
+
+ //get counts
+ for (int j = 0; j < seqLength; j++) {
+
+ if (m->control_pressed) { return consSeq; }
+
+ vector<int> counts; counts.resize(5, 0); //A,T,G,C,Gap
+ int numDots = 0;
+
+ 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, seqs.size()); }
+
+ 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();
+
+ }
+
+ for (int j = 0; j < seqLength; j++) {
+ outSummary << (binNumber + 1) << '\t' << (j+1) << '\t' << percentages[0][j] << '\t'<< percentages[1][j] << '\t'<< percentages[2][j] << '\t' << percentages[3][j] << '\t' << percentages[4][j] << '\t' << seqs.size() << '\t' << consSeq[j] << endl;
+ }
+
+ return consSeq;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ConsensusSeqsCommand", "getConsSeq");
+ exit(1);
+ }
+}
+//***************************************************************************************************************
+
+char ConsensusSeqsCommand::getBase(vector<int> counts, int size){ //A,T,G,C,Gap
+ try{
+ /* A = adenine
+ * C = cytosine
+ * G = guanine
+ * T = thymine
+ * R = G A (purine)
+ * Y = T C (pyrimidine)
+ * K = G T (keto)
+ * M = A C (amino)
+ * S = G C (strong bonds)
+ * W = A T (weak bonds)
+ * B = G T C (all but A)
+ * D = G A T (all but C)
+ * H = A C T (all but G)
+ * V = G C A (all but T)
+ * N = A G C T (any) */
+
+ char conBase = 'N';
+
+ //zero out counts that don't make the cutoff
+ float percentage = (100.0 - cutoff) / 100.0;
+ int zeroCutoff = percentage * size;
+
+ for (int i = 0; i < counts.size(); i++) {
+ if (counts[i] < zeroCutoff) { counts[i] = 0; }
+ }
+
+ //any
+ if ((counts[0] != 0) && (counts[1] != 0) && (counts[2] != 0) && (counts[3] != 0) && (counts[4] != 0)) { conBase = 'n'; }
+ //any no gap
+ else if ((counts[0] != 0) && (counts[1] != 0) && (counts[2] != 0) && (counts[3] != 0) && (counts[4] == 0)) { conBase = 'N'; }
+ //all but T
+ else if ((counts[0] != 0) && (counts[1] == 0) && (counts[2] != 0) && (counts[3] != 0) && (counts[4] != 0)) { conBase = 'v'; }
+ //all but T no gap
+ else if ((counts[0] != 0) && (counts[1] == 0) && (counts[2] != 0) && (counts[3] != 0) && (counts[4] == 0)) { conBase = 'V'; }
+ //all but G
+ else if ((counts[0] != 0) && (counts[1] != 0) && (counts[2] == 0) && (counts[3] != 0) && (counts[4] != 0)) { conBase = 'h'; }
+ //all but G no gap
+ else if ((counts[0] != 0) && (counts[1] != 0) && (counts[2] == 0) && (counts[3] != 0) && (counts[4] == 0)) { conBase = 'H'; }
+ //all but C
+ else if ((counts[0] != 0) && (counts[1] != 0) && (counts[2] != 0) && (counts[3] == 0) && (counts[4] != 0)) { conBase = 'd'; }
+ //all but C no gap
+ else if ((counts[0] != 0) && (counts[1] != 0) && (counts[2] != 0) && (counts[3] == 0) && (counts[4] == 0)) { conBase = 'D'; }
+ //all but A
+ else if ((counts[0] == 0) && (counts[1] != 0) && (counts[2] != 0) && (counts[3] != 0) && (counts[4] != 0)) { conBase = 'b'; }
+ //all but A no gap
+ else if ((counts[0] == 0) && (counts[1] != 0) && (counts[2] != 0) && (counts[3] != 0) && (counts[4] == 0)) { conBase = 'B'; }
+ //W = A T (weak bonds)
+ else if ((counts[0] != 0) && (counts[1] != 0) && (counts[2] == 0) && (counts[3] == 0) && (counts[4] != 0)) { conBase = 'w'; }
+ //W = A T (weak bonds) no gap
+ else if ((counts[0] != 0) && (counts[1] != 0) && (counts[2] == 0) && (counts[3] == 0) && (counts[4] == 0)) { conBase = 'W'; }
+ //S = G C (strong bonds)
+ else if ((counts[0] == 0) && (counts[1] == 0) && (counts[2] != 0) && (counts[3] != 0) && (counts[4] != 0)) { conBase = 's'; }
+ //S = G C (strong bonds) no gap
+ else if ((counts[0] == 0) && (counts[1] == 0) && (counts[2] != 0) && (counts[3] != 0) && (counts[4] == 0)) { conBase = 'S'; }
+ //M = A C (amino)
+ else if ((counts[0] != 0) && (counts[1] == 0) && (counts[2] == 0) && (counts[3] != 0) && (counts[4] != 0)) { conBase = 'm'; }
+ //M = A C (amino) no gap
+ else if ((counts[0] != 0) && (counts[1] == 0) && (counts[2] == 0) && (counts[3] != 0) && (counts[4] == 0)) { conBase = 'M'; }
+ //K = G T (keto)
+ else if ((counts[0] == 0) && (counts[1] != 0) && (counts[2] != 0) && (counts[3] == 0) && (counts[4] != 0)) { conBase = 'k'; }
+ //K = G T (keto) no gap
+ else if ((counts[0] == 0) && (counts[1] != 0) && (counts[2] != 0) && (counts[3] == 0) && (counts[4] == 0)) { conBase = 'K'; }
+ //Y = T C (pyrimidine)
+ else if ((counts[0] == 0) && (counts[1] != 0) && (counts[2] == 0) && (counts[3] != 0) && (counts[4] != 0)) { conBase = 'y'; }
+ //Y = T C (pyrimidine) no gap
+ else if ((counts[0] == 0) && (counts[1] != 0) && (counts[2] == 0) && (counts[3] != 0) && (counts[4] == 0)) { conBase = 'Y'; }
+ //R = G A (purine)
+ else if ((counts[0] != 0) && (counts[1] == 0) && (counts[2] != 0) && (counts[3] == 0) && (counts[4] != 0)) { conBase = 'r'; }
+ //R = G A (purine) no gap
+ else if ((counts[0] != 0) && (counts[1] == 0) && (counts[2] != 0) && (counts[3] == 0) && (counts[4] == 0)) { conBase = 'R'; }
+ //only A
+ else if ((counts[0] != 0) && (counts[1] == 0) && (counts[2] == 0) && (counts[3] == 0) && (counts[4] != 0)) { conBase = 'a'; }
+ //only A no gap
+ else if ((counts[0] != 0) && (counts[1] == 0) && (counts[2] == 0) && (counts[3] == 0) && (counts[4] == 0)) { conBase = 'A'; }
+ //only T
+ else if ((counts[0] == 0) && (counts[1] != 0) && (counts[2] == 0) && (counts[3] == 0) && (counts[4] != 0)) { conBase = 't'; }
+ //only T no gap
+ else if ((counts[0] == 0) && (counts[1] != 0) && (counts[2] == 0) && (counts[3] == 0) && (counts[4] == 0)) { conBase = 'T'; }
+ //only G
+ else if ((counts[0] == 0) && (counts[1] == 0) && (counts[2] != 0) && (counts[3] == 0) && (counts[4] != 0)) { conBase = 'g'; }
+ //only G no gap
+ else if ((counts[0] == 0) && (counts[1] == 0) && (counts[2] != 0) && (counts[3] == 0) && (counts[4] == 0)) { conBase = 'G'; }
+ //only C
+ else if ((counts[0] == 0) && (counts[1] == 0) && (counts[2] == 0) && (counts[3] != 0) && (counts[4] != 0)) { conBase = 'c'; }
+ //only C no gap
+ else if ((counts[0] == 0) && (counts[1] == 0) && (counts[2] == 0) && (counts[3] != 0) && (counts[4] == 0)) { conBase = 'C'; }
+ //only gap
+ else if ((counts[0] == 0) && (counts[1] == 0) && (counts[2] == 0) && (counts[3] == 0) && (counts[4] != 0)) { conBase = '-'; }
+ //cutoff removed all counts
+ else if ((counts[0] == 0) && (counts[1] == 0) && (counts[2] == 0) && (counts[3] == 0) && (counts[4] == 0)) { conBase = 'N'; }
+ else{ m->mothurOut("[ERROR]: cannot find consensus base."); m->mothurOutEndLine(); }
+
+ return conBase;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ConsensusSeqsCommand", "getBase");
+ exit(1);
+ }
+}
+
+//***************************************************************************************************************
+
+int ConsensusSeqsCommand::readFasta(){
+ try{
+
+ ifstream in;
+ m->openInputFile(fastafile, in);
+
+ while (!in.eof()) {
+
+ if (m->control_pressed) { break; }
+
+ Sequence seq(in); m->gobble(in);
+ string name = seq.getName();
+
+ if (name != "") {
+ fastaMap[name] = seq.getAligned();
+ nameMap[name] = name; //set nameMap incase no names file
+ nameFileMap[name] = name;
+ }
+ }
+
+ in.close();
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ConsensusSeqsCommand", "readFasta");
+ exit(1);
+ }
+}
+//***************************************************************************************************************
+
+int ConsensusSeqsCommand::readNames(){
+ try{
+
+ ifstream in;
+ m->openInputFile(namefile, in);
+
+ string thisname, repnames;
+ map<string, string>::iterator it;
+
+ bool error = false;
+
+ while(!in.eof()){
+
+ if (m->control_pressed) { break; }
+
+ in >> thisname; m->gobble(in); //read from first column
+ in >> repnames; //read from second column
+
+ it = nameMap.find(thisname);
+ if (it != nameMap.end()) { //then this sequence was in the fastafile
+
+ vector<string> splitRepNames;
+ m->splitAtComma(repnames, splitRepNames);
+
+ nameFileMap[thisname] = repnames; //for later when outputting the new namesFile if the list file is unique
+ for (int i = 0; i < splitRepNames.size(); i++) { nameMap[splitRepNames[i]] = thisname; }
+
+ }else{ m->mothurOut("[ERROR]: " + thisname + " is not in the fasta file, please correct."); m->mothurOutEndLine(); error = true; }
+
+ m->gobble(in);
+ }
+
+ in.close();
+
+ if (error) { m->control_pressed = true; }
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ConsensusSeqsCommand", "readNames");
+ exit(1);
+ }
+ }
+
+//***************************************************************************************************************
+
+
projects / mothur.git / blobdiff