X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=consensusseqscommand.cpp;h=d6158ba3ed3bc147027d54098aa71398182dc2f6;hb=dc383fb61b6d165a8d36e6108df8bc7129243ae6;hp=9d817a212cc2ad2ee3a330b982d96cffe251bdce;hpb=7ecb96ba54980d303fa066b4c29dae1e5a5be5b9;p=mothur.git diff --git a/consensusseqscommand.cpp b/consensusseqscommand.cpp index 9d817a2..d6158ba 100644 --- a/consensusseqscommand.cpp +++ b/consensusseqscommand.cpp @@ -53,6 +53,28 @@ string ConsensusSeqsCommand::getHelpString(){ exit(1); } } +//********************************************************************************************************************** +string ConsensusSeqsCommand::getOutputFileNameTag(string type, string inputName=""){ + try { + string outputFileName = ""; + map >::iterator it; + + //is this a type this command creates + it = outputTypes.find(type); + if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); } + else { + if (type == "fasta") { outputFileName = "cons.fasta"; } + else if (type == "name") { outputFileName = "cons.names"; } + else if (type == "summary") { outputFileName = "cons.summary"; } + else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; } + } + return outputFileName; + } + catch(exception& e) { + m->errorOut(e, "ConsensusSeqsCommand", "getOutputFileNameTag"); + exit(1); + } +} //********************************************************************************************************************** ConsensusSeqsCommand::ConsensusSeqsCommand(){ @@ -139,15 +161,17 @@ ConsensusSeqsCommand::ConsensusSeqsCommand(string option) { 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") { abort = true; } - else if (namefile == "not found") { namefile = ""; } + 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 = ""; } @@ -157,11 +181,15 @@ ConsensusSeqsCommand::ConsensusSeqsCommand(string option) { } string temp = validParameter.validFile(parameters, "cutoff", false); if (temp == "not found") { temp = "100"; } - convert(temp, cutoff); + 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 files; files.push_back(fastafile); + parser.getNameFile(files); + } } } catch(exception& e) { @@ -188,7 +216,7 @@ int ConsensusSeqsCommand::execute(){ if (listfile == "") { ofstream outSummary; - string outputSummaryFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "cons.summary"; + string outputSummaryFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("summary"); m->openOutputFile(outputSummaryFile, outSummary); outSummary.setf(ios::fixed, ios::floatfield); outSummary.setf(ios::showpoint); outputNames.push_back(outputSummaryFile); outputTypes["summary"].push_back(outputSummaryFile); @@ -196,7 +224,7 @@ int ConsensusSeqsCommand::execute(){ outSummary << "PositioninAlignment\tA\tT\tG\tC\tGap\tNumberofSeqs\tConsensusBase" << endl; ofstream outFasta; - string outputFastaFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "cons.fasta"; + string outputFastaFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("fasta"); m->openOutputFile(outputFastaFile, outFasta); outputNames.push_back(outputFastaFile); outputTypes["fasta"].push_back(outputFastaFile); @@ -204,7 +232,7 @@ int ConsensusSeqsCommand::execute(){ int seqLength = 0; for (map::iterator it = nameMap.begin(); it != nameMap.end(); it++) { - if (m->control_pressed) { outSummary.close(); outFasta.close(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; } + 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); @@ -221,7 +249,7 @@ int ConsensusSeqsCommand::execute(){ //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++) { remove(outputNames[i].c_str()); } return 0; } + if (m->control_pressed) { outSummary.close(); outFasta.close(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; } vector counts; counts.resize(5, 0); //A,T,G,C,Gap int numDots = 0; @@ -274,7 +302,7 @@ int ConsensusSeqsCommand::execute(){ //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 (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){ @@ -312,7 +340,7 @@ int ConsensusSeqsCommand::execute(){ } - 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; } + 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::iterator it; @@ -364,18 +392,18 @@ int ConsensusSeqsCommand::processList(ListVector*& list){ try{ ofstream outSummary; - string outputSummaryFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + list->getLabel() + ".cons.summary"; + string outputSummaryFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + list->getLabel() + getOutputFileNameTag("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"; + string outputNameFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + list->getLabel() + getOutputFileNameTag("name"); 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"; + string outputFastaFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + list->getLabel() + getOutputFileNameTag("fasta"); m->openOutputFile(outputFastaFile, outFasta); outputNames.push_back(outputFastaFile); outputTypes["fasta"].push_back(outputFastaFile); @@ -647,38 +675,29 @@ int ConsensusSeqsCommand::readFasta(){ int ConsensusSeqsCommand::readNames(){ try{ - - ifstream in; - m->openInputFile(namefile, in); - - string thisname, repnames; - map::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); + map temp; + map::iterator it; + bool error = false; + + m->readNames(namefile, temp); //use central buffered read + + for (map::iterator itTemp = temp.begin(); itTemp != temp.end(); itTemp++) { + string thisname, repnames; + thisname = itTemp->first; + repnames = itTemp->second; + + it = nameMap.find(thisname); if (it != nameMap.end()) { //then this sequence was in the fastafile - + nameFileMap[thisname] = repnames; //for later when outputting the new namesFile if the list file is unique + vector 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;