X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=deuniqueseqscommand.cpp;fp=deuniqueseqscommand.cpp;h=7481416f649ddad983877ab02cac08e5668316d1;hb=0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc;hp=0000000000000000000000000000000000000000;hpb=1b73ff67c83892a025e597dabd9df6fe7b58206a;p=mothur.git diff --git a/deuniqueseqscommand.cpp b/deuniqueseqscommand.cpp new file mode 100644 index 0000000..7481416 --- /dev/null +++ b/deuniqueseqscommand.cpp @@ -0,0 +1,256 @@ +/* + * deuniqueseqscommand.cpp + * Mothur + * + * Created by westcott on 10/19/10. + * Copyright 2010 Schloss Lab. All rights reserved. + * + */ + +#include "deuniqueseqscommand.h" +#include "sequence.hpp" + +//********************************************************************************************************************** +vector DeUniqueSeqsCommand::setParameters(){ + try { + CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta); + CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pname); + CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir); + CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir); + + vector myArray; + for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); } + return myArray; + } + catch(exception& e) { + m->errorOut(e, "DeUniqueSeqsCommand", "setParameters"); + exit(1); + } +} +//********************************************************************************************************************** +string DeUniqueSeqsCommand::getHelpString(){ + try { + string helpString = ""; + helpString += "The deunique.seqs command reads a fastafile and namefile, and creates a fastafile containing all the sequences.\n"; + helpString += "The deunique.seqs command parameters are fasta and name, both are required, unless you have valid current name and fasta files.\n"; + helpString += "The deunique.seqs command should be in the following format: \n"; + helpString += "deunique.seqs(fasta=yourFastaFile, name=yourNameFile) \n"; + helpString += "Example deunique.seqs(fasta=abrecovery.unique.fasta, name=abrecovery.names).\n"; + helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n"; + return helpString; + } + catch(exception& e) { + m->errorOut(e, "DeUniqueSeqsCommand", "getHelpString"); + exit(1); + } +} +//********************************************************************************************************************** +DeUniqueSeqsCommand::DeUniqueSeqsCommand(){ + try { + abort = true; calledHelp = true; + setParameters(); + vector tempOutNames; + outputTypes["fasta"] = tempOutNames; + } + catch(exception& e) { + m->errorOut(e, "DeUniqueSeqsCommand", "DeconvoluteCommand"); + exit(1); + } +} +/**************************************************************************************/ +DeUniqueSeqsCommand::DeUniqueSeqsCommand(string option) { + try { + abort = false; calledHelp = false; + + //allow user to run help + if(option == "help") { help(); abort = true; calledHelp = true; } + else if(option == "citation") { citation(); abort = true; calledHelp = true;} + + else { + vector myArray = setParameters(); + + OptionParser parser(option); + map parameters = parser.getParameters(); + + ValidParameters validParameter; + map::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 tempOutNames; + outputTypes["fasta"] = 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; } + } + } + + + //check for required 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); } + + //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 = ""; + outputDir += m->hasPath(fastaFile); //if user entered a file with a path then preserve it + } + + nameFile = validParameter.validFile(parameters, "name", true); + if (nameFile == "not open") { abort = true; } + else if (nameFile == "not found"){ + nameFile = m->getNameFile(); + if (nameFile != "") { m->mothurOut("Using " + nameFile + " as input file for the name parameter."); m->mothurOutEndLine(); } + else { m->mothurOut("You have no current namefile and the name parameter is required."); m->mothurOutEndLine(); abort = true; } + }else { m->setNameFile(nameFile); } + } + + } + catch(exception& e) { + m->errorOut(e, "DeUniqueSeqsCommand", "DeUniqueSeqsCommand"); + exit(1); + } +} +/**************************************************************************************/ +int DeUniqueSeqsCommand::execute() { + try { + + if (abort == true) { if (calledHelp) { return 0; } return 2; } + + //prepare filenames and open files + ofstream out; + string outFastaFile = m->getRootName(m->getSimpleName(fastaFile)); + int pos = outFastaFile.find("unique"); + if (pos != string::npos) { + outFastaFile = outputDir + outFastaFile.substr(0, pos) + "redundant" + m->getExtension(fastaFile); + }else{ + outFastaFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "redundant" + m->getExtension(fastaFile); + } + m->openOutputFile(outFastaFile, out); + + readNamesFile(); + if (m->control_pressed) { out.close(); outputTypes.clear(); m->mothurRemove(outFastaFile); return 0; } + + ifstream in; + m->openInputFile(fastaFile, in); + + while (!in.eof()) { + + if (m->control_pressed) { in.close(); out.close(); outputTypes.clear(); m->mothurRemove(outFastaFile); return 0; } + + Sequence seq(in); m->gobble(in); + + if (seq.getName() != "") { + + //look for sequence name in nameMap + map::iterator it = nameMap.find(seq.getName()); + + if (it == nameMap.end()) { m->mothurOut("[ERROR]: Your namefile does not contain " + seq.getName() + ", aborting."); m->mothurOutEndLine(); m->control_pressed = true; } + else { + vector names; + m->splitAtComma(it->second, names); + + //output sequences + for (int i = 0; i < names.size(); i++) { + out << ">" << names[i] << endl; + out << seq.getAligned() << endl; + } + + //remove seq from name map so we can check for seqs in namefile not in fastafile later + nameMap.erase(it); + } + } + } + in.close(); + out.close(); + + if (nameMap.size() != 0) { //then there are names in the namefile not in the fastafile + for (map::iterator it = nameMap.begin(); it != nameMap.end(); it++) { + m->mothurOut(it->first + " is not in your fasta file, but is in your name file. Please correct."); m->mothurOutEndLine(); + } + } + + if (m->control_pressed) { outputTypes.clear(); m->mothurRemove(outFastaFile); return 0; } + + m->mothurOutEndLine(); + m->mothurOut("Output File Names: "); m->mothurOutEndLine(); + m->mothurOut(outFastaFile); m->mothurOutEndLine(); + outputNames.push_back(outFastaFile); outputTypes["fasta"].push_back(outFastaFile); + m->mothurOutEndLine(); + + //set fasta file as new current fastafile + string current = ""; + itTypes = outputTypes.find("fasta"); + if (itTypes != outputTypes.end()) { + if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); } + } + + return 0; + } + catch(exception& e) { + m->errorOut(e, "DeUniqueSeqsCommand", "execute"); + exit(1); + } +} +//********************************************************************************************************************** +int DeUniqueSeqsCommand::readNamesFile() { + try { + + ifstream inNames; + m->openInputFile(nameFile, inNames); + + string name, names; + map::iterator it; + + while(inNames){ + + if(m->control_pressed) { break; } + + inNames >> name; m->gobble(inNames); + inNames >> names; + + it = nameMap.find(name); + + if (it == nameMap.end()) { nameMap[name] = names; } + else { m->mothurOut("[ERROR]: Your namefile already contains " + name + ", aborting."); m->mothurOutEndLine(); m->control_pressed = true; } + + m->gobble(inNames); + } + inNames.close(); + + return 0; + + } + catch(exception& e) { + m->errorOut(e, "DeUniqueSeqsCommand", "readNamesFile"); + exit(1); + } +} + +/**************************************************************************************/