X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=deuniqueseqscommand.cpp;fp=deuniqueseqscommand.cpp;h=0000000000000000000000000000000000000000;hb=4a877efa127e56e81a21f53cfdbbfd3bfbe8c4ff;hp=7481416f649ddad983877ab02cac08e5668316d1;hpb=a6cf29fa4dac0909c7582cb1094151d34093ee76;p=mothur.git diff --git a/deuniqueseqscommand.cpp b/deuniqueseqscommand.cpp deleted file mode 100644 index 7481416..0000000 --- a/deuniqueseqscommand.cpp +++ /dev/null @@ -1,256 +0,0 @@ -/* - * 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); - } -} - -/**************************************************************************************/