#include "removelineagecommand.h"
#include "parsefastaqcommand.h"
#include "pipelinepdscommand.h"
+#include "deuniqueseqscommand.h"
+
/*******************************************************/
commands["get.lineage"] = "get.lineage";
commands["remove.lineage"] = "remove.lineage";
commands["fastq.info"] = "fastq.info";
+ commands["deunique.seqs"] = "deunique.seqs";
commands["pipeline.pds"] = "MPIEnabled";
commands["classify.seqs"] = "MPIEnabled";
commands["dist.seqs"] = "MPIEnabled";
else if(commandName == "remove.lineage") { command = new RemoveLineageCommand(optionString); }
else if(commandName == "fastq.info") { command = new ParseFastaQCommand(optionString); }
else if(commandName == "pipeline.pds") { command = new PipelineCommand(optionString); }
+ else if(commandName == "deunique.seqs") { command = new DeUniqueSeqsCommand(optionString); }
else { command = new NoCommand(optionString); }
return command;
else if(commandName == "get.lineage") { pipecommand = new GetLineageCommand(optionString); }
else if(commandName == "remove.lineage") { pipecommand = new RemoveLineageCommand(optionString); }
else if(commandName == "fastq.info") { pipecommand = new ParseFastaQCommand(optionString); }
+ else if(commandName == "deunique.seqs") { pipecommand = new DeUniqueSeqsCommand(optionString); }
else { pipecommand = new NoCommand(optionString); }
return pipecommand;
else if(commandName == "get.lineage") { shellcommand = new GetLineageCommand(); }
else if(commandName == "remove.lineage") { shellcommand = new RemoveLineageCommand(); }
else if(commandName == "fastq.info") { shellcommand = new ParseFastaQCommand(); }
+ else if(commandName == "deunique.seqs") { shellcommand = new DeUniqueSeqsCommand(); }
else { shellcommand = new NoCommand(); }
return shellcommand;
--- /dev/null
+/*
+ * deuniqueseqscommand.cpp
+ * Mothur
+ *
+ * Created by westcott on 10/19/10.
+ * Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "deuniqueseqscommand.h"
+#include "sequence.hpp"
+
+//**********************************************************************************************************************
+vector<string> DeUniqueSeqsCommand::getValidParameters(){
+ try {
+ string Array[] = {"fasta", "name","outputdir","inputdir"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "DeUniqueSeqsCommand", "getValidParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+DeUniqueSeqsCommand::DeUniqueSeqsCommand(){
+ try {
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["fasta"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "DeUniqueSeqsCommand", "DeconvoluteCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> DeUniqueSeqsCommand::getRequiredParameters(){
+ try {
+ string Array[] = {"fasta","name"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "DeUniqueSeqsCommand", "getRequiredParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> DeUniqueSeqsCommand::getRequiredFiles(){
+ try {
+ vector<string> myArray;
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "DeUniqueSeqsCommand", "getRequiredFiles");
+ exit(1);
+ }
+}
+/**************************************************************************************/
+DeUniqueSeqsCommand::DeUniqueSeqsCommand(string option) {
+ try {
+ abort = false;
+
+ //allow user to run help
+ if(option == "help") { help(); abort = true; }
+
+ else {
+ //valid paramters for this command
+ string Array[] = {"fasta", "name","outputdir","inputdir"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+
+ 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;
+
+ //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->mothurOut("fasta is a required parameter for the deunique.seqs command."); m->mothurOutEndLine(); abort = true; }
+
+ //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->mothurOut("name is a required parameter for the deunique.seqs command."); m->mothurOutEndLine(); abort = true; }
+ }
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "DeUniqueSeqsCommand", "DeUniqueSeqsCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+void DeUniqueSeqsCommand::help(){
+ try {
+ m->mothurOut("The deunique.seqs command reads a fastafile and namefile, and creates a fastafile containing all the sequences.\n");
+ m->mothurOut("The deunique.seqs command parameters are fasta and name, both are required.\n");
+ m->mothurOut("The deunique.seqs command should be in the following format: \n");
+ m->mothurOut("deunique.seqs(fasta=yourFastaFile, name=yourNameFile) \n");
+ m->mothurOut("Example deunique.seqs(fasta=abrecovery.unique.fasta, name=abrecovery.names).\n");
+ m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n");
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "DeUniqueSeqsCommand", "help");
+ exit(1);
+ }
+}
+
+/**************************************************************************************/
+int DeUniqueSeqsCommand::execute() {
+ try {
+
+ if (abort == true) { return 0; }
+
+ //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(); remove(outFastaFile.c_str()); return 0; }
+
+ ifstream in;
+ m->openInputFile(fastaFile, in);
+
+ while (!in.eof()) {
+
+ if (m->control_pressed) { in.close(); out.close(); outputTypes.clear(); remove(outFastaFile.c_str()); return 0; }
+
+ Sequence seq(in); m->gobble(in);
+
+ if (seq.getName() != "") {
+
+ //look for sequence name in nameMap
+ map<string, string>::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<string> 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<string, string>::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(); remove(outFastaFile.c_str()); 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();
+
+ 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<string, string>::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);
+ }
+}
+
+/**************************************************************************************/
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