+++ /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::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<string> 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<string> 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<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;
-
- //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<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(); 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<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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