#include "deconvolutecommand.h"
+//**********************************************************************************************************************
+vector<string> DeconvoluteCommand::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, "DeconvoluteCommand", "getValidParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+DeconvoluteCommand::DeconvoluteCommand(){
+ try {
+ abort = true;
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["fasta"] = tempOutNames;
+ outputTypes["name"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "DeconvoluteCommand", "DeconvoluteCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> DeconvoluteCommand::getRequiredParameters(){
+ try {
+ string Array[] = {"fasta"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "DeconvoluteCommand", "getRequiredParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> DeconvoluteCommand::getRequiredFiles(){
+ try {
+ vector<string> myArray;
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "DeconvoluteCommand", "getRequiredFiles");
+ exit(1);
+ }
+}
+/**************************************************************************************/
+DeconvoluteCommand::DeconvoluteCommand(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;
+ outputTypes["name"] = 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
+ inFastaName = validParameter.validFile(parameters, "fasta", true);
+ if (inFastaName == "not open") { abort = true; }
+ else if (inFastaName == "not found") { inFastaName = ""; m->mothurOut("fasta is a required parameter for the unique.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(inFastaName); //if user entered a file with a path then preserve it
+ }
+
+ oldNameMapFName = validParameter.validFile(parameters, "name", true);
+ if (oldNameMapFName == "not open") { abort = true; }
+ else if (oldNameMapFName == "not found"){ oldNameMapFName = ""; }
+ }
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "DeconvoluteCommand", "DeconvoluteCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+void DeconvoluteCommand::help(){
+ try {
+ m->mothurOut("The unique.seqs command reads a fastafile and creates a namesfile.\n");
+ m->mothurOut("It creates a file where the first column is the groupname and the second column is a list of sequence names who have the same sequence. \n");
+ m->mothurOut("If the sequence is unique the second column will just contain its name. \n");
+ m->mothurOut("The unique.seqs command parameter is fasta and it is required.\n");
+ m->mothurOut("The unique.seqs command should be in the following format: \n");
+ m->mothurOut("unique.seqs(fasta=yourFastaFile) \n");
+ }
+ catch(exception& e) {
+ m->errorOut(e, "DeconvoluteCommand", "help");
+ exit(1);
+ }
+}
+
/**************************************************************************************/
int DeconvoluteCommand::execute() {
try {
- globaldata = GlobalData::getInstance();
-
+
+ if (abort == true) { return 0; }
+
//prepare filenames and open files
- filename = globaldata->getFastaFile();
- outputFileName = (getRootName(filename) + "names");
- outFastafile = (getRootName(filename) + "unique.fasta");
+ string outNameFile = outputDir + m->getRootName(m->getSimpleName(inFastaName)) + "names";
+ string outFastaFile = outputDir + m->getRootName(m->getSimpleName(inFastaName)) + "unique" + m->getExtension(inFastaName);
- openInputFile(filename, in);
- openOutputFile(outputFileName, out);
- openOutputFile(outFastafile, outFasta);
-
- //constructor reads in file and store internally
- fastamap = new FastaMap();
-
- //two columns separated by tabs sequence name and then sequence
- fastamap->readFastaFile(in);
-
- //print out new names file
- //file contains 2 columns separated by tabs. the first column is the groupname(name of first sequence found.
- //the second column is the list of names of identical sequences separated by ','.
- fastamap->print(out);
- fastamap->printCondensedFasta(outFasta);
+ FastaMap fastamap;
+ if(oldNameMapFName == "") { fastamap.readFastaFile(inFastaName); }
+ else { fastamap.readFastaFile(inFastaName, oldNameMapFName); }
+
+ if (m->control_pressed) { return 0; }
+
+ fastamap.printCondensedFasta(outFastaFile);
+ fastamap.printNamesFile(outNameFile);
+
+ if (m->control_pressed) { outputTypes.clear(); remove(outFastaFile.c_str()); remove(outNameFile.c_str()); return 0; }
+
+ m->mothurOutEndLine();
+ m->mothurOut("Output File Names: "); m->mothurOutEndLine();
+ m->mothurOut(outFastaFile); m->mothurOutEndLine();
+ m->mothurOut(outNameFile); m->mothurOutEndLine();
+ outputNames.push_back(outFastaFile); outputNames.push_back(outNameFile); outputTypes["fasta"].push_back(outFastaFile); outputTypes["name"].push_back(outNameFile);
+ m->mothurOutEndLine();
+
+
+
return 0;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the DeconvoluteCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the DeconvoluteCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "DeconvoluteCommand", "execute");
exit(1);
}
}
projects / mothur.git / blobdiff