#include "sequence.hpp"
//**********************************************************************************************************************
-vector<string> DeUniqueSeqsCommand::getValidParameters(){
+vector<string> DeUniqueSeqsCommand::setParameters(){
try {
- string Array[] = {"fasta", "name","outputdir","inputdir"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","fasta",false,true,true); parameters.push_back(pfasta);
+ CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none","",false,true,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", "getValidParameters");
+ m->errorOut(e, "DeUniqueSeqsCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
-DeUniqueSeqsCommand::DeUniqueSeqsCommand(){
+string DeUniqueSeqsCommand::getHelpString(){
try {
- abort = true; calledHelp = true;
- vector<string> tempOutNames;
- outputTypes["fasta"] = tempOutNames;
+ 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", "DeconvoluteCommand");
+ m->errorOut(e, "DeUniqueSeqsCommand", "getHelpString");
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);
- }
+string DeUniqueSeqsCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
+
+ if (type == "fasta") { pattern = "[filename],redundant.fasta"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "DeUniqueSeqsCommand", "getOutputPattern");
+ exit(1);
+ }
}
//**********************************************************************************************************************
-vector<string> DeUniqueSeqsCommand::getRequiredFiles(){
+DeUniqueSeqsCommand::DeUniqueSeqsCommand(){
try {
- vector<string> myArray;
- return myArray;
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["fasta"] = tempOutNames;
}
catch(exception& e) {
- m->errorOut(e, "DeUniqueSeqsCommand", "getRequiredFiles");
+ m->errorOut(e, "DeUniqueSeqsCommand", "DeconvoluteCommand");
exit(1);
}
}
//allow user to run help
if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else {
- //valid paramters for this command
- string Array[] = {"fasta", "name","outputdir","inputdir"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ vector<string> myArray = setParameters();
OptionParser parser(option);
map<string,string> parameters = parser.getParameters();
//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; }
+ 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"){
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; }
+ 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); }
}
}
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 {
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);
- }
+ if (pos != string::npos) { outFastaFile = outputDir + outFastaFile.substr(0, pos); }
+ else { outFastaFile = outputDir + outFastaFile; }
+ map<string, string> variables;
+ variables["[filename]"] = outFastaFile;
+ outFastaFile = getOutputFileName("fasta", variables);
m->openOutputFile(outFastaFile, out);
readNamesFile();
- if (m->control_pressed) { out.close(); outputTypes.clear(); remove(outFastaFile.c_str()); return 0; }
+ 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(); remove(outFastaFile.c_str()); return 0; }
+ if (m->control_pressed) { in.close(); out.close(); outputTypes.clear(); m->mothurRemove(outFastaFile); return 0; }
Sequence seq(in); m->gobble(in);
}
}
- if (m->control_pressed) { outputTypes.clear(); remove(outFastaFile.c_str()); return 0; }
+ if (m->control_pressed) { outputTypes.clear(); m->mothurRemove(outFastaFile); return 0; }
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
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