//***************************************************************************************************************
-ReverseSeqsCommand::ReverseSeqsCommand(){
+ReverseSeqsCommand::ReverseSeqsCommand(string option) {
try {
- globaldata = GlobalData::getInstance();
- if(globaldata->getFastaFile() == "") { cout << "you need to at least enter a fasta file name" << endl; }
+ abort = false;
+
+ //allow user to run help
+ if(option == "help") { help(); abort = true; }
+
+ else {
+ //valid paramters for this command
+ string Array[] = {"fasta", "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; }
+ }
+
+ //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 = 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; }
+ }
+ }
+
+ //check for required parameters
+ fasta = validParameter.validFile(parameters, "fasta", true);
+ if (fasta == "not open") { abort = true; }
+ else if (fasta == "not found") { fasta = ""; m->mothurOut("fasta is a required parameter for the reverse.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 += hasPath(fasta); //if user entered a file with a path then preserve it
+ }
+
+ }
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the SeqCoordCommand class Function SeqCoordCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "ReverseSeqsCommand", "ReverseSeqsCommand");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the SeqCoordCommand class function SeqCoordCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+}
+//**********************************************************************************************************************
+
+void ReverseSeqsCommand::help(){
+ try {
+ m->mothurOut("The reverse.seqs command reads a fastafile and ....\n");
+ m->mothurOut("The reverse.seqs command parameter is fasta and it is required.\n");
+ m->mothurOut("The reverse.seqs command should be in the following format: \n");
+ m->mothurOut("reverse.seqs(fasta=yourFastaFile) \n");
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ReverseSeqsCommand", "help");
exit(1);
- }
+ }
}
//***************************************************************************************************************
int ReverseSeqsCommand::execute(){
try{
+ if (abort == true) { return 0; }
+
ifstream inFASTA;
- openInputFile(globaldata->getFastaFile(), inFASTA);
+ openInputFile(fasta, inFASTA);
ofstream outFASTA;
- string reverseFile = getRootName(globaldata->getFastaFile()) + "rc" + getExtension(globaldata->getFastaFile());
+ string reverseFile = outputDir + getRootName(getSimpleName(fasta)) + "rc" + getExtension(fasta);
openOutputFile(reverseFile, outFASTA);
while(!inFASTA.eof()){
- Sequence currSeq(inFASTA);
- currSeq.reverseComplement();
- currSeq.printSequence(outFASTA);
+ if (m->control_pressed) { inFASTA.close(); outFASTA.close(); remove(reverseFile.c_str()); return 0; }
+
+ Sequence currSeq(inFASTA); gobble(inFASTA);
+ if (currSeq.getName() != "") {
+ currSeq.reverseComplement();
+ currSeq.printSequence(outFASTA);
+ }
}
inFASTA.close();
outFASTA.close();
+ if (m->control_pressed) { remove(reverseFile.c_str()); return 0; }
+
+ m->mothurOutEndLine();
+ m->mothurOut("Output File Name: "); m->mothurOutEndLine();
+ m->mothurOut(reverseFile); m->mothurOutEndLine();
+ m->mothurOutEndLine();
+
+
return 0;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the FilterSeqsCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the FilterSeqsCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "ReverseSeqsCommand", "execute");
exit(1);
}
}