#include "reversecommand.h"
#include "sequence.hpp"
-
+//**********************************************************************************************************************
+vector<string> ReverseSeqsCommand::getValidParameters(){
+ try {
+ string Array[] = {"fasta", "outputdir","inputdir"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ReverseSeqsCommand", "getValidParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+ReverseSeqsCommand::ReverseSeqsCommand(){
+ try {
+ abort = true;
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["fasta"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ReverseSeqsCommand", "ReverseSeqsCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> ReverseSeqsCommand::getRequiredParameters(){
+ try {
+ string Array[] = {"fasta"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ReverseSeqsCommand", "getRequiredParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> ReverseSeqsCommand::getRequiredFiles(){
+ try {
+ vector<string> myArray;
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ReverseSeqsCommand", "getRequiredFiles");
+ exit(1);
+ }
+}
//***************************************************************************************************************
-ReverseSeqsCommand::ReverseSeqsCommand(string option){
+ReverseSeqsCommand::ReverseSeqsCommand(string option) {
try {
- globaldata = GlobalData::getInstance();
abort = false;
//allow user to run help
else {
//valid paramters for this command
- string Array[] = {"fasta"};
+ string Array[] = {"fasta", "outputdir","inputdir"};
vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
- parser = new OptionParser();
- parser->parse(option, parameters); delete parser;
+ OptionParser parser(option);
+ map<string,string> parameters = parser.getParameters();
+
+ ValidParameters validParameter;
+ map<string,string>::iterator it;
- ValidParameters* validParameter = new ValidParameters();
-
//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 (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; }
+ }
+ }
+
//check for required parameters
- fasta = validParameter->validFile(parameters, "fasta", true);
+ fasta = validParameter.validFile(parameters, "fasta", true);
if (fasta == "not open") { abort = true; }
- else if (fasta == "not found") { fasta = ""; cout << "fasta is a required parameter for the reverse.seqs command." << endl; abort = true; }
- else { globaldata->setFastaFile(fasta); globaldata->setFormat("fasta"); }
+ else if (fasta == "not found") { fasta = ""; m->mothurOut("fasta is a required parameter for the reverse.seqs command."); m->mothurOutEndLine(); abort = true; }
- delete validParameter;
+ //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(fasta); //if user entered a file with a path then preserve it
+ }
+
}
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the ReverseSeqsCommand class Function ReverseSeqsCommand. 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 ReverseSeqsCommand class function ReverseSeqsCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
}
//**********************************************************************************************************************
void ReverseSeqsCommand::help(){
try {
- cout << "The reverse.seqs command reads a fastafile and ...." << "\n";
- cout << "The reverse.seqs command parameter is fasta and it is required." << "\n";
- cout << "The reverse.seqs command should be in the following format: " << "\n";
- cout << "reverse.seqs(fasta=yourFastaFile) " << "\n";
+ m->mothurOut("The reverse.seqs command reads a fastafile and outputs a fasta file containing the reverse compliment.\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) {
- cout << "Standard Error: " << e.what() << " has occurred in the ReverseSeqsCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "ReverseSeqsCommand", "help");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the ReverseSeqsCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
}
//***************************************************************************************************************
if (abort == true) { return 0; }
ifstream inFASTA;
- openInputFile(fasta, inFASTA);
+ m->openInputFile(fasta, inFASTA);
ofstream outFASTA;
- string reverseFile = getRootName(fasta) + "rc" + getExtension(fasta);
- openOutputFile(reverseFile, outFASTA);
+ string reverseFile = outputDir + m->getRootName(m->getSimpleName(fasta)) + "rc" + m->getExtension(fasta);
+ m->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); m->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(); outputNames.push_back(reverseFile); outputTypes["fasta"].push_back(reverseFile);
+ m->mothurOutEndLine();
+
+
return 0;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the ReverseSeqsCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the ReverseSeqsCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "ReverseSeqsCommand", "execute");
exit(1);
}
}
projects / mothur.git / blobdiff