#include "deconvolutecommand.h"
+/**************************************************************************************/
+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"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+
+ OptionParser parser(option);
+ map<string,string> parameters = parser.getParameters();
+
+ ValidParameters validParameter;
+
+ //check to make sure all parameters are valid for command
+ for (map<string, string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
+ if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
+ }
+
+ //check for required parameters
+ filename = validParameter.validFile(parameters, "fasta", true);
+ if (filename == "not open") { abort = true; }
+ else if (filename == "not found") { filename = ""; cout << "fasta is a required parameter for the unique.seqs command." << endl; abort = true; }
+
+ }
+
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the DeconvoluteCommand class Function DeconvoluteCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the DeconvoluteCommand class function DeconvoluteCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+void DeconvoluteCommand::help(){
+ try {
+ cout << "The unique.seqs command reads a fastafile and creates a namesfile." << "\n";
+ cout << "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";
+ cout << "If the sequence is unique the second column will just contain its name. " << "\n";
+ cout << "The unique.seqs command parameter is fasta and it is required." << "\n";
+ cout << "The unique.seqs command should be in the following format: " << "\n";
+ cout << "unique.seqs(fasta=yourFastaFile) " << "\n";
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the DeconvoluteCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the DeconvoluteCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ 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");
+
openInputFile(filename, in);
openOutputFile(outputFileName, out);
-
+ openOutputFile(outFastafile, outFasta);
+
//constructor reads in file and store internally
fastamap = new FastaMap();
//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->printNamesFile(out);
+ fastamap->printCondensedFasta(outFasta);
+
+ in.close();
+ out.close();
+ outFasta.close();
return 0;
}