else {
//valid paramters for this command
- string Array[] = {"fasta"};
+ 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 (map<string, string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
+ 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; }
+ }
+
+ it = parameters.find("name");
+ //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["name"] = inputDir + it->second; }
+ }
+ }
+
+
//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; }
+ inFastaName = validParameter.validFile(parameters, "fasta", true);
+ if (inFastaName == "not open") { abort = true; }
+ else if (inFastaName == "not found") { inFastaName = ""; mothurOut("fasta is a required parameter for the unique.seqs command."); 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(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) {
- 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";
+ errorOut(e, "DeconvoluteCommand", "DeconvoluteCommand");
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";
+ mothurOut("The unique.seqs command reads a fastafile and creates a namesfile.\n");
+ 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");
+ mothurOut("If the sequence is unique the second column will just contain its name. \n");
+ mothurOut("The unique.seqs command parameter is fasta and it is required.\n");
+ mothurOut("The unique.seqs command should be in the following format: \n");
+ mothurOut("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";
+ errorOut(e, "DeconvoluteCommand", "help");
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);
- }
}
/**************************************************************************************/
try {
if (abort == true) { return 0; }
-
+
//prepare filenames and open files
- outputFileName = (getRootName(filename) + "names");
- outFastafile = (getRootName(filename) + "unique.fasta");
+ string outNameFile = outputDir + getRootName(getSimpleName(inFastaName)) + "names";
+ string outFastaFile = outputDir + getRootName(getSimpleName(inFastaName)) + "unique" + getExtension(inFastaName);
- openInputFile(filename, in);
- openOutputFile(outputFileName, out);
- openOutputFile(outFastafile, outFasta);
-
- //constructor reads in file and store internally
- fastamap = new FastaMap();
+ FastaMap fastamap;
- //two columns separated by tabs sequence name and then sequence
- fastamap->readFastaFile(in);
+ if(oldNameMapFName == "") { fastamap.readFastaFile(inFastaName); }
+ else { fastamap.readFastaFile(inFastaName, oldNameMapFName); }
- //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->printNamesFile(out);
- fastamap->printCondensedFasta(outFasta);
+ fastamap.printCondensedFasta(outFastaFile);
+ fastamap.printNamesFile(outNameFile);
- in.close();
- out.close();
- outFasta.close();
-
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";
+ errorOut(e, "DeconvoluteCommand", "execute");
exit(1);
}
}
projects / mothur.git / blobdiff