chimera.seqs pintail is working.

[mothur.git] / deconvolutecommand.cpp

diff --git a/deconvolutecommand.cpp b/deconvolutecommand.cpp
index 3ec5f734eebb393c6ff630a1adc8d7e94ab6729f..a936c820b56f88609e621894565359892384224a 100644 (file)
--- a/deconvolutecommand.cpp
+++ b/deconvolutecommand.cpp
@@ -19,7 +19,7 @@ DeconvoluteCommand::DeconvoluteCommand(string option) {
                
                else {
                        //valid paramters for this command
-                       string Array[] =  {"fasta"};
+                       string Array[] =  {"fasta", "name"};
                        vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
                        
                        OptionParser parser(option);
@@ -33,19 +33,18 @@ DeconvoluteCommand::DeconvoluteCommand(string option) {
                        }
                        
                        //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;  }  
                        
+                       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);
        }
 }
@@ -53,21 +52,17 @@ DeconvoluteCommand::DeconvoluteCommand(string option) {
 
 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);
-       }       
 }
 
 /**************************************************************************************/
@@ -75,38 +70,23 @@ int DeconvoluteCommand::execute() {
        try {
                
                if (abort == true) { return 0; }
-       
+
                //prepare filenames and open files
-               outputFileName = (getRootName(filename) + "names");
-               outFastafile = (getRootName(filename) + "unique.fasta");
+               string outNameFile = (getRootName(inFastaName) + "names");
+               string outFastaFile = (getRootName(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);
                
-               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);
        }
 }