deconvolutecommand.cpp

   1 /*
   2  *  deconvolute.cpp
   3  *  Mothur
   4  *
   5  *  Created by Sarah Westcott on 1/21/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "deconvolutecommand.h"
  11
  12 /**************************************************************************************/
  13 int DeconvoluteCommand::execute() {
  14         try {
  15                 globaldata = GlobalData::getInstance();
  16
  17                 //prepare filenames and open files
  18                 filename = globaldata->getFastaFile();
  19                 outputFileName = (getRootName(filename) + "names");
  20                 outFastafile = (getRootName(filename) + "unique.fasta");
  21
  22                 openInputFile(filename, in);
  23                 openOutputFile(outputFileName, out);
  24                 openOutputFile(outFastafile, outFasta);
  25
  26                 //constructor reads in file and store internally
  27                 fastamap = new FastaMap();
  28
  29                 //two columns separated by tabs sequence name and then sequence
  30                 fastamap->readFastaFile(in);
  31
  32                 //print out new names file
  33                 //file contains 2 columns separated by tabs.  the first column is the groupname(name of first sequence found.
  34                 //the second column is the list of names of identical sequences separated by ','.
  35                 fastamap->printNamesFile(out);
  36                 fastamap->printCondensedFasta(outFasta);
  37
  38                 return 0;
  39         }
  40         catch(exception& e) {
  41                 cout << "Standard Error: " << e.what() << " has occurred in the DeconvoluteCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  42                 exit(1);
  43         }
  44         catch(...) {
  45                 cout << "An unknown error has occurred in the DeconvoluteCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  46                 exit(1);
  47         }
  48 }
  49 /**************************************************************************************/