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 DeconvoluteCommand::DeconvoluteCommand(string option) {
  14         try {
  15                 abort = false;
  16
  17                 //allow user to run help
  18                 if(option == "help") { help(); abort = true; }
  19
  20                 else {
  21                         //valid paramters for this command
  22                         string Array[] =  {"fasta", "name"};
  23                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  24
  25                         OptionParser parser(option);
  26                         map<string,string> parameters = parser.getParameters();
  27
  28                         ValidParameters validParameter;
  29
  30                         //check to make sure all parameters are valid for command
  31                         for (map<string, string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
  32                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  33                         }
  34
  35                         //check for required parameters
  36                         inFastaName = validParameter.validFile(parameters, "fasta", true);
  37                         if (inFastaName == "not open") { abort = true; }
  38                         else if (inFastaName == "not found") { inFastaName = ""; mothurOut("fasta is a required parameter for the unique.seqs command."); mothurOutEndLine(); abort = true;  }
  39
  40                         oldNameMapFName = validParameter.validFile(parameters, "name", true);
  41                         if (oldNameMapFName == "not open") { abort = true; }
  42                         else if (oldNameMapFName == "not found"){       oldNameMapFName = "";   }
  43                 }
  44
  45         }
  46         catch(exception& e) {
  47                 errorOut(e, "DeconvoluteCommand", "DeconvoluteCommand");
  48                 exit(1);
  49         }
  50 }
  51 //**********************************************************************************************************************
  52
  53 void DeconvoluteCommand::help(){
  54         try {
  55                 mothurOut("The unique.seqs command reads a fastafile and creates a namesfile.\n");
  56                 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");
  57                 mothurOut("If the sequence is unique the second column will just contain its name. \n");
  58                 mothurOut("The unique.seqs command parameter is fasta and it is required.\n");
  59                 mothurOut("The unique.seqs command should be in the following format: \n");
  60                 mothurOut("unique.seqs(fasta=yourFastaFile) \n");
  61         }
  62         catch(exception& e) {
  63                 errorOut(e, "DeconvoluteCommand", "help");
  64                 exit(1);
  65         }
  66 }
  67
  68 /**************************************************************************************/
  69 int DeconvoluteCommand::execute() {
  70         try {
  71
  72                 if (abort == true) { return 0; }
  73
  74                 //prepare filenames and open files
  75                 string outNameFile = (getRootName(inFastaName) + "names");
  76                 string outFastaFile = (getRootName(inFastaName) + "unique" + getExtension(inFastaName));
  77
  78                 FastaMap fastamap;
  79
  80                 if(oldNameMapFName == "")       {       fastamap.readFastaFile(inFastaName);                                    }
  81                 else                                            {       fastamap.readFastaFile(inFastaName, oldNameMapFName);   }
  82
  83                 fastamap.printCondensedFasta(outFastaFile);
  84                 fastamap.printNamesFile(outNameFile);
  85
  86                 return 0;
  87         }
  88         catch(exception& e) {
  89                 errorOut(e, "DeconvoluteCommand", "execute");
  90                 exit(1);
  91         }
  92 }
  93 /**************************************************************************************/