reversecommand.cpp

   1 /*
   2  *  reversecommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by Pat Schloss on 6/6/09.
   6  *  Copyright 2009 Patrick D. Schloss. All rights reserved.
   7  *
   8  */
   9
  10 #include "reversecommand.h"
  11 #include "sequence.hpp"
  12
  13
  14 //***************************************************************************************************************
  15
  16 ReverseSeqsCommand::ReverseSeqsCommand(string option){
  17         try {
  18                 globaldata = GlobalData::getInstance();
  19                 abort = false;
  20
  21                 //allow user to run help
  22                 if(option == "help") { help(); abort = true; }
  23
  24                 else {
  25                         //valid paramters for this command
  26                         string Array[] =  {"fasta"};
  27                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  28
  29                         parser = new OptionParser();
  30                         parser->parse(option, parameters);  delete parser;
  31
  32                         ValidParameters* validParameter = new ValidParameters();
  33
  34                         //check to make sure all parameters are valid for command
  35                         for (it = parameters.begin(); it != parameters.end(); it++) {
  36                                 if (validParameter->isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  37                         }
  38
  39                         //check for required parameters
  40                         fasta = validParameter->validFile(parameters, "fasta", true);
  41                         if (fasta == "not open") { abort = true; }
  42                         else if (fasta == "not found") { fasta = ""; cout << "fasta is a required parameter for the reverse.seqs command." << endl; abort = true;  }
  43                         else {  globaldata->setFastaFile(fasta);  globaldata->setFormat("fasta");       }
  44
  45                         delete validParameter;
  46                 }
  47         }
  48         catch(exception& e) {
  49                 cout << "Standard Error: " << e.what() << " has occurred in the ReverseSeqsCommand class Function ReverseSeqsCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  50                 exit(1);
  51         }
  52         catch(...) {
  53                 cout << "An unknown error has occurred in the ReverseSeqsCommand class function ReverseSeqsCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  54                 exit(1);
  55         }
  56 }
  57 //**********************************************************************************************************************
  58
  59 void ReverseSeqsCommand::help(){
  60         try {
  61                 cout << "The reverse.seqs command reads a fastafile and ...." << "\n";
  62                 cout << "The reverse.seqs command parameter is fasta and it is required." << "\n";
  63                 cout << "The reverse.seqs command should be in the following format: " << "\n";
  64                 cout << "reverse.seqs(fasta=yourFastaFile) " << "\n";
  65         }
  66         catch(exception& e) {
  67                 cout << "Standard Error: " << e.what() << " has occurred in the ReverseSeqsCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  68                 exit(1);
  69         }
  70         catch(...) {
  71                 cout << "An unknown error has occurred in the ReverseSeqsCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  72                 exit(1);
  73         }
  74 }
  75
  76 //***************************************************************************************************************
  77
  78 ReverseSeqsCommand::~ReverseSeqsCommand(){      /*      do nothing      */      }
  79
  80 //***************************************************************************************************************
  81
  82
  83 int ReverseSeqsCommand::execute(){
  84         try{
  85
  86                 if (abort == true) { return 0; }
  87
  88                 ifstream inFASTA;
  89                 openInputFile(fasta, inFASTA);
  90
  91                 ofstream outFASTA;
  92                 string reverseFile = getRootName(fasta) + "rc" + getExtension(fasta);
  93                 openOutputFile(reverseFile, outFASTA);
  94
  95                 while(!inFASTA.eof()){
  96                         Sequence currSeq(inFASTA);
  97                         currSeq.reverseComplement();
  98                         currSeq.printSequence(outFASTA);
  99                 }
 100                 inFASTA.close();
 101                 outFASTA.close();
 102
 103                 return 0;
 104
 105         }
 106         catch(exception& e) {
 107                 cout << "Standard Error: " << e.what() << " has occurred in the ReverseSeqsCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 108                 exit(1);
 109         }
 110         catch(...) {
 111                 cout << "An unknown error has occurred in the ReverseSeqsCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 112                 exit(1);
 113         }
 114 }
 115
 116 //***************************************************************************************************************