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                 abort = false;
  19
  20                 //allow user to run help
  21                 if(option == "help") { help(); abort = true; }
  22
  23                 else {
  24                         //valid paramters for this command
  25                         string Array[] =  {"fasta"};
  26                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  27
  28                         OptionParser parser(option);
  29                         map<string,string> parameters = parser.getParameters();
  30
  31                         ValidParameters validParameter;
  32
  33                         //check to make sure all parameters are valid for command
  34                         for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
  35                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  36                         }
  37
  38                         //check for required parameters
  39                         fasta = validParameter.validFile(parameters, "fasta", true);
  40                         if (fasta == "not open") { abort = true; }
  41                         else if (fasta == "not found") { fasta = ""; mothurOut("fasta is a required parameter for the reverse.seqs command."); mothurOutEndLine(); abort = true;  }
  42
  43                 }
  44         }
  45         catch(exception& e) {
  46                 errorOut(e, "ReverseSeqsCommand", "ReverseSeqsCommand");
  47                 exit(1);
  48         }
  49 }
  50 //**********************************************************************************************************************
  51
  52 void ReverseSeqsCommand::help(){
  53         try {
  54                 mothurOut("The reverse.seqs command reads a fastafile and ....\n");
  55                 mothurOut("The reverse.seqs command parameter is fasta and it is required.\n");
  56                 mothurOut("The reverse.seqs command should be in the following format: \n");
  57                 mothurOut("reverse.seqs(fasta=yourFastaFile) \n");
  58         }
  59         catch(exception& e) {
  60                 errorOut(e, "ReverseSeqsCommand", "help");
  61                 exit(1);
  62         }
  63 }
  64
  65 //***************************************************************************************************************
  66
  67 ReverseSeqsCommand::~ReverseSeqsCommand(){      /*      do nothing      */      }
  68
  69 //***************************************************************************************************************
  70
  71
  72 int ReverseSeqsCommand::execute(){
  73         try{
  74
  75                 if (abort == true) { return 0; }
  76
  77                 ifstream inFASTA;
  78                 openInputFile(fasta, inFASTA);
  79
  80                 ofstream outFASTA;
  81                 string reverseFile = getRootName(fasta) + "rc" + getExtension(fasta);
  82                 openOutputFile(reverseFile, outFASTA);
  83
  84                 while(!inFASTA.eof()){
  85                         Sequence currSeq(inFASTA);
  86                         currSeq.reverseComplement();
  87                         currSeq.printSequence(outFASTA);
  88                 }
  89                 inFASTA.close();
  90                 outFASTA.close();
  91
  92                 return 0;
  93
  94         }
  95         catch(exception& e) {
  96                 errorOut(e, "ReverseSeqsCommand", "execute");
  97                 exit(1);
  98         }
  99 }
 100
 101 //***************************************************************************************************************