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", "outputdir","inputdir"};
  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                         map<string,string>::iterator it;
  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                         //if the user changes the input directory command factory will send this info to us in the output parameter
  40                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
  41                         if (inputDir == "not found"){   inputDir = "";          }
  42                         else {
  43                                 string path;
  44                                 it = parameters.find("fasta");
  45                                 //user has given a template file
  46                                 if(it != parameters.end()){
  47                                         path = hasPath(it->second);
  48                                         //if the user has not given a path then, add inputdir. else leave path alone.
  49                                         if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
  50                                 }
  51                         }
  52
  53                         //check for required parameters
  54                         fasta = validParameter.validFile(parameters, "fasta", true);
  55                         if (fasta == "not open") { abort = true; }
  56                         else if (fasta == "not found") { fasta = ""; m->mothurOut("fasta is a required parameter for the reverse.seqs command."); m->mothurOutEndLine(); abort = true;  }
  57
  58                         //if the user changes the output directory command factory will send this info to us in the output parameter
  59                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
  60                                 outputDir = "";
  61                                 outputDir += hasPath(fasta); //if user entered a file with a path then preserve it
  62                         }
  63
  64                 }
  65         }
  66         catch(exception& e) {
  67                 m->errorOut(e, "ReverseSeqsCommand", "ReverseSeqsCommand");
  68                 exit(1);
  69         }
  70 }
  71 //**********************************************************************************************************************
  72
  73 void ReverseSeqsCommand::help(){
  74         try {
  75                 m->mothurOut("The reverse.seqs command reads a fastafile and ....\n");
  76                 m->mothurOut("The reverse.seqs command parameter is fasta and it is required.\n");
  77                 m->mothurOut("The reverse.seqs command should be in the following format: \n");
  78                 m->mothurOut("reverse.seqs(fasta=yourFastaFile) \n");
  79         }
  80         catch(exception& e) {
  81                 m->errorOut(e, "ReverseSeqsCommand", "help");
  82                 exit(1);
  83         }
  84 }
  85
  86 //***************************************************************************************************************
  87
  88 ReverseSeqsCommand::~ReverseSeqsCommand(){      /*      do nothing      */      }
  89
  90 //***************************************************************************************************************
  91
  92
  93 int ReverseSeqsCommand::execute(){
  94         try{
  95
  96                 if (abort == true) { return 0; }
  97
  98                 ifstream inFASTA;
  99                 openInputFile(fasta, inFASTA);
 100
 101                 ofstream outFASTA;
 102                 string reverseFile = outputDir + getRootName(getSimpleName(fasta)) + "rc" + getExtension(fasta);
 103                 openOutputFile(reverseFile, outFASTA);
 104
 105                 while(!inFASTA.eof()){
 106                         Sequence currSeq(inFASTA);  gobble(inFASTA);
 107                         if (currSeq.getName() != "") {
 108                                 currSeq.reverseComplement();
 109                                 currSeq.printSequence(outFASTA);
 110                         }
 111                 }
 112                 inFASTA.close();
 113                 outFASTA.close();
 114
 115                 m->mothurOutEndLine();
 116                 m->mothurOut("Output File Name: "); m->mothurOutEndLine();
 117                 m->mothurOut(reverseFile); m->mothurOutEndLine();
 118                 m->mothurOutEndLine();
 119
 120
 121                 return 0;
 122
 123         }
 124         catch(exception& e) {
 125                 m->errorOut(e, "ReverseSeqsCommand", "execute");
 126                 exit(1);
 127         }
 128 }
 129
 130 //***************************************************************************************************************