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 vector<string> ReverseSeqsCommand::getValidParameters(){
  15         try {
  16                 string Array[] =  {"fasta", "outputdir","inputdir"};
  17                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  18                 return myArray;
  19         }
  20         catch(exception& e) {
  21                 m->errorOut(e, "ReverseSeqsCommand", "getValidParameters");
  22                 exit(1);
  23         }
  24 }
  25 //**********************************************************************************************************************
  26 ReverseSeqsCommand::ReverseSeqsCommand(){
  27         try {
  28                 //initialize outputTypes
  29                 vector<string> tempOutNames;
  30                 outputTypes["fasta"] = tempOutNames;
  31         }
  32         catch(exception& e) {
  33                 m->errorOut(e, "ReverseSeqsCommand", "ReverseSeqsCommand");
  34                 exit(1);
  35         }
  36 }
  37 //**********************************************************************************************************************
  38 vector<string> ReverseSeqsCommand::getRequiredParameters(){
  39         try {
  40                 string Array[] =  {"fasta"};
  41                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  42                 return myArray;
  43         }
  44         catch(exception& e) {
  45                 m->errorOut(e, "ReverseSeqsCommand", "getRequiredParameters");
  46                 exit(1);
  47         }
  48 }
  49 //**********************************************************************************************************************
  50 vector<string> ReverseSeqsCommand::getRequiredFiles(){
  51         try {
  52                 vector<string> myArray;
  53                 return myArray;
  54         }
  55         catch(exception& e) {
  56                 m->errorOut(e, "ReverseSeqsCommand", "getRequiredFiles");
  57                 exit(1);
  58         }
  59 }
  60 //***************************************************************************************************************
  61
  62 ReverseSeqsCommand::ReverseSeqsCommand(string option)  {
  63         try {
  64                 abort = false;
  65
  66                 //allow user to run help
  67                 if(option == "help") { help(); abort = true; }
  68
  69                 else {
  70                         //valid paramters for this command
  71                         string Array[] =  {"fasta", "outputdir","inputdir"};
  72                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  73
  74                         OptionParser parser(option);
  75                         map<string,string> parameters = parser.getParameters();
  76
  77                         ValidParameters validParameter;
  78                         map<string,string>::iterator it;
  79
  80                         //check to make sure all parameters are valid for command
  81                         for (it = parameters.begin(); it != parameters.end(); it++) {
  82                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  83                         }
  84
  85                         //initialize outputTypes
  86                         vector<string> tempOutNames;
  87                         outputTypes["fasta"] = tempOutNames;
  88
  89                         //if the user changes the input directory command factory will send this info to us in the output parameter
  90                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
  91                         if (inputDir == "not found"){   inputDir = "";          }
  92                         else {
  93                                 string path;
  94                                 it = parameters.find("fasta");
  95                                 //user has given a template file
  96                                 if(it != parameters.end()){
  97                                         path = m->hasPath(it->second);
  98                                         //if the user has not given a path then, add inputdir. else leave path alone.
  99                                         if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
 100                                 }
 101                         }
 102
 103                         //check for required parameters
 104                         fasta = validParameter.validFile(parameters, "fasta", true);
 105                         if (fasta == "not open") { abort = true; }
 106                         else if (fasta == "not found") { fasta = ""; m->mothurOut("fasta is a required parameter for the reverse.seqs command."); m->mothurOutEndLine(); abort = true;  }
 107
 108                         //if the user changes the output directory command factory will send this info to us in the output parameter
 109                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
 110                                 outputDir = "";
 111                                 outputDir += m->hasPath(fasta); //if user entered a file with a path then preserve it
 112                         }
 113
 114                 }
 115         }
 116         catch(exception& e) {
 117                 m->errorOut(e, "ReverseSeqsCommand", "ReverseSeqsCommand");
 118                 exit(1);
 119         }
 120 }
 121 //**********************************************************************************************************************
 122
 123 void ReverseSeqsCommand::help(){
 124         try {
 125                 m->mothurOut("The reverse.seqs command reads a fastafile and outputs a fasta file containing the reverse compliment.\n");
 126                 m->mothurOut("The reverse.seqs command parameter is fasta and it is required.\n");
 127                 m->mothurOut("The reverse.seqs command should be in the following format: \n");
 128                 m->mothurOut("reverse.seqs(fasta=yourFastaFile) \n");
 129         }
 130         catch(exception& e) {
 131                 m->errorOut(e, "ReverseSeqsCommand", "help");
 132                 exit(1);
 133         }
 134 }
 135
 136 //***************************************************************************************************************
 137
 138 ReverseSeqsCommand::~ReverseSeqsCommand(){      /*      do nothing      */      }
 139
 140 //***************************************************************************************************************
 141
 142
 143 int ReverseSeqsCommand::execute(){
 144         try{
 145
 146                 if (abort == true) { return 0; }
 147
 148                 ifstream inFASTA;
 149                 m->openInputFile(fasta, inFASTA);
 150
 151                 ofstream outFASTA;
 152                 string reverseFile = outputDir + m->getRootName(m->getSimpleName(fasta)) + "rc" + m->getExtension(fasta);
 153                 m->openOutputFile(reverseFile, outFASTA);
 154
 155                 while(!inFASTA.eof()){
 156                         if (m->control_pressed) {  inFASTA.close();  outFASTA.close(); remove(reverseFile.c_str()); return 0; }
 157
 158                         Sequence currSeq(inFASTA);  m->gobble(inFASTA);
 159                         if (currSeq.getName() != "") {
 160                                 currSeq.reverseComplement();
 161                                 currSeq.printSequence(outFASTA);
 162                         }
 163                 }
 164                 inFASTA.close();
 165                 outFASTA.close();
 166
 167                 if (m->control_pressed) {  remove(reverseFile.c_str()); return 0; }
 168
 169                 m->mothurOutEndLine();
 170                 m->mothurOut("Output File Name: "); m->mothurOutEndLine();
 171                 m->mothurOut(reverseFile); m->mothurOutEndLine();       outputNames.push_back(reverseFile); outputTypes["fasta"].push_back(reverseFile);
 172                 m->mothurOutEndLine();
 173
 174
 175                 return 0;
 176
 177         }
 178         catch(exception& e) {
 179                 m->errorOut(e, "ReverseSeqsCommand", "execute");
 180                 exit(1);
 181         }
 182 }
 183
 184 //***************************************************************************************************************