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                 abort = true;
  29                 //initialize outputTypes
  30                 vector<string> tempOutNames;
  31                 outputTypes["fasta"] = tempOutNames;
  32         }
  33         catch(exception& e) {
  34                 m->errorOut(e, "ReverseSeqsCommand", "ReverseSeqsCommand");
  35                 exit(1);
  36         }
  37 }
  38 //**********************************************************************************************************************
  39 vector<string> ReverseSeqsCommand::getRequiredParameters(){
  40         try {
  41                 string Array[] =  {"fasta"};
  42                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  43                 return myArray;
  44         }
  45         catch(exception& e) {
  46                 m->errorOut(e, "ReverseSeqsCommand", "getRequiredParameters");
  47                 exit(1);
  48         }
  49 }
  50 //**********************************************************************************************************************
  51 vector<string> ReverseSeqsCommand::getRequiredFiles(){
  52         try {
  53                 vector<string> myArray;
  54                 return myArray;
  55         }
  56         catch(exception& e) {
  57                 m->errorOut(e, "ReverseSeqsCommand", "getRequiredFiles");
  58                 exit(1);
  59         }
  60 }
  61 //***************************************************************************************************************
  62
  63 ReverseSeqsCommand::ReverseSeqsCommand(string option)  {
  64         try {
  65                 abort = false;
  66
  67                 //allow user to run help
  68                 if(option == "help") { help(); abort = true; }
  69
  70                 else {
  71                         //valid paramters for this command
  72                         string Array[] =  {"fasta", "outputdir","inputdir"};
  73                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  74
  75                         OptionParser parser(option);
  76                         map<string,string> parameters = parser.getParameters();
  77
  78                         ValidParameters validParameter;
  79                         map<string,string>::iterator it;
  80
  81                         //check to make sure all parameters are valid for command
  82                         for (it = parameters.begin(); it != parameters.end(); it++) {
  83                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  84                         }
  85
  86                         //initialize outputTypes
  87                         vector<string> tempOutNames;
  88                         outputTypes["fasta"] = tempOutNames;
  89
  90                         //if the user changes the input directory command factory will send this info to us in the output parameter
  91                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
  92                         if (inputDir == "not found"){   inputDir = "";          }
  93                         else {
  94                                 string path;
  95                                 it = parameters.find("fasta");
  96                                 //user has given a template file
  97                                 if(it != parameters.end()){
  98                                         path = m->hasPath(it->second);
  99                                         //if the user has not given a path then, add inputdir. else leave path alone.
 100                                         if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
 101                                 }
 102                         }
 103
 104                         //check for required parameters
 105                         fasta = validParameter.validFile(parameters, "fasta", true);
 106                         if (fasta == "not open") { abort = true; }
 107                         else if (fasta == "not found") { fasta = ""; m->mothurOut("fasta is a required parameter for the reverse.seqs command."); m->mothurOutEndLine(); abort = true;  }
 108
 109                         //if the user changes the output directory command factory will send this info to us in the output parameter
 110                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
 111                                 outputDir = "";
 112                                 outputDir += m->hasPath(fasta); //if user entered a file with a path then preserve it
 113                         }
 114
 115                 }
 116         }
 117         catch(exception& e) {
 118                 m->errorOut(e, "ReverseSeqsCommand", "ReverseSeqsCommand");
 119                 exit(1);
 120         }
 121 }
 122 //**********************************************************************************************************************
 123
 124 void ReverseSeqsCommand::help(){
 125         try {
 126                 m->mothurOut("The reverse.seqs command reads a fastafile and outputs a fasta file containing the reverse compliment.\n");
 127                 m->mothurOut("The reverse.seqs command parameter is fasta and it is required.\n");
 128                 m->mothurOut("The reverse.seqs command should be in the following format: \n");
 129                 m->mothurOut("reverse.seqs(fasta=yourFastaFile) \n");
 130         }
 131         catch(exception& e) {
 132                 m->errorOut(e, "ReverseSeqsCommand", "help");
 133                 exit(1);
 134         }
 135 }
 136
 137 //***************************************************************************************************************
 138
 139 ReverseSeqsCommand::~ReverseSeqsCommand(){      /*      do nothing      */      }
 140
 141 //***************************************************************************************************************
 142
 143
 144 int ReverseSeqsCommand::execute(){
 145         try{
 146
 147                 if (abort == true) { return 0; }
 148
 149                 ifstream inFASTA;
 150                 m->openInputFile(fasta, inFASTA);
 151
 152                 ofstream outFASTA;
 153                 string reverseFile = outputDir + m->getRootName(m->getSimpleName(fasta)) + "rc" + m->getExtension(fasta);
 154                 m->openOutputFile(reverseFile, outFASTA);
 155
 156                 while(!inFASTA.eof()){
 157                         if (m->control_pressed) {  inFASTA.close();  outFASTA.close(); remove(reverseFile.c_str()); return 0; }
 158
 159                         Sequence currSeq(inFASTA);  m->gobble(inFASTA);
 160                         if (currSeq.getName() != "") {
 161                                 currSeq.reverseComplement();
 162                                 currSeq.printSequence(outFASTA);
 163                         }
 164                 }
 165                 inFASTA.close();
 166                 outFASTA.close();
 167
 168                 if (m->control_pressed) {  remove(reverseFile.c_str()); return 0; }
 169
 170                 m->mothurOutEndLine();
 171                 m->mothurOut("Output File Name: "); m->mothurOutEndLine();
 172                 m->mothurOut(reverseFile); m->mothurOutEndLine();       outputNames.push_back(reverseFile); outputTypes["fasta"].push_back(reverseFile);
 173                 m->mothurOutEndLine();
 174
 175
 176                 return 0;
 177
 178         }
 179         catch(exception& e) {
 180                 m->errorOut(e, "ReverseSeqsCommand", "execute");
 181                 exit(1);
 182         }
 183 }
 184
 185 //***************************************************************************************************************