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 #include "qualityscores.h"
  13
  14 //**********************************************************************************************************************
  15 vector<string> ReverseSeqsCommand::getValidParameters(){
  16         try {
  17                 string Array[] =  {"fasta", "qfile", "outputdir", "inputdir"};
  18                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  19                 return myArray;
  20         }
  21         catch(exception& e) {
  22                 m->errorOut(e, "ReverseSeqsCommand", "getValidParameters");
  23                 exit(1);
  24         }
  25 }
  26 //**********************************************************************************************************************
  27 ReverseSeqsCommand::ReverseSeqsCommand(){
  28         try {
  29                 abort = true; calledHelp = true;
  30                 vector<string> tempOutNames;
  31                 outputTypes["fasta"] = tempOutNames;
  32                 outputTypes["qfile"] = tempOutNames;
  33         }
  34         catch(exception& e) {
  35                 m->errorOut(e, "ReverseSeqsCommand", "ReverseSeqsCommand");
  36                 exit(1);
  37         }
  38 }
  39 //**********************************************************************************************************************
  40
  41 vector<string> ReverseSeqsCommand::getRequiredParameters(){
  42         try {
  43                 string Array[] =  {"fasta", "qfile"};
  44                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  45                 return myArray;
  46         }
  47         catch(exception& e) {
  48                 m->errorOut(e, "ReverseSeqsCommand", "getRequiredParameters");
  49                 exit(1);
  50         }
  51 }
  52
  53 //**********************************************************************************************************************
  54
  55 vector<string> ReverseSeqsCommand::getRequiredFiles(){
  56         try {
  57                 vector<string> myArray;
  58                 return myArray;
  59         }
  60         catch(exception& e) {
  61                 m->errorOut(e, "ReverseSeqsCommand", "getRequiredFiles");
  62                 exit(1);
  63         }
  64 }//***************************************************************************************************************
  65
  66 ReverseSeqsCommand::ReverseSeqsCommand(string option)  {
  67         try {
  68                 abort = false; calledHelp = false;
  69
  70                 //allow user to run help
  71                 if(option == "help") { help(); abort = true; calledHelp = true; }
  72
  73                 else {
  74                         //valid paramters for this command
  75                         string Array[] =  {"fasta", "qfile", "outputdir","inputdir"};
  76                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  77
  78                         OptionParser parser(option);
  79                         map<string,string> parameters = parser.getParameters();
  80
  81                         ValidParameters validParameter;
  82                         map<string,string>::iterator it;
  83
  84                         //check to make sure all parameters are valid for command
  85                         for (it = parameters.begin(); it != parameters.end(); it++) {
  86                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  87                         }
  88
  89                         //initialize outputTypes
  90                         vector<string> tempOutNames;
  91                         outputTypes["fasta"] = tempOutNames;
  92                         outputTypes["qfile"] = tempOutNames;
  93
  94                         //if the user changes the input directory command factory will send this info to us in the output parameter
  95                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
  96                         if (inputDir == "not found"){   inputDir = "";          }
  97                         else {
  98                                 string path;
  99                                 it = parameters.find("fasta");
 100                                 //user has given a template file
 101                                 if(it != parameters.end()){
 102                                         path = m->hasPath(it->second);
 103                                         //if the user has not given a path then, add inputdir. else leave path alone.
 104                                         if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
 105                                 }
 106                         }
 107
 108                         //check for required parameters
 109                         fastaFileName = validParameter.validFile(parameters, "fasta", true);
 110                         if (fastaFileName == "not open") { abort = true; }
 111                         else if (fastaFileName == "not found") { fastaFileName = "";}// m->mothurOut("fasta is a required parameter for the reverse.seqs command."); m->mothurOutEndLine(); abort = true;  }
 112
 113                         qualFileName = validParameter.validFile(parameters, "qfile", true);
 114                         if (qualFileName == "not open") { abort = true; }
 115                         else if (qualFileName == "not found") { qualFileName = ""; }//m->mothurOut("fasta is a required parameter for the reverse.seqs command."); m->mothurOutEndLine(); abort = true;  }
 116
 117                         if(fastaFileName == "not open" && qualFileName == "not open"){
 118                                 m->mothurOut("fasta or qfile is a required parameter for the reverse.seqs command.");
 119                                 m->mothurOutEndLine();
 120                                 abort = true;
 121                         }
 122
 123                         //if the user changes the output directory command factory will send this info to us in the output parameter
 124                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
 125                                 outputDir = "";
 126                                 outputDir += m->hasPath(fastaFileName); //if user entered a file with a path then preserve it
 127                         }
 128
 129                 }
 130         }
 131         catch(exception& e) {
 132                 m->errorOut(e, "ReverseSeqsCommand", "ReverseSeqsCommand");
 133                 exit(1);
 134         }
 135 }
 136 //**********************************************************************************************************************
 137
 138 void ReverseSeqsCommand::help(){
 139         try {
 140                 m->mothurOut("The reverse.seqs command reads a fastafile and outputs a fasta file containing the reverse compliment.\n");
 141                 m->mothurOut("The reverse.seqs command parameters fasta or qfile are required.\n");
 142                 m->mothurOut("The reverse.seqs command should be in the following format: \n");
 143                 m->mothurOut("reverse.seqs(fasta=yourFastaFile) \n");
 144         }
 145         catch(exception& e) {
 146                 m->errorOut(e, "ReverseSeqsCommand", "help");
 147                 exit(1);
 148         }
 149 }
 150
 151 //***************************************************************************************************************
 152
 153 ReverseSeqsCommand::~ReverseSeqsCommand(){      /*      do nothing      */      }
 154
 155 //***************************************************************************************************************
 156
 157
 158 int ReverseSeqsCommand::execute(){
 159         try{
 160
 161                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 162
 163                 string fastaReverseFileName;
 164
 165                 if(fastaFileName != ""){
 166                         ifstream inFASTA;
 167                         m->openInputFile(fastaFileName, inFASTA);
 168
 169                         ofstream outFASTA;
 170                         fastaReverseFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileName)) + "rc" + m->getExtension(fastaFileName);
 171                         m->openOutputFile(fastaReverseFileName, outFASTA);
 172
 173                         while(!inFASTA.eof()){
 174                                 if (m->control_pressed) {  inFASTA.close();  outFASTA.close(); remove(fastaReverseFileName.c_str()); return 0; }
 175
 176                                 Sequence currSeq(inFASTA);  m->gobble(inFASTA);
 177                                 if (currSeq.getName() != "") {
 178                                         currSeq.reverseComplement();
 179                                         currSeq.printSequence(outFASTA);
 180                                 }
 181                         }
 182                         inFASTA.close();
 183                         outFASTA.close();
 184                         outputNames.push_back(fastaReverseFileName); outputTypes["fasta"].push_back(fastaReverseFileName);
 185                 }
 186
 187                 string qualReverseFileName;
 188
 189                 if(qualFileName != ""){
 190                         QualityScores currQual;
 191
 192                         ifstream inQual;
 193                         m->openInputFile(qualFileName, inQual);
 194
 195                         ofstream outQual;
 196                         string qualReverseFileName = outputDir + m->getRootName(m->getSimpleName(qualFileName)) + "rc" + m->getExtension(qualFileName);
 197                         m->openOutputFile(qualReverseFileName, outQual);
 198
 199                         while(!inQual.eof()){
 200                                 if (m->control_pressed) {  inQual.close();  outQual.close(); remove(qualReverseFileName.c_str()); return 0; }
 201                                 currQual = QualityScores(inQual);  m->gobble(inQual);
 202                                 currQual.flipQScores();
 203                                 currQual.printQScores(outQual);
 204                         }
 205                         inQual.close();
 206                         outQual.close();
 207                         outputNames.push_back(qualReverseFileName); outputTypes["qfile"].push_back(qualReverseFileName);
 208                 }
 209
 210                 if (m->control_pressed) {  remove(qualReverseFileName.c_str()); remove(fastaReverseFileName.c_str()); return 0; }
 211
 212                 //set fasta file as new current fastafile
 213                 string current = "";
 214                 itTypes = outputTypes.find("fasta");
 215                 if (itTypes != outputTypes.end()) {
 216                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
 217                 }
 218
 219                 itTypes = outputTypes.find("qfile");
 220                 if (itTypes != outputTypes.end()) {
 221                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setQualFile(current); }
 222                 }
 223
 224
 225                 m->mothurOutEndLine();
 226                 m->mothurOut("Output File Name: "); m->mothurOutEndLine();
 227                 for(int i=0;i<outputNames.size();i++){
 228                         m->mothurOut(outputNames[i]);
 229                         m->mothurOutEndLine();
 230                 }
 231
 232
 233
 234                 return 0;
 235         }
 236         catch(exception& e) {
 237                 m->errorOut(e, "ReverseSeqsCommand", "execute");
 238                 exit(1);
 239         }
 240 }
 241
 242 //***************************************************************************************************************