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::setParameters(){
  16         try {
  17                 CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "fastaQual", "none",false,false); parameters.push_back(pfasta);
  18                 CommandParameter pqfile("qfile", "InputTypes", "", "", "none", "fastaQual", "none",false,false); parameters.push_back(pqfile);
  19                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
  20                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
  21
  22                 vector<string> myArray;
  23                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  24                 return myArray;
  25         }
  26         catch(exception& e) {
  27                 m->errorOut(e, "ReverseSeqsCommand", "setParameters");
  28                 exit(1);
  29         }
  30 }
  31 //**********************************************************************************************************************
  32 string ReverseSeqsCommand::getHelpString(){
  33         try {
  34                 string helpString = "";
  35                 helpString += "The reverse.seqs command reads a fastafile and outputs a fasta file containing the reverse compliment.\n";
  36                 helpString += "The reverse.seqs command parameters fasta or qfile are required.\n";
  37                 helpString += "The reverse.seqs command should be in the following format: \n";
  38                 helpString += "reverse.seqs(fasta=yourFastaFile) \n";
  39                 return helpString;
  40         }
  41         catch(exception& e) {
  42                 m->errorOut(e, "ReverseSeqsCommand", "getHelpString");
  43                 exit(1);
  44         }
  45 }
  46
  47 //**********************************************************************************************************************
  48 ReverseSeqsCommand::ReverseSeqsCommand(){
  49         try {
  50                 abort = true; calledHelp = true;
  51                 setParameters();
  52                 vector<string> tempOutNames;
  53                 outputTypes["fasta"] = tempOutNames;
  54                 outputTypes["qfile"] = tempOutNames;
  55         }
  56         catch(exception& e) {
  57                 m->errorOut(e, "ReverseSeqsCommand", "ReverseSeqsCommand");
  58                 exit(1);
  59         }
  60 }
  61 //***************************************************************************************************************
  62
  63 ReverseSeqsCommand::ReverseSeqsCommand(string option)  {
  64         try {
  65                 abort = false; calledHelp = false;
  66
  67                 //allow user to run help
  68                 if(option == "help") { help(); abort = true; calledHelp = true; }
  69                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
  70
  71                 else {
  72                         vector<string> myArray = setParameters();
  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                         outputTypes["qfile"] = 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                                 it = parameters.find("qfile");
 104                                 //user has given a template file
 105                                 if(it != parameters.end()){
 106                                         path = m->hasPath(it->second);
 107                                         //if the user has not given a path then, add inputdir. else leave path alone.
 108                                         if (path == "") {       parameters["qfile"] = inputDir + it->second;            }
 109                                 }
 110                         }
 111
 112                         //check for required parameters
 113                         fastaFileName = validParameter.validFile(parameters, "fasta", true);
 114                         if (fastaFileName == "not open") { abort = true; }
 115                         else if (fastaFileName == "not found") { fastaFileName = "";}// m->mothurOut("fasta is a required parameter for the reverse.seqs command."); m->mothurOutEndLine(); abort = true;  }
 116                         else { m->setFastaFile(fastaFileName); }
 117
 118                         qualFileName = validParameter.validFile(parameters, "qfile", true);
 119                         if (qualFileName == "not open") { abort = true; }
 120                         else if (qualFileName == "not found") { qualFileName = ""; }//m->mothurOut("fasta is a required parameter for the reverse.seqs command."); m->mothurOutEndLine(); abort = true;  }
 121                         else { m->setQualFile(qualFileName); }
 122
 123                         if((fastaFileName == "") && (qualFileName == "")){
 124                                 fastaFileName = m->getFastaFile();
 125                                 if (fastaFileName != "") {  m->mothurOut("Using " + fastaFileName + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
 126                                 else {
 127                                         qualFileName = m->getQualFile();
 128                                         if (qualFileName != "") {  m->mothurOut("Using " + qualFileName + " as input file for the qfile parameter."); m->mothurOutEndLine(); }
 129                                         else {
 130                                                 m->mothurOut("You have no current files for fasta or qfile, and fasta or qfile is a required parameter for the reverse.seqs command."); m->mothurOutEndLine();
 131                                                 abort = true;
 132                                         }
 133                                 }
 134                         }
 135
 136                         //if the user changes the output directory command factory will send this info to us in the output parameter
 137                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
 138                                 outputDir = "";
 139                         }
 140
 141                 }
 142         }
 143         catch(exception& e) {
 144                 m->errorOut(e, "ReverseSeqsCommand", "ReverseSeqsCommand");
 145                 exit(1);
 146         }
 147 }
 148 //***************************************************************************************************************
 149
 150
 151 int ReverseSeqsCommand::execute(){
 152         try{
 153
 154                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 155
 156                 string fastaReverseFileName;
 157
 158                 if(fastaFileName != ""){
 159                         ifstream inFASTA;
 160                         m->openInputFile(fastaFileName, inFASTA);
 161
 162                         ofstream outFASTA;
 163                         string tempOutputDir = outputDir;
 164                         if (outputDir == "") { tempOutputDir += m->hasPath(fastaFileName); } //if user entered a file with a path then preserve it
 165                         fastaReverseFileName = tempOutputDir + m->getRootName(m->getSimpleName(fastaFileName)) + "rc" + m->getExtension(fastaFileName);
 166                         m->openOutputFile(fastaReverseFileName, outFASTA);
 167
 168                         while(!inFASTA.eof()){
 169                                 if (m->control_pressed) {  inFASTA.close();  outFASTA.close(); m->mothurRemove(fastaReverseFileName); return 0; }
 170
 171                                 Sequence currSeq(inFASTA);  m->gobble(inFASTA);
 172                                 if (currSeq.getName() != "") {
 173                                         currSeq.reverseComplement();
 174                                         currSeq.printSequence(outFASTA);
 175                                 }
 176                         }
 177                         inFASTA.close();
 178                         outFASTA.close();
 179                         outputNames.push_back(fastaReverseFileName); outputTypes["fasta"].push_back(fastaReverseFileName);
 180                 }
 181
 182                 string qualReverseFileName;
 183
 184                 if(qualFileName != ""){
 185                         QualityScores currQual;
 186
 187                         ifstream inQual;
 188                         m->openInputFile(qualFileName, inQual);
 189
 190                         ofstream outQual;
 191                         string tempOutputDir = outputDir;
 192                         if (outputDir == "") { tempOutputDir += m->hasPath(qualFileName); } //if user entered a file with a path then preserve it
 193                         string qualReverseFileName = tempOutputDir + m->getRootName(m->getSimpleName(qualFileName)) + "rc" + m->getExtension(qualFileName);
 194                         m->openOutputFile(qualReverseFileName, outQual);
 195
 196                         while(!inQual.eof()){
 197                                 if (m->control_pressed) {  inQual.close();  outQual.close(); m->mothurRemove(qualReverseFileName); return 0; }
 198                                 currQual = QualityScores(inQual);  m->gobble(inQual);
 199                                 currQual.flipQScores();
 200                                 currQual.printQScores(outQual);
 201                         }
 202                         inQual.close();
 203                         outQual.close();
 204                         outputNames.push_back(qualReverseFileName); outputTypes["qfile"].push_back(qualReverseFileName);
 205                 }
 206
 207                 if (m->control_pressed) {  m->mothurRemove(qualReverseFileName); m->mothurRemove(fastaReverseFileName); return 0; }
 208
 209                 //set fasta file as new current fastafile
 210                 string current = "";
 211                 itTypes = outputTypes.find("fasta");
 212                 if (itTypes != outputTypes.end()) {
 213                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
 214                 }
 215
 216                 itTypes = outputTypes.find("qfile");
 217                 if (itTypes != outputTypes.end()) {
 218                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setQualFile(current); }
 219                 }
 220
 221
 222                 m->mothurOutEndLine();
 223                 m->mothurOut("Output File Name: "); m->mothurOutEndLine();
 224                 for(int i=0;i<outputNames.size();i++){
 225                         m->mothurOut(outputNames[i]);
 226                         m->mothurOutEndLine();
 227                 }
 228
 229
 230
 231                 return 0;
 232         }
 233         catch(exception& e) {
 234                 m->errorOut(e, "ReverseSeqsCommand", "execute");
 235                 exit(1);
 236         }
 237 }
 238
 239 //***************************************************************************************************************