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","fasta",false,false,true); parameters.push_back(pfasta);
  18                 CommandParameter pqfile("qfile", "InputTypes", "", "", "none", "fastaQual", "none","qfile",false,false,true); 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 string ReverseSeqsCommand::getOutputPattern(string type) {
  48     try {
  49         string pattern = "";
  50
  51         if (type == "fasta") {  pattern = "[filename],rc,[extension]"; }
  52         else if (type == "qfile") {  pattern = "[filename],rc,[extension]"; }
  53         else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
  54
  55         return pattern;
  56     }
  57     catch(exception& e) {
  58         m->errorOut(e, "ReverseSeqsCommand", "getOutputPattern");
  59         exit(1);
  60     }
  61 }
  62 //**********************************************************************************************************************
  63 ReverseSeqsCommand::ReverseSeqsCommand(){
  64         try {
  65                 abort = true; calledHelp = true;
  66                 setParameters();
  67                 vector<string> tempOutNames;
  68                 outputTypes["fasta"] = tempOutNames;
  69                 outputTypes["qfile"] = tempOutNames;
  70         }
  71         catch(exception& e) {
  72                 m->errorOut(e, "ReverseSeqsCommand", "ReverseSeqsCommand");
  73                 exit(1);
  74         }
  75 }
  76 //***************************************************************************************************************
  77
  78 ReverseSeqsCommand::ReverseSeqsCommand(string option)  {
  79         try {
  80                 abort = false; calledHelp = false;
  81
  82                 //allow user to run help
  83                 if(option == "help") { help(); abort = true; calledHelp = true; }
  84                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
  85
  86                 else {
  87                         vector<string> myArray = setParameters();
  88
  89                         OptionParser parser(option);
  90                         map<string,string> parameters = parser.getParameters();
  91
  92                         ValidParameters validParameter;
  93                         map<string,string>::iterator it;
  94
  95                         //check to make sure all parameters are valid for command
  96                         for (it = parameters.begin(); it != parameters.end(); it++) {
  97                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  98                         }
  99
 100                         //initialize outputTypes
 101                         vector<string> tempOutNames;
 102                         outputTypes["fasta"] = tempOutNames;
 103                         outputTypes["qfile"] = tempOutNames;
 104
 105                         //if the user changes the input directory command factory will send this info to us in the output parameter
 106                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 107                         if (inputDir == "not found"){   inputDir = "";          }
 108                         else {
 109                                 string path;
 110                                 it = parameters.find("fasta");
 111                                 //user has given a template file
 112                                 if(it != parameters.end()){
 113                                         path = m->hasPath(it->second);
 114                                         //if the user has not given a path then, add inputdir. else leave path alone.
 115                                         if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
 116                                 }
 117
 118                                 it = parameters.find("qfile");
 119                                 //user has given a template file
 120                                 if(it != parameters.end()){
 121                                         path = m->hasPath(it->second);
 122                                         //if the user has not given a path then, add inputdir. else leave path alone.
 123                                         if (path == "") {       parameters["qfile"] = inputDir + it->second;            }
 124                                 }
 125                         }
 126
 127                         //check for required parameters
 128                         fastaFileName = validParameter.validFile(parameters, "fasta", true);
 129                         if (fastaFileName == "not open") { abort = true; }
 130                         else if (fastaFileName == "not found") { fastaFileName = "";}// m->mothurOut("fasta is a required parameter for the reverse.seqs command."); m->mothurOutEndLine(); abort = true;  }
 131                         else { m->setFastaFile(fastaFileName); }
 132
 133                         qualFileName = validParameter.validFile(parameters, "qfile", true);
 134                         if (qualFileName == "not open") { abort = true; }
 135                         else if (qualFileName == "not found") { qualFileName = ""; }//m->mothurOut("fasta is a required parameter for the reverse.seqs command."); m->mothurOutEndLine(); abort = true;  }
 136                         else { m->setQualFile(qualFileName); }
 137
 138                         if((fastaFileName == "") && (qualFileName == "")){
 139                                 fastaFileName = m->getFastaFile();
 140                                 if (fastaFileName != "") {  m->mothurOut("Using " + fastaFileName + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
 141                                 else {
 142                                         qualFileName = m->getQualFile();
 143                                         if (qualFileName != "") {  m->mothurOut("Using " + qualFileName + " as input file for the qfile parameter."); m->mothurOutEndLine(); }
 144                                         else {
 145                                                 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();
 146                                                 abort = true;
 147                                         }
 148                                 }
 149                         }
 150
 151                         //if the user changes the output directory command factory will send this info to us in the output parameter
 152                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
 153                                 outputDir = "";
 154                         }
 155
 156                 }
 157         }
 158         catch(exception& e) {
 159                 m->errorOut(e, "ReverseSeqsCommand", "ReverseSeqsCommand");
 160                 exit(1);
 161         }
 162 }
 163 //***************************************************************************************************************
 164
 165
 166 int ReverseSeqsCommand::execute(){
 167         try{
 168
 169                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 170
 171                 string fastaReverseFileName;
 172
 173                 if(fastaFileName != ""){
 174                         ifstream inFASTA;
 175                         m->openInputFile(fastaFileName, inFASTA);
 176
 177                         ofstream outFASTA;
 178                         string tempOutputDir = outputDir;
 179                         if (outputDir == "") { tempOutputDir += m->hasPath(fastaFileName); } //if user entered a file with a path then preserve it
 180             map<string, string> variables;
 181             variables["[filename]"] = tempOutputDir + m->getRootName(m->getSimpleName(fastaFileName));
 182             variables["[extension]"] = m->getExtension(fastaFileName);
 183                         fastaReverseFileName = getOutputFileName("fasta", variables);
 184                         m->openOutputFile(fastaReverseFileName, outFASTA);
 185
 186                         while(!inFASTA.eof()){
 187                                 if (m->control_pressed) {  inFASTA.close();  outFASTA.close(); m->mothurRemove(fastaReverseFileName); return 0; }
 188
 189                                 Sequence currSeq(inFASTA);  m->gobble(inFASTA);
 190                                 if (currSeq.getName() != "") {
 191                                         currSeq.reverseComplement();
 192                                         currSeq.printSequence(outFASTA);
 193                                 }
 194                         }
 195                         inFASTA.close();
 196                         outFASTA.close();
 197                         outputNames.push_back(fastaReverseFileName); outputTypes["fasta"].push_back(fastaReverseFileName);
 198                 }
 199
 200                 string qualReverseFileName;
 201
 202                 if(qualFileName != ""){
 203                         QualityScores currQual;
 204
 205                         ifstream inQual;
 206                         m->openInputFile(qualFileName, inQual);
 207
 208                         ofstream outQual;
 209                         string tempOutputDir = outputDir;
 210                         if (outputDir == "") { tempOutputDir += m->hasPath(qualFileName); } //if user entered a file with a path then preserve it
 211             map<string, string> variables;
 212             variables["[filename]"] = tempOutputDir + m->getRootName(m->getSimpleName(qualFileName));
 213             variables["[extension]"] = m->getExtension(qualFileName);
 214                         string qualReverseFileName = getOutputFileName("qfile", variables);
 215             m->openOutputFile(qualReverseFileName, outQual);
 216
 217                         while(!inQual.eof()){
 218                                 if (m->control_pressed) {  inQual.close();  outQual.close(); m->mothurRemove(qualReverseFileName); return 0; }
 219                                 currQual = QualityScores(inQual);  m->gobble(inQual);
 220                                 currQual.flipQScores();
 221                                 currQual.printQScores(outQual);
 222                         }
 223                         inQual.close();
 224                         outQual.close();
 225                         outputNames.push_back(qualReverseFileName); outputTypes["qfile"].push_back(qualReverseFileName);
 226                 }
 227
 228                 if (m->control_pressed) {  m->mothurRemove(qualReverseFileName); m->mothurRemove(fastaReverseFileName); return 0; }
 229
 230                 //set fasta file as new current fastafile
 231                 string current = "";
 232                 itTypes = outputTypes.find("fasta");
 233                 if (itTypes != outputTypes.end()) {
 234                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
 235                 }
 236
 237                 itTypes = outputTypes.find("qfile");
 238                 if (itTypes != outputTypes.end()) {
 239                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setQualFile(current); }
 240                 }
 241
 242
 243                 m->mothurOutEndLine();
 244                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 245                 for(int i=0;i<outputNames.size();i++){
 246                         m->mothurOut(outputNames[i]);
 247                         m->mothurOutEndLine();
 248                 }
 249
 250
 251
 252                 return 0;
 253         }
 254         catch(exception& e) {
 255                 m->errorOut(e, "ReverseSeqsCommand", "execute");
 256                 exit(1);
 257         }
 258 }
 259
 260 //***************************************************************************************************************