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