deconvolutecommand.cpp

   1 /*
   2  *  deconvolute.cpp
   3  *  Mothur
   4  *
   5  *  Created by Sarah Westcott on 1/21/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "deconvolutecommand.h"
  11
  12 //**********************************************************************************************************************
  13 vector<string> DeconvoluteCommand::setParameters(){
  14         try {
  15                 CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
  16                 CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
  17                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
  18                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
  19
  20                 vector<string> myArray;
  21                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  22                 return myArray;
  23         }
  24         catch(exception& e) {
  25                 m->errorOut(e, "DeconvoluteCommand", "setParameters");
  26                 exit(1);
  27         }
  28 }
  29 //**********************************************************************************************************************
  30 string DeconvoluteCommand::getHelpString(){
  31         try {
  32                 string helpString = "";
  33                 helpString += "The unique.seqs command reads a fastafile and creates a namesfile.\n";
  34                 helpString += "It creates a file where the first column is the groupname and the second column is a list of sequence names who have the same sequence. \n";
  35                 helpString += "If the sequence is unique the second column will just contain its name. \n";
  36                 helpString += "The unique.seqs command parameters are fasta and name.  fasta is required, unless there is a valid current fasta file.\n";
  37                 helpString += "The unique.seqs command should be in the following format: \n";
  38                 helpString += "unique.seqs(fasta=yourFastaFile) \n";
  39                 return helpString;
  40         }
  41         catch(exception& e) {
  42                 m->errorOut(e, "DeconvoluteCommand", "getHelpString");
  43                 exit(1);
  44         }
  45 }
  46 //**********************************************************************************************************************
  47 DeconvoluteCommand::DeconvoluteCommand(){
  48         try {
  49                 abort = true; calledHelp = true;
  50                 setParameters();
  51                 vector<string> tempOutNames;
  52                 outputTypes["fasta"] = tempOutNames;
  53                 outputTypes["name"] = tempOutNames;
  54         }
  55         catch(exception& e) {
  56                 m->errorOut(e, "DeconvoluteCommand", "DeconvoluteCommand");
  57                 exit(1);
  58         }
  59 }
  60 /**************************************************************************************/
  61 DeconvoluteCommand::DeconvoluteCommand(string option)  {
  62         try {
  63                 abort = false; calledHelp = false;
  64
  65                 //allow user to run help
  66                 if(option == "help") { help(); abort = true; calledHelp = true; }
  67                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
  68
  69                 else {
  70                         vector<string> myArray = setParameters();
  71
  72                         OptionParser parser(option);
  73                         map<string,string> parameters = parser.getParameters();
  74
  75                         ValidParameters validParameter;
  76                         map<string, string>::iterator it;
  77
  78                         //check to make sure all parameters are valid for command
  79                         for (it = parameters.begin(); it != parameters.end(); it++) {
  80                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  81                         }
  82
  83                         //initialize outputTypes
  84                         vector<string> tempOutNames;
  85                         outputTypes["fasta"] = tempOutNames;
  86                         outputTypes["name"] = tempOutNames;
  87
  88                         //if the user changes the input directory command factory will send this info to us in the output parameter
  89                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
  90                         if (inputDir == "not found"){   inputDir = "";          }
  91                         else {
  92                                 string path;
  93                                 it = parameters.find("fasta");
  94                                 //user has given a template file
  95                                 if(it != parameters.end()){
  96                                         path = m->hasPath(it->second);
  97                                         //if the user has not given a path then, add inputdir. else leave path alone.
  98                                         if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
  99                                 }
 100
 101                                 it = parameters.find("name");
 102                                 //user has given a template file
 103                                 if(it != parameters.end()){
 104                                         path = m->hasPath(it->second);
 105                                         //if the user has not given a path then, add inputdir. else leave path alone.
 106                                         if (path == "") {       parameters["name"] = inputDir + it->second;             }
 107                                 }
 108                         }
 109
 110
 111                         //check for required parameters
 112                         inFastaName = validParameter.validFile(parameters, "fasta", true);
 113                         if (inFastaName == "not open") { abort = true; }
 114                         else if (inFastaName == "not found") {
 115                                 inFastaName = m->getFastaFile();
 116                                 if (inFastaName != "") { m->mothurOut("Using " + inFastaName + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
 117                                 else {  m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
 118                         }
 119
 120                         //if the user changes the output directory command factory will send this info to us in the output parameter
 121                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
 122                                 outputDir = "";
 123                                 outputDir += m->hasPath(inFastaName); //if user entered a file with a path then preserve it
 124                         }
 125
 126                         oldNameMapFName = validParameter.validFile(parameters, "name", true);
 127                         if (oldNameMapFName == "not open") { abort = true; }
 128                         else if (oldNameMapFName == "not found"){       oldNameMapFName = "";   }
 129                 }
 130
 131         }
 132         catch(exception& e) {
 133                 m->errorOut(e, "DeconvoluteCommand", "DeconvoluteCommand");
 134                 exit(1);
 135         }
 136 }
 137 /**************************************************************************************/
 138 int DeconvoluteCommand::execute() {
 139         try {
 140
 141                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 142
 143                 //prepare filenames and open files
 144                 string outNameFile = outputDir + m->getRootName(m->getSimpleName(inFastaName)) + "names";
 145                 string outFastaFile = outputDir + m->getRootName(m->getSimpleName(inFastaName)) + "unique" + m->getExtension(inFastaName);
 146
 147                 FastaMap fastamap;
 148
 149                 if(oldNameMapFName == "")       {       fastamap.readFastaFile(inFastaName);                                    }
 150                 else                                            {       fastamap.readFastaFile(inFastaName, oldNameMapFName);   }
 151
 152                 if (m->control_pressed) { return 0; }
 153
 154                 fastamap.printCondensedFasta(outFastaFile);
 155                 fastamap.printNamesFile(outNameFile);
 156
 157                 if (m->control_pressed) { outputTypes.clear(); remove(outFastaFile.c_str()); remove(outNameFile.c_str()); return 0; }
 158
 159                 m->mothurOutEndLine();
 160                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 161                 m->mothurOut(outFastaFile); m->mothurOutEndLine();
 162                 m->mothurOut(outNameFile); m->mothurOutEndLine();
 163                 outputNames.push_back(outFastaFile);  outputNames.push_back(outNameFile); outputTypes["fasta"].push_back(outFastaFile);  outputTypes["name"].push_back(outNameFile);
 164                 m->mothurOutEndLine();
 165
 166                 //set fasta file as new current fastafile
 167                 string current = "";
 168                 itTypes = outputTypes.find("fasta");
 169                 if (itTypes != outputTypes.end()) {
 170                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
 171                 }
 172
 173                 itTypes = outputTypes.find("name");
 174                 if (itTypes != outputTypes.end()) {
 175                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setNameFile(current); }
 176                 }
 177
 178                 return 0;
 179         }
 180         catch(exception& e) {
 181                 m->errorOut(e, "DeconvoluteCommand", "execute");
 182                 exit(1);
 183         }
 184 }
 185 /**************************************************************************************/