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
  68                 else {
  69                         vector<string> myArray = setParameters();
  70
  71                         OptionParser parser(option);
  72                         map<string,string> parameters = parser.getParameters();
  73
  74                         ValidParameters validParameter;
  75                         map<string, string>::iterator it;
  76
  77                         //check to make sure all parameters are valid for command
  78                         for (it = parameters.begin(); it != parameters.end(); it++) {
  79                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  80                         }
  81
  82                         //initialize outputTypes
  83                         vector<string> tempOutNames;
  84                         outputTypes["fasta"] = tempOutNames;
  85                         outputTypes["name"] = tempOutNames;
  86
  87                         //if the user changes the input directory command factory will send this info to us in the output parameter
  88                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
  89                         if (inputDir == "not found"){   inputDir = "";          }
  90                         else {
  91                                 string path;
  92                                 it = parameters.find("fasta");
  93                                 //user has given a template file
  94                                 if(it != parameters.end()){
  95                                         path = m->hasPath(it->second);
  96                                         //if the user has not given a path then, add inputdir. else leave path alone.
  97                                         if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
  98                                 }
  99
 100                                 it = parameters.find("name");
 101                                 //user has given a template file
 102                                 if(it != parameters.end()){
 103                                         path = m->hasPath(it->second);
 104                                         //if the user has not given a path then, add inputdir. else leave path alone.
 105                                         if (path == "") {       parameters["name"] = inputDir + it->second;             }
 106                                 }
 107                         }
 108
 109
 110                         //check for required parameters
 111                         inFastaName = validParameter.validFile(parameters, "fasta", true);
 112                         if (inFastaName == "not open") { abort = true; }
 113                         else if (inFastaName == "not found") {
 114                                 inFastaName = m->getFastaFile();
 115                                 if (inFastaName != "") { m->mothurOut("Using " + inFastaName + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
 116                                 else {  m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
 117                         }
 118
 119                         //if the user changes the output directory command factory will send this info to us in the output parameter
 120                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
 121                                 outputDir = "";
 122                                 outputDir += m->hasPath(inFastaName); //if user entered a file with a path then preserve it
 123                         }
 124
 125                         oldNameMapFName = validParameter.validFile(parameters, "name", true);
 126                         if (oldNameMapFName == "not open") { abort = true; }
 127                         else if (oldNameMapFName == "not found"){       oldNameMapFName = "";   }
 128                 }
 129
 130         }
 131         catch(exception& e) {
 132                 m->errorOut(e, "DeconvoluteCommand", "DeconvoluteCommand");
 133                 exit(1);
 134         }
 135 }
 136 /**************************************************************************************/
 137 int DeconvoluteCommand::execute() {
 138         try {
 139
 140                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 141
 142                 //prepare filenames and open files
 143                 string outNameFile = outputDir + m->getRootName(m->getSimpleName(inFastaName)) + "names";
 144                 string outFastaFile = outputDir + m->getRootName(m->getSimpleName(inFastaName)) + "unique" + m->getExtension(inFastaName);
 145
 146                 FastaMap fastamap;
 147
 148                 if(oldNameMapFName == "")       {       fastamap.readFastaFile(inFastaName);                                    }
 149                 else                                            {       fastamap.readFastaFile(inFastaName, oldNameMapFName);   }
 150
 151                 if (m->control_pressed) { return 0; }
 152
 153                 fastamap.printCondensedFasta(outFastaFile);
 154                 fastamap.printNamesFile(outNameFile);
 155
 156                 if (m->control_pressed) { outputTypes.clear(); remove(outFastaFile.c_str()); remove(outNameFile.c_str()); return 0; }
 157
 158                 m->mothurOutEndLine();
 159                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 160                 m->mothurOut(outFastaFile); m->mothurOutEndLine();
 161                 m->mothurOut(outNameFile); m->mothurOutEndLine();
 162                 outputNames.push_back(outFastaFile);  outputNames.push_back(outNameFile); outputTypes["fasta"].push_back(outFastaFile);  outputTypes["name"].push_back(outNameFile);
 163                 m->mothurOutEndLine();
 164
 165                 //set fasta file as new current fastafile
 166                 string current = "";
 167                 itTypes = outputTypes.find("fasta");
 168                 if (itTypes != outputTypes.end()) {
 169                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
 170                 }
 171
 172                 itTypes = outputTypes.find("name");
 173                 if (itTypes != outputTypes.end()) {
 174                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setNameFile(current); }
 175                 }
 176
 177                 return 0;
 178         }
 179         catch(exception& e) {
 180                 m->errorOut(e, "DeconvoluteCommand", "execute");
 181                 exit(1);
 182         }
 183 }
 184 /**************************************************************************************/