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 DeconvoluteCommand::DeconvoluteCommand(string option)  {
  14         try {
  15                 abort = false;
  16
  17                 //allow user to run help
  18                 if(option == "help") { help(); abort = true; }
  19
  20                 else {
  21                         //valid paramters for this command
  22                         string Array[] =  {"fasta", "name","outputdir","inputdir"};
  23                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  24
  25                         OptionParser parser(option);
  26                         map<string,string> parameters = parser.getParameters();
  27
  28                         ValidParameters validParameter;
  29                         map<string, string>::iterator it;
  30
  31                         //check to make sure all parameters are valid for command
  32                         for (it = parameters.begin(); it != parameters.end(); it++) {
  33                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  34                         }
  35
  36                         //if the user changes the input directory command factory will send this info to us in the output parameter
  37                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
  38                         if (inputDir == "not found"){   inputDir = "";          }
  39                         else {
  40                                 string path;
  41                                 it = parameters.find("fasta");
  42                                 //user has given a template file
  43                                 if(it != parameters.end()){
  44                                         path = m->hasPath(it->second);
  45                                         //if the user has not given a path then, add inputdir. else leave path alone.
  46                                         if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
  47                                 }
  48
  49                                 it = parameters.find("name");
  50                                 //user has given a template file
  51                                 if(it != parameters.end()){
  52                                         path = m->hasPath(it->second);
  53                                         //if the user has not given a path then, add inputdir. else leave path alone.
  54                                         if (path == "") {       parameters["name"] = inputDir + it->second;             }
  55                                 }
  56                         }
  57
  58
  59                         //check for required parameters
  60                         inFastaName = validParameter.validFile(parameters, "fasta", true);
  61                         if (inFastaName == "not open") { abort = true; }
  62                         else if (inFastaName == "not found") { inFastaName = ""; m->mothurOut("fasta is a required parameter for the unique.seqs command."); m->mothurOutEndLine(); abort = true;  }
  63
  64                         //if the user changes the output directory command factory will send this info to us in the output parameter
  65                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
  66                                 outputDir = "";
  67                                 outputDir += m->hasPath(inFastaName); //if user entered a file with a path then preserve it
  68                         }
  69
  70                         oldNameMapFName = validParameter.validFile(parameters, "name", true);
  71                         if (oldNameMapFName == "not open") { abort = true; }
  72                         else if (oldNameMapFName == "not found"){       oldNameMapFName = "";   }
  73                 }
  74
  75         }
  76         catch(exception& e) {
  77                 m->errorOut(e, "DeconvoluteCommand", "DeconvoluteCommand");
  78                 exit(1);
  79         }
  80 }
  81 //**********************************************************************************************************************
  82
  83 void DeconvoluteCommand::help(){
  84         try {
  85                 m->mothurOut("The unique.seqs command reads a fastafile and creates a namesfile.\n");
  86                 m->mothurOut("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");
  87                 m->mothurOut("If the sequence is unique the second column will just contain its name. \n");
  88                 m->mothurOut("The unique.seqs command parameter is fasta and it is required.\n");
  89                 m->mothurOut("The unique.seqs command should be in the following format: \n");
  90                 m->mothurOut("unique.seqs(fasta=yourFastaFile) \n");
  91         }
  92         catch(exception& e) {
  93                 m->errorOut(e, "DeconvoluteCommand", "help");
  94                 exit(1);
  95         }
  96 }
  97
  98 /**************************************************************************************/
  99 int DeconvoluteCommand::execute() {
 100         try {
 101
 102                 if (abort == true) { return 0; }
 103
 104                 //prepare filenames and open files
 105                 string outNameFile = outputDir + m->getRootName(m->getSimpleName(inFastaName)) + "names";
 106                 string outFastaFile = outputDir + m->getRootName(m->getSimpleName(inFastaName)) + "unique" + m->getExtension(inFastaName);
 107
 108                 FastaMap fastamap;
 109
 110                 if(oldNameMapFName == "")       {       fastamap.readFastaFile(inFastaName);                                    }
 111                 else                                            {       fastamap.readFastaFile(inFastaName, oldNameMapFName);   }
 112
 113                 if (m->control_pressed) { return 0; }
 114
 115                 fastamap.printCondensedFasta(outFastaFile);
 116                 fastamap.printNamesFile(outNameFile);
 117
 118                 if (m->control_pressed) { remove(outFastaFile.c_str()); remove(outNameFile.c_str()); return 0; }
 119
 120                 m->mothurOutEndLine();
 121                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 122                 m->mothurOut(outFastaFile); m->mothurOutEndLine();
 123                 m->mothurOut(outNameFile); m->mothurOutEndLine();
 124                 m->mothurOutEndLine();
 125
 126
 127
 128                 return 0;
 129         }
 130         catch(exception& e) {
 131                 m->errorOut(e, "DeconvoluteCommand", "execute");
 132                 exit(1);
 133         }
 134 }
 135 /**************************************************************************************/