chimeraseqscommand.cpp

   1 /*
   2  *  chimeraseqscommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by Sarah Westcott on 6/29/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "chimeraseqscommand.h"
  11 #include "bellerophon.h"
  12 #include "pintail.h"
  13
  14 //***************************************************************************************************************
  15
  16 ChimeraSeqsCommand::ChimeraSeqsCommand(string option){
  17         try {
  18                 abort = false;
  19
  20                 //allow user to run help
  21                 if(option == "help") { help(); abort = true; }
  22
  23                 else {
  24                         //valid paramters for this command
  25                         string Array[] =  {"fasta", "filter", "correction", "processors", "method", "window", "increment", "template" };
  26                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  27
  28                         OptionParser parser(option);
  29                         map<string,string> parameters = parser.getParameters();
  30
  31                         ValidParameters validParameter;
  32
  33                         //check to make sure all parameters are valid for command
  34                         for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
  35                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  36                         }
  37
  38                         //check for required parameters
  39                         fastafile = validParameter.validFile(parameters, "fasta", true);
  40                         if (fastafile == "not open") { abort = true; }
  41                         else if (fastafile == "not found") { fastafile = ""; mothurOut("fasta is a required parameter for the chimera.seqs command."); mothurOutEndLine(); abort = true;  }
  42
  43                         templatefile = validParameter.validFile(parameters, "template", true);
  44                         if (templatefile == "not open") { abort = true; }
  45                         else if (templatefile == "not found") { templatefile = "";  }
  46
  47
  48                         string temp;
  49                         temp = validParameter.validFile(parameters, "filter", false);                   if (temp == "not found") { temp = "T"; }
  50                         filter = isTrue(temp);
  51
  52                         temp = validParameter.validFile(parameters, "correction", false);               if (temp == "not found") { temp = "T"; }
  53                         correction = isTrue(temp);
  54
  55                         temp = validParameter.validFile(parameters, "processors", false);               if (temp == "not found") { temp = "1"; }
  56                         convert(temp, processors);
  57
  58                         temp = validParameter.validFile(parameters, "window", false);                   if (temp == "not found") { temp = "0"; }
  59                         convert(temp, window);
  60
  61                         temp = validParameter.validFile(parameters, "increment", false);                        if (temp == "not found") { temp = "10"; }
  62                         convert(temp, increment);
  63
  64                         method = validParameter.validFile(parameters, "method", false);         if (method == "not found") { method = "pintail"; }
  65
  66                         if ((method == "pintail") && (templatefile == "")) { mothurOut("You must provide a template file with the pintail method."); mothurOutEndLine(); abort = true;  }
  67
  68
  69                 }
  70         }
  71         catch(exception& e) {
  72                 errorOut(e, "ChimeraSeqsCommand", "ChimeraSeqsCommand");
  73                 exit(1);
  74         }
  75 }
  76 //**********************************************************************************************************************
  77
  78 void ChimeraSeqsCommand::help(){
  79         try {
  80                 mothurOut("The chimera.seqs command reads a fastafile and creates a sorted priority score list of potentially chimeric sequences (ideally, the sequences should already be aligned).\n");
  81                 mothurOut("The chimera.seqs command parameters are fasta, filter, correction, processors and method.  fasta is required.\n");
  82                 mothurOut("The filter parameter allows you to specify if you would like to apply a 50% soft filter.  The default is false. \n");
  83                 mothurOut("The correction parameter allows you to put more emphasis on the distance between highly similar sequences and less emphasis on the differences between remote homologs.   The default is true. \n");
  84                 mothurOut("The processors parameter allows you to specify how many processors you would like to use.  The default is 1. \n");
  85                 mothurOut("The method parameter allows you to specify the method for finding chimeric sequences.  The default is pintail. \n");
  86                 mothurOut("The chimera.seqs command should be in the following format: \n");
  87                 mothurOut("chimera.seqs(fasta=yourFastaFile, filter=yourFilter, correction=yourCorrection, processors=yourProcessors, method=bellerophon) \n");
  88                 mothurOut("Example: chimera.seqs(fasta=AD.align, filter=True, correction=true, processors=2, method=yourMethod) \n");
  89                 mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n\n");
  90         }
  91         catch(exception& e) {
  92                 errorOut(e, "ChimeraSeqsCommand", "help");
  93                 exit(1);
  94         }
  95 }
  96
  97 //***************************************************************************************************************
  98
  99 ChimeraSeqsCommand::~ChimeraSeqsCommand(){      /*      do nothing      */      }
 100
 101 //***************************************************************************************************************
 102
 103 int ChimeraSeqsCommand::execute(){
 104         try{
 105
 106                 if (abort == true) { return 0; }
 107
 108                 if (method == "bellerophon")    {       chimera = new Bellerophon(fastafile);   }
 109                 else if (method == "pintail")   {       chimera = new Pintail(fastafile);               }
 110                 else { mothurOut("Not a valid method."); mothurOutEndLine(); return 0;          }
 111
 112                 //set user options
 113                 chimera->setFilter(filter);
 114                 chimera->setCorrection(correction);
 115                 chimera->setProcessors(processors);
 116                 chimera->setWindow(window);
 117                 chimera->setIncrement(increment);
 118                 chimera->setTemplate(templatefile);
 119
 120                 //find chimeras
 121                 chimera->getChimeras();
 122
 123                 string outputFileName = getRootName(fastafile) + method + ".chimeras";
 124                 ofstream out;
 125                 openOutputFile(outputFileName, out);
 126
 127                 //print results
 128                 chimera->print(out);
 129
 130                 out.close();
 131
 132                 delete chimera;
 133
 134                 return 0;
 135
 136         }
 137         catch(exception& e) {
 138                 errorOut(e, "ChimeraSeqsCommand", "execute");
 139                 exit(1);
 140         }
 141 }
 142
 143 /**************************************************************************************************/
 144