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", "conservation", "quantile", "mask" };
  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                         consfile = validParameter.validFile(parameters, "conservation", true);
  48                         if (consfile == "not open") { abort = true; }
  49                         else if (consfile == "not found") { consfile = "";  }
  50
  51                         quanfile = validParameter.validFile(parameters, "quantile", true);
  52                         if (quanfile == "not open") { abort = true; }
  53                         else if (quanfile == "not found") { quanfile = "";  }
  54
  55                         maskfile = validParameter.validFile(parameters, "mask", true);
  56                         if (maskfile == "not open") { abort = true; }
  57                         else if (maskfile == "not found") { maskfile = "";  }
  58
  59
  60
  61                         string temp;
  62                         temp = validParameter.validFile(parameters, "filter", false);                   if (temp == "not found") { temp = "T"; }
  63                         filter = isTrue(temp);
  64
  65                         temp = validParameter.validFile(parameters, "correction", false);               if (temp == "not found") { temp = "T"; }
  66                         correction = isTrue(temp);
  67
  68                         temp = validParameter.validFile(parameters, "processors", false);               if (temp == "not found") { temp = "1"; }
  69                         convert(temp, processors);
  70
  71                         temp = validParameter.validFile(parameters, "window", false);                   if (temp == "not found") { temp = "0"; }
  72                         convert(temp, window);
  73
  74                         temp = validParameter.validFile(parameters, "increment", false);                        if (temp == "not found") { temp = "25"; }
  75                         convert(temp, increment);
  76
  77                         method = validParameter.validFile(parameters, "method", false);         if (method == "not found") { method = "pintail"; }
  78
  79                         if ((method == "pintail") && (templatefile == "")) { mothurOut("You must provide a template file with the pintail method."); mothurOutEndLine(); abort = true;  }
  80
  81
  82                 }
  83         }
  84         catch(exception& e) {
  85                 errorOut(e, "ChimeraSeqsCommand", "ChimeraSeqsCommand");
  86                 exit(1);
  87         }
  88 }
  89 //**********************************************************************************************************************
  90
  91 void ChimeraSeqsCommand::help(){
  92         try {
  93                 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");
  94                 mothurOut("The chimera.seqs command parameters are fasta, filter, correction, processors, mask and method.  fasta is required.\n");
  95                 mothurOut("The filter parameter allows you to specify if you would like to apply a 50% soft filter.  The default is false. \n");
  96                 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");
  97                 mothurOut("The processors parameter allows you to specify how many processors you would like to use.  The default is 1. \n");
  98                 mothurOut("The method parameter allows you to specify the method for finding chimeric sequences.  The default is pintail. \n");
  99                 mothurOut("The mask parameter allows you to specify a file containing one sequence you wish to use as a mask for the pintail and mallard method.  The default is 236627 EU009184.1 Shigella dysenteriae str. FBD013. \n");
 100                 mothurOut("The chimera.seqs command should be in the following format: \n");
 101                 mothurOut("chimera.seqs(fasta=yourFastaFile, filter=yourFilter, correction=yourCorrection, processors=yourProcessors, method=bellerophon) \n");
 102                 mothurOut("Example: chimera.seqs(fasta=AD.align, filter=True, correction=true, processors=2, method=yourMethod) \n");
 103                 mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n\n");
 104         }
 105         catch(exception& e) {
 106                 errorOut(e, "ChimeraSeqsCommand", "help");
 107                 exit(1);
 108         }
 109 }
 110
 111 //***************************************************************************************************************
 112
 113 ChimeraSeqsCommand::~ChimeraSeqsCommand(){      /*      do nothing      */      }
 114
 115 //***************************************************************************************************************
 116
 117 int ChimeraSeqsCommand::execute(){
 118         try{
 119
 120                 if (abort == true) { return 0; }
 121
 122                 if (method == "bellerophon")    {               chimera = new Bellerophon(fastafile);                   }
 123                 else if (method == "pintail")   {               chimera = new Pintail(fastafile, templatefile);
 124                         //saves time to avoid generating it
 125                         if (consfile != "")                     {               chimera->setCons(consfile);                                             }
 126                         else                                            {               chimera->setCons("");                                                   }
 127
 128                         //saves time to avoid generating it
 129                         if (quanfile != "")                     {               chimera->setQuantiles(quanfile);                                }
 130                         else                                            {               chimera->setQuantiles("");                                              }
 131
 132                         if (maskfile == "") { mothurOut("You have not provided a mask, so I am using the default 236627 EU009184.1 Shigella dysenteriae str. FBD013."); mothurOutEndLine();  }
 133                         chimera->setMask(maskfile);
 134
 135                 }else { mothurOut("Not a valid method."); mothurOutEndLine(); return 0;         }
 136
 137                 //set user options
 138                 chimera->setFilter(filter);
 139                 chimera->setCorrection(correction);
 140                 chimera->setProcessors(processors);
 141                 chimera->setWindow(window);
 142                 chimera->setIncrement(increment);
 143
 144                 //find chimeras
 145                 chimera->getChimeras();
 146
 147                 string outputFileName = getRootName(fastafile) + method + ".chimeras";
 148                 ofstream out;
 149                 openOutputFile(outputFileName, out);
 150
 151                 //print results
 152                 chimera->print(out);
 153
 154                 out.close();
 155
 156                 delete chimera;
 157
 158                 return 0;
 159
 160         }
 161         catch(exception& e) {
 162                 errorOut(e, "ChimeraSeqsCommand", "execute");
 163                 exit(1);
 164         }
 165 }
 166 /**************************************************************************************************/
 167