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", false);
  56                         if (maskfile == "not found") { maskfile = "";  }
  57                         else if (maskfile != "default")  {
  58                                 ifstream in;
  59                                 int     ableToOpen = openInputFile(maskfile, in);
  60                                 if (ableToOpen == 1) { abort = true; }
  61                                 in.close();
  62                         }
  63
  64
  65
  66
  67                         string temp;
  68                         temp = validParameter.validFile(parameters, "filter", false);                   if (temp == "not found") { temp = "T"; }
  69                         filter = isTrue(temp);
  70
  71                         temp = validParameter.validFile(parameters, "correction", false);               if (temp == "not found") { temp = "T"; }
  72                         correction = isTrue(temp);
  73
  74                         temp = validParameter.validFile(parameters, "processors", false);               if (temp == "not found") { temp = "1"; }
  75                         convert(temp, processors);
  76
  77                         temp = validParameter.validFile(parameters, "window", false);                   if (temp == "not found") { temp = "0"; }
  78                         convert(temp, window);
  79
  80                         temp = validParameter.validFile(parameters, "increment", false);                        if (temp == "not found") { temp = "25"; }
  81                         convert(temp, increment);
  82
  83                         method = validParameter.validFile(parameters, "method", false);         if (method == "not found") { method = "pintail"; }
  84
  85                         if ((method == "pintail") && (templatefile == "")) { mothurOut("You must provide a template file with the pintail method."); mothurOutEndLine(); abort = true;  }
  86
  87
  88                 }
  89         }
  90         catch(exception& e) {
  91                 errorOut(e, "ChimeraSeqsCommand", "ChimeraSeqsCommand");
  92                 exit(1);
  93         }
  94 }
  95 //**********************************************************************************************************************
  96
  97 void ChimeraSeqsCommand::help(){
  98         try {
  99                 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");
 100                 mothurOut("The chimera.seqs command parameters are fasta, filter, correction, processors, mask and method.  fasta is required.\n");
 101                 mothurOut("The filter parameter allows you to specify if you would like to apply a 50% soft filter.  The default is false. \n");
 102                 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");
 103                 mothurOut("The processors parameter allows you to specify how many processors you would like to use.  The default is 1. \n");
 104                 mothurOut("The method parameter allows you to specify the method for finding chimeric sequences.  The default is pintail. \n");
 105                 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");
 106                 mothurOut("The chimera.seqs command should be in the following format: \n");
 107                 mothurOut("chimera.seqs(fasta=yourFastaFile, filter=yourFilter, correction=yourCorrection, processors=yourProcessors, method=bellerophon) \n");
 108                 mothurOut("Example: chimera.seqs(fasta=AD.align, filter=True, correction=true, processors=2, method=yourMethod) \n");
 109                 mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n\n");
 110         }
 111         catch(exception& e) {
 112                 errorOut(e, "ChimeraSeqsCommand", "help");
 113                 exit(1);
 114         }
 115 }
 116
 117 //***************************************************************************************************************
 118
 119 ChimeraSeqsCommand::~ChimeraSeqsCommand(){      /*      do nothing      */      }
 120
 121 //***************************************************************************************************************
 122
 123 int ChimeraSeqsCommand::execute(){
 124         try{
 125
 126                 if (abort == true) { return 0; }
 127
 128                 if (method == "bellerophon")    {               chimera = new Bellerophon(fastafile);                   }
 129                 else if (method == "pintail")   {               chimera = new Pintail(fastafile, templatefile);
 130                         //saves time to avoid generating it
 131                         if (consfile != "")                     {               chimera->setCons(consfile);                                             }
 132                         else                                            {               chimera->setCons("");                                                   }
 133
 134                         //saves time to avoid generating it
 135                         if (quanfile != "")                     {               chimera->setQuantiles(quanfile);                                }
 136                         else                                            {               chimera->setQuantiles("");                                              }
 137
 138                         if (maskfile == "default") { mothurOut("I am using the default 236627 EU009184.1 Shigella dysenteriae str. FBD013."); mothurOutEndLine();  }
 139                         chimera->setMask(maskfile);
 140
 141                 }else { mothurOut("Not a valid method."); mothurOutEndLine(); return 0;         }
 142
 143                 //set user options
 144                 chimera->setFilter(filter);
 145                 chimera->setCorrection(correction);
 146                 chimera->setProcessors(processors);
 147                 chimera->setWindow(window);
 148                 chimera->setIncrement(increment);
 149
 150                 //find chimeras
 151                 chimera->getChimeras();
 152
 153                 string outputFileName = getRootName(fastafile) + method + ".chimeras";
 154                 ofstream out;
 155                 openOutputFile(outputFileName, out);
 156
 157                 //print results
 158                 chimera->print(out);
 159
 160                 out.close();
 161
 162                 delete chimera;
 163
 164                 return 0;
 165
 166         }
 167         catch(exception& e) {
 168                 errorOut(e, "ChimeraSeqsCommand", "execute");
 169                 exit(1);
 170         }
 171 }
 172 /**************************************************************************************************/
 173