chimerabellerophoncommand.cpp

   1 /*
   2  *  chimerabellerophoncommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by westcott on 4/1/10.
   6  *  Copyright 2010 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "chimerabellerophoncommand.h"
  11 #include "bellerophon.h"
  12
  13 //***************************************************************************************************************
  14
  15 ChimeraBellerophonCommand::ChimeraBellerophonCommand(string option)  {
  16         try {
  17                 abort = false;
  18
  19                 //allow user to run help
  20                 if(option == "help") { help(); abort = true; }
  21
  22                 else {
  23                         //valid paramters for this command
  24                         string Array[] =  {"fasta","filter","correction","processors","window","increment","outputdir","inputdir"};
  25                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  26
  27                         OptionParser parser(option);
  28                         map<string,string> parameters = parser.getParameters();
  29
  30                         ValidParameters validParameter;
  31                         map<string,string>::iterator it;
  32
  33                         //check to make sure all parameters are valid for command
  34                         for (it = parameters.begin(); it != parameters.end(); it++) {
  35                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  36                         }
  37
  38                         //if the user changes the input directory command factory will send this info to us in the output parameter
  39                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
  40                         if (inputDir == "not found"){   inputDir = "";          }
  41                         else {
  42                                 string path;
  43                                 it = parameters.find("fasta");
  44                                 //user has given a template file
  45                                 if(it != parameters.end()){
  46                                         path = hasPath(it->second);
  47                                         //if the user has not given a path then, add inputdir. else leave path alone.
  48                                         if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
  49                                 }
  50                         }
  51
  52
  53                         //check for required parameters
  54                         fastafile = validParameter.validFile(parameters, "fasta", true);
  55                         if (fastafile == "not open") { abort = true; }
  56                         else if (fastafile == "not found") { fastafile = ""; m->mothurOut("fasta is a required parameter for the chimera.bellerophon command."); m->mothurOutEndLine(); abort = true;  }
  57
  58                         //if the user changes the output directory command factory will send this info to us in the output parameter
  59                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
  60                                 outputDir = "";
  61                                 outputDir += hasPath(fastafile); //if user entered a file with a path then preserve it
  62                         }
  63
  64                         string temp;
  65                         temp = validParameter.validFile(parameters, "filter", false);                   if (temp == "not found") { temp = "F"; }
  66                         filter = isTrue(temp);
  67
  68                         temp = validParameter.validFile(parameters, "correction", false);               if (temp == "not found") { temp = "T"; }
  69                         correction = isTrue(temp);
  70
  71                         temp = validParameter.validFile(parameters, "processors", false);               if (temp == "not found") { temp = "1"; }
  72                         convert(temp, processors);
  73
  74                         temp = validParameter.validFile(parameters, "window", false);                   if (temp == "not found") { temp = "0"; }
  75                         convert(temp, window);
  76
  77                         temp = validParameter.validFile(parameters, "increment", false);                if (temp == "not found") { temp = "25"; }
  78                         convert(temp, increment);
  79                 }
  80         }
  81         catch(exception& e) {
  82                 m->errorOut(e, "ChimeraBellerophonCommand", "ChimeraBellerophonCommand");
  83                 exit(1);
  84         }
  85 }
  86 //**********************************************************************************************************************
  87
  88 void ChimeraBellerophonCommand::help(){
  89         try {
  90                 m->mothurOut("The chimera.bellerophon command reads a fastafile and creates list of potentially chimeric sequences.\n");
  91                 m->mothurOut("The chimera.bellerophon command parameters are fasta, filter, correction, processors, window, increment. The fasta parameter is required.\n");
  92                 m->mothurOut("The filter parameter allows you to specify if you would like to apply a vertical and 50% soft filter, default=false. \n");
  93                 m->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, default=true.\n");
  94                 m->mothurOut("The processors parameter allows you to specify how many processors you would like to use.  The default is 1. \n");
  95                 #ifdef USE_MPI
  96                 m->mothurOut("When using MPI, the processors parameter is set to the number of MPI processes running. \n");
  97                 #endif
  98                 m->mothurOut("The window parameter allows you to specify the window size for searching for chimeras, default is 1/4 sequence length. \n");
  99                 m->mothurOut("The increment parameter allows you to specify how far you move each window while finding chimeric sequences, default is 25.\n");
 100                 m->mothurOut("chimera.bellerophon(fasta=yourFastaFile, filter=yourFilter, correction=yourCorrection, processors=yourProcessors) \n");
 101                 m->mothurOut("Example: chimera.seqs(fasta=AD.align, filter=True, correction=true, window=200) \n");
 102                 m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n\n");
 103         }
 104         catch(exception& e) {
 105                 m->errorOut(e, "ChimeraBellerophonCommand", "help");
 106                 exit(1);
 107         }
 108 }
 109
 110 //***************************************************************************************************************
 111
 112 ChimeraBellerophonCommand::~ChimeraBellerophonCommand(){        /*      do nothing      */      }
 113
 114 //***************************************************************************************************************
 115
 116 int ChimeraBellerophonCommand::execute(){
 117         try{
 118
 119                 if (abort == true) { return 0; }
 120
 121                 int start = time(NULL);
 122
 123                 chimera = new Bellerophon(fastafile, filter, correction, window, increment, processors, outputDir);
 124
 125                 string outputFileName = outputDir + getRootName(getSimpleName(fastafile)) +  "bellerophon.chimeras";
 126                 string accnosFileName = outputDir + getRootName(getSimpleName(fastafile)) + "bellerophon.accnos";
 127                 bool hasAccnos = true;
 128
 129                 chimera->getChimeras();
 130
 131                 if (m->control_pressed) { delete chimera;       return 0;       }
 132
 133         #ifdef USE_MPI
 134                 MPI_File outMPI;
 135                 MPI_File outMPIAccnos;
 136
 137                 int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 138
 139                 //char* outFilename = new char[accnosFileName.length()];
 140                 //memcpy(outFilename, accnosFileName.c_str(), accnosFileName.length());
 141
 142                 char outFilename[1024];
 143                 strcpy(outFilename, accnosFileName.c_str());
 144
 145                 //char* FileName = new char[outputFileName.length()];
 146                 //memcpy(FileName, outputFileName.c_str(), outputFileName.length());
 147
 148                 char FileName[1024];
 149                 strcpy(FileName, outputFileName.c_str());
 150
 151                 MPI_File_open(MPI_COMM_WORLD, FileName, outMode, MPI_INFO_NULL, &outMPI);  //comm, filename, mode, info, filepointer
 152                 MPI_File_open(MPI_COMM_WORLD, outFilename, outMode, MPI_INFO_NULL, &outMPIAccnos);
 153
 154                 //delete FileName;
 155                 //delete outFilename;
 156
 157                 numSeqs = chimera->print(outMPI, outMPIAccnos);
 158
 159                 MPI_File_close(&outMPI);
 160                 MPI_File_close(&outMPIAccnos);
 161
 162         #else
 163
 164                 ofstream out;
 165                 openOutputFile(outputFileName, out);
 166
 167                 ofstream out2;
 168                 openOutputFile(accnosFileName, out2);
 169
 170                 numSeqs = chimera->print(out, out2);
 171                 out.close();
 172                 out2.close();
 173
 174         #endif
 175
 176                 if (m->control_pressed) { remove(accnosFileName.c_str()); remove(outputFileName.c_str()); delete chimera;       return 0;       }
 177
 178                 //delete accnos file if its blank
 179                 if (isBlank(accnosFileName)) {  remove(accnosFileName.c_str());  hasAccnos = false; }
 180
 181                 m->mothurOutEndLine();
 182                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 183                 m->mothurOut(outputFileName); m->mothurOutEndLine();
 184                 if (hasAccnos) {  m->mothurOut(accnosFileName); m->mothurOutEndLine();  }
 185                 m->mothurOutEndLine();
 186                 m->mothurOutEndLine(); m->mothurOut("It took " + toString(time(NULL) - start) + " secs to check " + toString(numSeqs) + " sequences."); m->mothurOutEndLine();
 187
 188                 delete chimera;
 189
 190                 return 0;
 191
 192         }
 193         catch(exception& e) {
 194                 m->errorOut(e, "ChimeraBellerophonCommand", "execute");
 195                 exit(1);
 196         }
 197 }
 198 //**********************************************************************************************************************
 199