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 vector<string> DeconvoluteCommand::getValidParameters(){
  14         try {
  15                 string Array[] =  {"fasta", "name","outputdir","inputdir"};
  16                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  17                 return myArray;
  18         }
  19         catch(exception& e) {
  20                 m->errorOut(e, "DeconvoluteCommand", "getValidParameters");
  21                 exit(1);
  22         }
  23 }
  24 //**********************************************************************************************************************
  25 DeconvoluteCommand::DeconvoluteCommand(){
  26         try {
  27                 abort = true; calledHelp = true;
  28                 vector<string> tempOutNames;
  29                 outputTypes["fasta"] = tempOutNames;
  30                 outputTypes["name"] = tempOutNames;
  31         }
  32         catch(exception& e) {
  33                 m->errorOut(e, "DeconvoluteCommand", "DeconvoluteCommand");
  34                 exit(1);
  35         }
  36 }
  37 //**********************************************************************************************************************
  38 vector<string> DeconvoluteCommand::getRequiredParameters(){
  39         try {
  40                 string Array[] =  {"fasta"};
  41                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  42                 return myArray;
  43         }
  44         catch(exception& e) {
  45                 m->errorOut(e, "DeconvoluteCommand", "getRequiredParameters");
  46                 exit(1);
  47         }
  48 }
  49 //**********************************************************************************************************************
  50 vector<string> DeconvoluteCommand::getRequiredFiles(){
  51         try {
  52                 vector<string> myArray;
  53                 return myArray;
  54         }
  55         catch(exception& e) {
  56                 m->errorOut(e, "DeconvoluteCommand", "getRequiredFiles");
  57                 exit(1);
  58         }
  59 }
  60 /**************************************************************************************/
  61 DeconvoluteCommand::DeconvoluteCommand(string option)  {
  62         try {
  63                 abort = false; calledHelp = false;
  64
  65                 //allow user to run help
  66                 if(option == "help") { help(); abort = true; calledHelp = true; }
  67
  68                 else {
  69                         //valid paramters for this command
  70                         string Array[] =  {"fasta", "name","outputdir","inputdir"};
  71                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  72
  73                         OptionParser parser(option);
  74                         map<string,string> parameters = parser.getParameters();
  75
  76                         ValidParameters validParameter;
  77                         map<string, string>::iterator it;
  78
  79                         //check to make sure all parameters are valid for command
  80                         for (it = parameters.begin(); it != parameters.end(); it++) {
  81                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  82                         }
  83
  84                         //initialize outputTypes
  85                         vector<string> tempOutNames;
  86                         outputTypes["fasta"] = tempOutNames;
  87                         outputTypes["name"] = tempOutNames;
  88
  89                         //if the user changes the input directory command factory will send this info to us in the output parameter
  90                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
  91                         if (inputDir == "not found"){   inputDir = "";          }
  92                         else {
  93                                 string path;
  94                                 it = parameters.find("fasta");
  95                                 //user has given a template file
  96                                 if(it != parameters.end()){
  97                                         path = m->hasPath(it->second);
  98                                         //if the user has not given a path then, add inputdir. else leave path alone.
  99                                         if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
 100                                 }
 101
 102                                 it = parameters.find("name");
 103                                 //user has given a template file
 104                                 if(it != parameters.end()){
 105                                         path = m->hasPath(it->second);
 106                                         //if the user has not given a path then, add inputdir. else leave path alone.
 107                                         if (path == "") {       parameters["name"] = inputDir + it->second;             }
 108                                 }
 109                         }
 110
 111
 112                         //check for required parameters
 113                         inFastaName = validParameter.validFile(parameters, "fasta", true);
 114                         if (inFastaName == "not open") { abort = true; }
 115                         else if (inFastaName == "not found") { inFastaName = ""; m->mothurOut("fasta is a required parameter for the unique.seqs command."); m->mothurOutEndLine(); abort = true;  }
 116
 117                         //if the user changes the output directory command factory will send this info to us in the output parameter
 118                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
 119                                 outputDir = "";
 120                                 outputDir += m->hasPath(inFastaName); //if user entered a file with a path then preserve it
 121                         }
 122
 123                         oldNameMapFName = validParameter.validFile(parameters, "name", true);
 124                         if (oldNameMapFName == "not open") { abort = true; }
 125                         else if (oldNameMapFName == "not found"){       oldNameMapFName = "";   }
 126                 }
 127
 128         }
 129         catch(exception& e) {
 130                 m->errorOut(e, "DeconvoluteCommand", "DeconvoluteCommand");
 131                 exit(1);
 132         }
 133 }
 134 //**********************************************************************************************************************
 135
 136 void DeconvoluteCommand::help(){
 137         try {
 138                 m->mothurOut("The unique.seqs command reads a fastafile and creates a namesfile.\n");
 139                 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");
 140                 m->mothurOut("If the sequence is unique the second column will just contain its name. \n");
 141                 m->mothurOut("The unique.seqs command parameter is fasta and it is required.\n");
 142                 m->mothurOut("The unique.seqs command should be in the following format: \n");
 143                 m->mothurOut("unique.seqs(fasta=yourFastaFile) \n");
 144         }
 145         catch(exception& e) {
 146                 m->errorOut(e, "DeconvoluteCommand", "help");
 147                 exit(1);
 148         }
 149 }
 150
 151 /**************************************************************************************/
 152 int DeconvoluteCommand::execute() {
 153         try {
 154
 155                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 156
 157                 //prepare filenames and open files
 158                 string outNameFile = outputDir + m->getRootName(m->getSimpleName(inFastaName)) + "names";
 159                 string outFastaFile = outputDir + m->getRootName(m->getSimpleName(inFastaName)) + "unique" + m->getExtension(inFastaName);
 160
 161                 FastaMap fastamap;
 162
 163                 if(oldNameMapFName == "")       {       fastamap.readFastaFile(inFastaName);                                    }
 164                 else                                            {       fastamap.readFastaFile(inFastaName, oldNameMapFName);   }
 165
 166                 if (m->control_pressed) { return 0; }
 167
 168                 fastamap.printCondensedFasta(outFastaFile);
 169                 fastamap.printNamesFile(outNameFile);
 170
 171                 if (m->control_pressed) { outputTypes.clear(); remove(outFastaFile.c_str()); remove(outNameFile.c_str()); return 0; }
 172
 173                 m->mothurOutEndLine();
 174                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 175                 m->mothurOut(outFastaFile); m->mothurOutEndLine();
 176                 m->mothurOut(outNameFile); m->mothurOutEndLine();
 177                 outputNames.push_back(outFastaFile);  outputNames.push_back(outNameFile); outputTypes["fasta"].push_back(outFastaFile);  outputTypes["name"].push_back(outNameFile);
 178                 m->mothurOutEndLine();
 179
 180                 //set fasta file as new current fastafile
 181                 string current = "";
 182                 itTypes = outputTypes.find("fasta");
 183                 if (itTypes != outputTypes.end()) {
 184                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
 185                 }
 186
 187                 itTypes = outputTypes.find("name");
 188                 if (itTypes != outputTypes.end()) {
 189                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setNameFile(current); }
 190                 }
 191
 192                 return 0;
 193         }
 194         catch(exception& e) {
 195                 m->errorOut(e, "DeconvoluteCommand", "execute");
 196                 exit(1);
 197         }
 198 }
 199 /**************************************************************************************/