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