filterseqscommand.cpp

   1 /*
   2  *  filterseqscommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by Thomas Ryabin on 5/4/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "filterseqscommand.h"
  11
  12 /**************************************************************************************/
  13
  14 FilterSeqsCommand::FilterSeqsCommand(){
  15         globaldata = GlobalData::getInstance();
  16
  17         if(globaldata->getFastaFile() == "")            {       cout << "You must enter a fasta formatted file" << endl;        }
  18         trump = globaldata->getTrump()[0];
  19         vertical =
  20 //      readSeqs->read();
  21 //      db = readSeqs->getDB();
  22 //      numSeqs = db->size();
  23 //
  24 //      alignmentLength = db->get(0).getAlignLength();
  25 //
  26 //      filter = string(alignmentLength, '1');
  27 }
  28
  29 /**************************************************************************************/
  30
  31 void FilterSeqsCommand::doHard() {
  32
  33 //      string hardName = globaldata->getHard();
  34 //      string hardFilter = "";
  35 //
  36 //      ifstream fileHandle;
  37 //      openInputFile(hardName, fileHandle);
  38 //
  39 //      fileHandle >> hardFilter;
  40 //
  41 //      if(hardFilter.length() != filter.length()){
  42 //              cout << "The hard filter is not the same length as the alignment: Hard filter will not be applied." << endl;
  43 //      }
  44 //      else{
  45 //              filter = hardFilter;
  46 //      }
  47
  48 }
  49
  50 /**************************************************************************************/
  51
  52 void FilterSeqsCommand::doTrump() {
  53
  54
  55         for(int i = 0; i < numSeqs; i++) {
  56                 string curAligned = db->get(i).getAligned();;
  57
  58                 for(int j = 0; j < alignmentLength; j++) {
  59                         if(curAligned[j] == trump){
  60                                 filter[j] = '0';
  61                         }
  62                 }
  63         }
  64
  65 }
  66
  67 /**************************************************************************************/
  68
  69 void FilterSeqsCommand::doVertical() {
  70
  71 //      vector<int> counts(alignmentLength, 0);
  72 //
  73 //      for(int i = 0; i < numSeqs; i++) {
  74 //              string curAligned = db->get(i).getAligned();;
  75 //
  76 //              for(int j = 0; j < alignmentLength; j++) {
  77 //                      if(curAligned[j] == '-' || curAligned[j] == '.'){
  78 //                              counts[j]++;
  79 //                      }
  80 //              }
  81 //      }
  82 //      for(int i=0;i<alignmentLength;i++){
  83 //              if(counts[i] == numSeqs)        {       filter[i] = '0';                }
  84 //      }
  85 }
  86
  87 /**************************************************************************************/
  88
  89 void FilterSeqsCommand::doSoft() {
  90
  91 //      int softThreshold = numSeqs * (float)atoi(globaldata->getSoft().c_str()) / 100.0;
  92 //
  93 //      vector<int> a(alignmentLength, 0);
  94 //      vector<int> t(alignmentLength, 0);
  95 //      vector<int> g(alignmentLength, 0);
  96 //      vector<int> c(alignmentLength, 0);
  97 //      vector<int> x(alignmentLength, 0);
  98 //
  99 //      for(int i=0;i<numSeqs;i++){
 100 //              string curAligned = db->get(i).getAligned();;
 101 //
 102 //              for(int j=0;j<alignmentLength;j++){
 103 //                      if(toupper(curAligned[j]) == 'A')                                                                               {       a[j]++; }
 104 //                      else if(toupper(curAligned[j]) == 'T' || toupper(curAligned[i]) == 'U') {       t[j]++; }
 105 //                      else if(toupper(curAligned[j]) == 'G')                                                                  {       g[j]++; }
 106 //                      else if(toupper(curAligned[j]) == 'C')                                                                  {       c[j]++; }
 107 //              }
 108 //      }
 109 //
 110 //      for(int i=0;i<alignmentLength;i++){
 111 //              if(a[i] < softThreshold && t[i] < softThreshold && g[i] < softThreshold && c[i] < softThreshold){
 112 //                      filter[i] = '0';
 113 //              }
 114 //      }
 115 }
 116
 117 /**************************************************************************************/
 118
 119 int FilterSeqsCommand::execute() {
 120         try {
 121
 122                 ifstream inFASTA;
 123                 openInputFile(globaldata->getFastaFile(), inFASTA);
 124
 125                 Sequence currSequence(inFASTA);
 126                 alignmentLength = currSequence.getAlignLength();
 127
 128                 //while
 129
 130
 131                 if(globaldata->getHard().compare("") != 0)      {       doHard();               }       //      has to be applied first!
 132                 if(globaldata->getTrump().compare("") != 0)     {       doTrump();              }
 133                 if(isTrue(globaldata->getVertical()))           {       doVertical();   }
 134                 if(globaldata->getSoft().compare("") != 0)      {       doSoft();               }
 135
 136
 137
 138
 139
 140
 141
 142                 ofstream outfile;
 143                 string filterFile = getRootName(globaldata->inputFileName) + "filter";
 144                 openOutputFile(filterFile, outfile);
 145
 146                 outfile << filter << endl;
 147                 outfile.close();
 148
 149                 string filteredFasta = getRootName(globaldata->inputFileName) + "filter.fasta";
 150                 openOutputFile(filteredFasta, outfile);
 151
 152                 for(int i=0;i<numSeqs;i++){
 153                         string curAligned = db->get(i).getAligned();
 154                         outfile << '>' << db->get(i).getName() << endl;
 155                         for(int j=0;j<alignmentLength;j++){
 156                                 if(filter[j] == '1'){
 157                                         outfile << curAligned[j];
 158                                 }
 159                         }
 160                         outfile << endl;
 161                 }
 162                 outfile.close();
 163
 164                 int filteredLength = 0;
 165                 for(int i=0;i<alignmentLength;i++){
 166                         if(filter[i] == '1'){   filteredLength++;       }
 167                 }
 168
 169                 cout << endl;
 170                 cout << "Length of filtered alignment: " << filteredLength << endl;
 171                 cout << "Number of columns removed: " << alignmentLength-filteredLength << endl;
 172                 cout << "Length of the original alignment: " << alignmentLength << endl;
 173                 cout << "Number of sequences used to construct filter: " << numSeqs << endl;
 174
 175                 globaldata->clear();
 176
 177                 return 0;
 178
 179         }
 180         catch(exception& e) {
 181                 cout << "Standard Error: " << e.what() << " has occurred in the FilterSeqsCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 182                 exit(1);
 183         }
 184         catch(...) {
 185                 cout << "An unknown error has occurred in the FilterSeqsCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 186                 exit(1);
 187         }
 188 }
 189
 190 /**************************************************************************************/