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(Sequence seq) {
  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(Sequence seq) {
  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(Sequence seq) {
  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                 ifstream inFASTA;
 122                 openInputFile(globaldata->getFastaFile(), inFASTA);
 123
 124                 Sequence testSeq(inFASTA);
 125                 alignmentLength = testSeq.getAlignLength();
 126                 inFASTA.seekg(0);
 127                 int numSeqs = 0;
 128
 129                 if(globaldata->getHard().compare("") != 0)      {       doHard();                                                               }
 130                 else                                                                            {       filter = string(alignmentLength, '1');  }
 131                 while(!inFASTA.eof()){
 132                         Sequence seq(inFASTA);
 133                         if(globaldata->getTrump().compare("") != 0)     {       doTrump(seq);           }
 134                         if(isTrue(globaldata->getVertical()) == 1)      {       doVertical(seq);        }
 135 //                      if(globaldata->getSoft().compare("") != 0)      {       doSoft(seq);            }
 136                         numSeqs++;
 137                 }
 138
 139                 ofstream outfile;
 140                 string filterFile = getRootName(globaldata->inputFileName) + "filter";
 141                 openOutputFile(filterFile, outfile);
 142
 143                 outfile << filter << endl;
 144                 outfile.close();
 145
 146                 string filteredFasta = getRootName(globaldata->inputFileName) + "filter.fasta";
 147                 openOutputFile(filteredFasta, outfile);
 148
 149 //              for(int i=0;i<numSeqs;i++){
 150 //                      string curAligned = db->get(i).getAligned();
 151 //                      outfile << '>' << db->get(i).getName() << endl;
 152 //                      for(int j=0;j<alignmentLength;j++){
 153 //                              if(filter[j] == '1'){
 154 //                                      outfile << curAligned[j];
 155 //                              }
 156 //                      }
 157 //                      outfile << endl;
 158 //              }
 159 //              outfile.close();
 160
 161                 int filteredLength = 0;
 162                 for(int i=0;i<alignmentLength;i++){
 163                         if(filter[i] == '1'){   filteredLength++;       }
 164                 }
 165
 166                 cout << endl;
 167                 cout << "Length of filtered alignment: " << filteredLength << endl;
 168                 cout << "Number of columns removed: " << alignmentLength-filteredLength << endl;
 169                 cout << "Length of the original alignment: " << alignmentLength << endl;
 170                 cout << "Number of sequences used to construct filter: " << numSeqs << endl;
 171
 172                 globaldata->clear();
 173
 174                 return 0;
 175
 176         }
 177         catch(exception& e) {
 178                 cout << "Standard Error: " << e.what() << " has occurred in the FilterSeqsCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 179                 exit(1);
 180         }
 181         catch(...) {
 182                 cout << "An unknown error has occurred in the FilterSeqsCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 183                 exit(1);
 184         }
 185 }
 186
 187 /**************************************************************************************/