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