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(string option){
  15         try {
  16                 globaldata = GlobalData::getInstance();
  17                 abort = false;
  18
  19                 //allow user to run help
  20                 if(option == "help") { help(); abort = true; }
  21
  22                 else {
  23                         //valid paramters for this command
  24                         string Array[] =  {"fasta", "trump", "soft", "hard", "vertical"};
  25                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  26
  27                         parser = new OptionParser();
  28                         parser->parse(option, parameters);  delete parser;
  29
  30                         ValidParameters* validParameter = new ValidParameters();
  31
  32                         //check to make sure all parameters are valid for command
  33                         for (it = parameters.begin(); it != parameters.end(); it++) {
  34                                 if (validParameter->isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  35                         }
  36
  37                         //check for required parameters
  38                         fastafile = validParameter->validFile(parameters, "fasta", true);
  39                         if (fastafile == "not found") { cout << "fasta is a required parameter for the filter.seqs command." << endl; abort = true; }
  40                         else if (fastafile == "not open") { abort = true; }
  41                         else {
  42                                 globaldata->setFastaFile(fastafile);
  43                         }
  44
  45                         //check for optional parameter and set defaults
  46                         // ...at some point should added some additional type checking...
  47
  48                         string temp;
  49                         temp = validParameter->validFile(parameters, "trump", false);                           if (temp == "not found") { temp = "."; }
  50                         trump = temp[0];
  51
  52                         temp = validParameter->validFile(parameters, "soft", false);                            if (temp == "not found") { soft = 0; }
  53                         else {  soft = (float)atoi(temp.c_str()) / 100.0;  }
  54
  55                         hard = validParameter->validFile(parameters, "hard", true);                                     if (hard == "not found") { hard = ""; }
  56                         else if (hard == "not open") { abort = true; }
  57
  58                         vertical = validParameter->validFile(parameters, "vertical", false);            if (vertical == "not found") { vertical = "F"; }
  59
  60                         delete validParameter;
  61
  62                         numSeqs = 0;
  63
  64                 }
  65
  66         }
  67         catch(exception& e) {
  68                 cout << "Standard Error: " << e.what() << " has occurred in the FilterSeqsCommand class Function FilterSeqsCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  69                 exit(1);
  70         }
  71         catch(...) {
  72                 cout << "An unknown error has occurred in the FilterSeqsCommand class function FilterSeqsCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  73                 exit(1);
  74         }
  75 }
  76
  77 //**********************************************************************************************************************
  78
  79 void FilterSeqsCommand::help(){
  80         try {
  81                 cout << "The filter.seqs command reads a file containing sequences and creates a .filter and .filter.fasta file." << "\n";
  82                 cout << "The filter.seqs command parameters are fasta, trump, soft, hard and vertical.  " << "\n";
  83                 cout << "The fasta parameter is required." << "\n";
  84                 cout << "The trump parameter .... The default is '.'" << "\n";
  85                 cout << "The soft parameter .... The default is ...." << "\n";
  86                 cout << "The hard parameter .... The default is ...." << "\n";
  87                 cout << "The vertical parameter .... The default is F." << "\n";
  88                 cout << "The filter.seqs command should be in the following format: " << "\n";
  89                 cout << "filter.seqs(fasta=yourFastaFile, trump=yourTrump, soft=yourSoft, hard=yourHard, vertical=yourVertical) " << "\n";
  90                 cout << "Example filter.seqs(fasta=abrecovery.fasta, trump=..., soft=..., hard=..., vertical=T)." << "\n";
  91                 cout << "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta)." << "\n" << "\n";
  92
  93         }
  94         catch(exception& e) {
  95                 cout << "Standard Error: " << e.what() << " has occurred in the FilterSeqsCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  96                 exit(1);
  97         }
  98         catch(...) {
  99                 cout << "An unknown error has occurred in the FilterSeqsCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 100                 exit(1);
 101         }
 102 }
 103
 104 /**************************************************************************************/
 105
 106 void FilterSeqsCommand::doHard() {
 107
 108         ifstream fileHandle;
 109         openInputFile(hard, fileHandle);
 110
 111         fileHandle >> filter;
 112
 113 }
 114
 115 /**************************************************************************************/
 116
 117 void FilterSeqsCommand::doTrump(Sequence seq) {
 118
 119         string curAligned = seq.getAligned();
 120
 121         for(int j = 0; j < alignmentLength; j++) {
 122                 if(curAligned[j] == trump){
 123                         filter[j] = '0';
 124                 }
 125         }
 126
 127 }
 128
 129 /**************************************************************************************/
 130
 131 void FilterSeqsCommand::doVertical() {
 132
 133         for(int i=0;i<alignmentLength;i++){
 134                 if(gap[i] == numSeqs)   {       filter[i] = '0';        }
 135         }
 136
 137 }
 138
 139 /**************************************************************************************/
 140
 141 void FilterSeqsCommand::doSoft() {
 142
 143         int threshold = int (soft * numSeqs);
 144         bool keep = 0;
 145
 146         for(int i=0;i<alignmentLength;i++){
 147                 if(a[i] >= threshold)           {       keep = 1;       }
 148                 else if(t[i] >= threshold)      {       keep = 1;       }
 149                 else if(g[i] >= threshold)      {       keep = 1;       }
 150                 else if(c[i] >= threshold)      {       keep = 1;       }
 151
 152                 if(keep == 0)   {       filter[i] = 0;          }
 153         }
 154 }
 155
 156 /**************************************************************************************/
 157
 158 void FilterSeqsCommand::getFreqs(Sequence seq) {
 159
 160         string curAligned = seq.getAligned();;
 161
 162         for(int j=0;j<alignmentLength;j++){
 163                 if(toupper(curAligned[j]) == 'A')                                                                               {       a[j]++;         }
 164                 else if(toupper(curAligned[j]) == 'T' || toupper(curAligned[j]) == 'U') {       t[j]++;         }
 165                 else if(toupper(curAligned[j]) == 'G')                                                                  {       g[j]++;         }
 166                 else if(toupper(curAligned[j]) == 'C')                                                                  {       c[j]++;         }
 167                 else if(curAligned[j] == '-' || curAligned[j] == '.')                                   {       gap[j]++;       }
 168         }
 169
 170 }
 171
 172 /**************************************************************************************/
 173
 174 int FilterSeqsCommand::execute() {
 175         try {
 176
 177                 if (abort == true) { return 0; }
 178
 179                 ifstream inFASTA;
 180                 openInputFile(fastafile, inFASTA);
 181
 182                 Sequence testSeq(inFASTA);
 183                 alignmentLength = testSeq.getAlignLength();
 184                 inFASTA.seekg(0);
 185
 186                 if(soft != 0 || isTrue(vertical)){
 187                         a.assign(alignmentLength, 0);
 188                         t.assign(alignmentLength, 0);
 189                         g.assign(alignmentLength, 0);
 190                         c.assign(alignmentLength, 0);
 191                         gap.assign(alignmentLength, 0);
 192                 }
 193
 194                 if(hard.compare("") != 0)       {       doHard();               }
 195                 else                                            {       filter = string(alignmentLength, '1');  }
 196
 197                 if(isTrue(vertical) || soft != 0){
 198
 199                         while(!inFASTA.eof()){
 200                                 Sequence seq(inFASTA);
 201                                 doTrump(seq);
 202                                 if(isTrue(vertical) || soft != 0){      getFreqs(seq);  }
 203                                 numSeqs++;
 204                                 cout.flush();
 205                         }
 206
 207                 }
 208                 inFASTA.close();
 209
 210                 if(isTrue(vertical) == 1)       {       doVertical();   }
 211                 if(soft != 0)   {       doSoft();               }
 212
 213                 ofstream outFilter;
 214                 string filterFile = getRootName(fastafile) + "filter";
 215                 openOutputFile(filterFile, outFilter);
 216                 outFilter << filter << endl;
 217                 outFilter.close();
 218
 219
 220                 openInputFile(fastafile, inFASTA);
 221                 string filteredFasta = getRootName(fastafile) + "filter.fasta";
 222                 ofstream outFASTA;
 223                 openOutputFile(filteredFasta, outFASTA);
 224
 225                 numSeqs = 0;
 226                 while(!inFASTA.eof()){
 227                         Sequence seq(inFASTA);
 228                         string align = seq.getAligned();
 229                         string filterSeq = "";
 230
 231                         for(int j=0;j<alignmentLength;j++){
 232                                 if(filter[j] == '1'){
 233                                         filterSeq += align[j];
 234                                 }
 235                         }
 236
 237                         outFASTA << '>' << seq.getName() << endl << filterSeq << endl;
 238                         numSeqs++;
 239                         gobble(inFASTA);
 240                 }
 241                 outFASTA.close();
 242                 inFASTA.close();
 243
 244
 245                 int filteredLength = 0;
 246                 for(int i=0;i<alignmentLength;i++){
 247                         if(filter[i] == '1'){   filteredLength++;       }
 248                 }
 249
 250                 cout << endl;
 251                 cout << "Length of filtered alignment: " << filteredLength << endl;
 252                 cout << "Number of columns removed: " << alignmentLength-filteredLength << endl;
 253                 cout << "Length of the original alignment: " << alignmentLength << endl;
 254                 cout << "Number of sequences used to construct filter: " << numSeqs << endl;
 255
 256                 globaldata->clear();
 257
 258                 return 0;
 259
 260         }
 261         catch(exception& e) {
 262                 cout << "Standard Error: " << e.what() << " has occurred in the FilterSeqsCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 263                 exit(1);
 264         }
 265         catch(...) {
 266                 cout << "An unknown error has occurred in the FilterSeqsCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 267                 exit(1);
 268         }
 269 }
 270
 271 /**************************************************************************************/