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 #include "sequence.hpp"
  12
  13 /**************************************************************************************/
  14
  15 FilterSeqsCommand::FilterSeqsCommand(string option)  {
  16         try {
  17                 abort = false;
  18                 filterFileName = "";
  19
  20                 //allow user to run help
  21                 if(option == "help") { help(); abort = true; }
  22
  23                 else {
  24                         //valid paramters for this command
  25                         string Array[] =  {"fasta", "trump", "soft", "hard", "vertical", "outputdir","inputdir"};
  26                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  27
  28                         OptionParser parser(option);
  29                         map<string,string> parameters = parser.getParameters();
  30
  31                         ValidParameters validParameter;
  32                         map<string,string>::iterator it;
  33
  34                         //check to make sure all parameters are valid for command
  35                         for (it = parameters.begin(); it != parameters.end(); it++) {
  36                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  37                         }
  38
  39                         //if the user changes the input directory command factory will send this info to us in the output parameter
  40                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
  41                         if (inputDir == "not found"){   inputDir = "";          }
  42                         else {
  43                                 string path;
  44                                 it = parameters.find("fasta");
  45                                 //user has given a template file
  46                                 if(it != parameters.end()){
  47                                         path = hasPath(it->second);
  48                                         //if the user has not given a path then, add inputdir. else leave path alone.
  49                                         if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
  50                                 }
  51
  52                                 it = parameters.find("hard");
  53                                 //user has given a template file
  54                                 if(it != parameters.end()){
  55                                         path = hasPath(it->second);
  56                                         //if the user has not given a path then, add inputdir. else leave path alone.
  57                                         if (path == "") {       parameters["hard"] = inputDir + it->second;             }
  58                                 }
  59                         }
  60
  61                         //check for required parameters
  62                         fasta = validParameter.validFile(parameters, "fasta", false);
  63                         if (fasta == "not found") { m->mothurOut("fasta is a required parameter for the filter.seqs command."); m->mothurOutEndLine(); abort = true;  }
  64                         else {
  65                                 splitAtDash(fasta, fastafileNames);
  66
  67                                 //go through files and make sure they are good, if not, then disregard them
  68                                 for (int i = 0; i < fastafileNames.size(); i++) {
  69                                         if (inputDir != "") {
  70                                                 string path = hasPath(fastafileNames[i]);
  71                                                 //if the user has not given a path then, add inputdir. else leave path alone.
  72                                                 if (path == "") {       fastafileNames[i] = inputDir + fastafileNames[i];               }
  73                                         }
  74
  75                                         int ableToOpen;
  76                                         ifstream in;
  77                                         ableToOpen = openInputFile(fastafileNames[i], in);
  78                                         if (ableToOpen == 1) {
  79                                                 m->mothurOut(fastafileNames[i] + " will be disregarded."); m->mothurOutEndLine();
  80                                                 //erase from file list
  81                                                 fastafileNames.erase(fastafileNames.begin()+i);
  82                                                 i--;
  83                                         }else{
  84                                                 string simpleName = getSimpleName(fastafileNames[i]);
  85                                                 filterFileName += simpleName.substr(0, simpleName.find_first_of('.'));
  86                                         }
  87                                         in.close();
  88                                 }
  89
  90                                 //make sure there is at least one valid file left
  91                                 if (fastafileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
  92                         }
  93
  94                         if (!abort) {
  95                                 //if the user changes the output directory command factory will send this info to us in the output parameter
  96                                 outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
  97                                         outputDir = "";
  98                                         outputDir += hasPath(fastafileNames[0]); //if user entered a file with a path then preserve it
  99                                 }
 100                         }
 101                         //check for optional parameter and set defaults
 102                         // ...at some point should added some additional type checking...
 103
 104                         string temp;
 105                         temp = validParameter.validFile(parameters, "trump", false);                    if (temp == "not found") { temp = "*"; }
 106                         trump = temp[0];
 107
 108                         temp = validParameter.validFile(parameters, "soft", false);                             if (temp == "not found") { soft = 0; }
 109                         else {  soft = (float)atoi(temp.c_str()) / 100.0;  }
 110
 111                         hard = validParameter.validFile(parameters, "hard", true);                              if (hard == "not found") { hard = ""; }
 112                         else if (hard == "not open") { abort = true; }
 113
 114                         vertical = validParameter.validFile(parameters, "vertical", false);             if (vertical == "not found") { vertical = "T"; }
 115
 116                         numSeqs = 0;
 117
 118                         if (abort == false) {
 119
 120                                 if (soft != 0)                  {  F.setSoft(soft);             }
 121                                 if (trump != '*')               {  F.setTrump(trump);   }
 122
 123                         }
 124
 125                 }
 126
 127         }
 128         catch(exception& e) {
 129                 m->errorOut(e, "FilterSeqsCommand", "FilterSeqsCommand");
 130                 exit(1);
 131         }
 132 }
 133
 134 //**********************************************************************************************************************
 135
 136 void FilterSeqsCommand::help(){
 137         try {
 138                 m->mothurOut("The filter.seqs command reads a file containing sequences and creates a .filter and .filter.fasta file.\n");
 139                 m->mothurOut("The filter.seqs command parameters are fasta, trump, soft, hard and vertical. \n");
 140                 m->mothurOut("The fasta parameter is required. You may enter several fasta files to build the filter from and filter, by separating their names with -'s.\n");
 141                 m->mothurOut("For example: fasta=abrecovery.fasta-amazon.fasta \n");
 142                 m->mothurOut("The trump parameter .... The default is ...\n");
 143                 m->mothurOut("The soft parameter .... The default is ....\n");
 144                 m->mothurOut("The hard parameter .... The default is ....\n");
 145                 m->mothurOut("The vertical parameter .... The default is T.\n");
 146                 m->mothurOut("The filter.seqs command should be in the following format: \n");
 147                 m->mothurOut("filter.seqs(fasta=yourFastaFile, trump=yourTrump, soft=yourSoft, hard=yourHard, vertical=yourVertical) \n");
 148                 m->mothurOut("Example filter.seqs(fasta=abrecovery.fasta, trump=..., soft=..., hard=..., vertical=T).\n");
 149                 m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n");
 150
 151         }
 152         catch(exception& e) {
 153                 m->errorOut(e, "FilterSeqsCommand", "help");
 154                 exit(1);
 155         }
 156 }
 157
 158 /**************************************************************************************/
 159
 160 int FilterSeqsCommand::execute() {
 161         try {
 162
 163                 if (abort == true) { return 0; }
 164                 vector<string> outputNames;
 165
 166                 ifstream inFASTA;
 167                 openInputFile(fastafileNames[0], inFASTA);
 168
 169                 Sequence testSeq(inFASTA);
 170                 alignmentLength = testSeq.getAlignLength();
 171                 inFASTA.close();
 172
 173                 F.setLength(alignmentLength);
 174
 175                 if(soft != 0 || isTrue(vertical)){
 176                         F.initialize();
 177                 }
 178
 179                 if(hard.compare("") != 0)       {       F.doHard(hard);         }
 180                 else                                            {       F.setFilter(string(alignmentLength, '1'));      }
 181
 182                 if(trump != '*' || isTrue(vertical) || soft != 0){
 183                         for (int i = 0; i < fastafileNames.size(); i++) {
 184                                 ifstream in;
 185                                 openInputFile(fastafileNames[i], in);
 186
 187                                 while(!in.eof()){       //read through and create the filter...
 188                                         Sequence seq(in);
 189                                         if (seq.getName() != "") {
 190                                                 if(trump != '*'){       F.doTrump(seq); }
 191                                                 if(isTrue(vertical) || soft != 0){      F.getFreqs(seq);        }
 192                                                 numSeqs++;
 193                                                 cout.flush();
 194                                         }
 195                                 }
 196                                 in.close();
 197                         }
 198
 199                 }
 200                 F.setNumSeqs(numSeqs);
 201
 202
 203                 if(isTrue(vertical) == 1)       {       F.doVertical(); }
 204                 if(soft != 0)                           {       F.doSoft();             }
 205
 206                 filter = F.getFilter();
 207
 208                 ofstream outFilter;
 209
 210                 string filterFile = outputDir + filterFileName + ".filter";
 211                 openOutputFile(filterFile, outFilter);
 212                 outFilter << filter << endl;
 213                 outFilter.close();
 214                 outputNames.push_back(filterFile);
 215
 216                 numSeqs = 0;
 217                 for (int i = 0; i < fastafileNames.size(); i++) {
 218                         ifstream in;
 219                         openInputFile(fastafileNames[i], in);
 220                         string filteredFasta = outputDir + getRootName(getSimpleName(fastafileNames[i])) + "filter.fasta";
 221                         ofstream outFASTA;
 222                         openOutputFile(filteredFasta, outFASTA);
 223                         outputNames.push_back(filteredFasta);
 224
 225
 226                         while(!in.eof()){
 227                                 Sequence seq(in);
 228                                 if (seq.getName() != "") {
 229                                         string align = seq.getAligned();
 230                                         string filterSeq = "";
 231
 232                                         for(int j=0;j<alignmentLength;j++){
 233                                                 if(filter[j] == '1'){
 234                                                         filterSeq += align[j];
 235                                                 }
 236                                         }
 237
 238                                         outFASTA << '>' << seq.getName() << endl << filterSeq << endl;
 239                                         numSeqs++;
 240                                 }
 241                                 gobble(in);
 242                         }
 243                         outFASTA.close();
 244                         in.close();
 245                 }
 246
 247                 int filteredLength = 0;
 248                 for(int i=0;i<alignmentLength;i++){
 249                         if(filter[i] == '1'){   filteredLength++;       }
 250                 }
 251
 252                 m->mothurOutEndLine();
 253                 m->mothurOut("Length of filtered alignment: " + toString(filteredLength)); m->mothurOutEndLine();
 254                 m->mothurOut("Number of columns removed: " + toString((alignmentLength-filteredLength))); m->mothurOutEndLine();
 255                 m->mothurOut("Length of the original alignment: " + toString(alignmentLength)); m->mothurOutEndLine();
 256                 m->mothurOut("Number of sequences used to construct filter: " + toString(numSeqs)); m->mothurOutEndLine();
 257
 258
 259                 m->mothurOutEndLine();
 260                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 261                 for(int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();      }
 262                 m->mothurOutEndLine();
 263
 264                 return 0;
 265
 266         }
 267         catch(exception& e) {
 268                 m->errorOut(e, "FilterSeqsCommand", "execute");
 269                 exit(1);
 270         }
 271 }
 272
 273 /**************************************************************************************/