preclustercommand.cpp

   1 /*
   2  *  preclustercommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by westcott on 12/21/09.
   6  *  Copyright 2009 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "preclustercommand.h"
  11
  12 //**********************************************************************************************************************
  13 inline bool comparePriority(seqPNode first, seqPNode second) {  return (first.numIdentical > second.numIdentical); }
  14 //**********************************************************************************************************************
  15
  16 PreClusterCommand::PreClusterCommand(string option){
  17         try {
  18                 abort = false;
  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", "name", "diffs"};
  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
  33                         //check to make sure all parameters are valid for command
  34                         for (map<string, string>::iterator it2 = parameters.begin(); it2 != parameters.end(); it2++) {
  35                                 if (validParameter.isValidParameter(it2->first, myArray, it2->second) != true) {  abort = true;  }
  36                         }
  37
  38                         //check for required parameters
  39                         fastafile = validParameter.validFile(parameters, "fasta", true);
  40                         if (fastafile == "not found") { mothurOut("fasta is a required parameter for the pre.cluster command."); mothurOutEndLine(); abort = true; }
  41                         else if (fastafile == "not open") { abort = true; }
  42
  43                         //check for optional parameter and set defaults
  44                         // ...at some point should added some additional type checking...
  45                         namefile = validParameter.validFile(parameters, "name", true);
  46                         if (namefile == "not found") { namefile =  "";  }
  47                         else if (namefile == "not open") { abort = true; }
  48                         else {  readNameFile();  }
  49
  50                         string temp     = validParameter.validFile(parameters, "diffs", false);                         if(temp == "not found"){        temp = "1"; }
  51                         convert(temp, diffs);
  52                 }
  53
  54         }
  55         catch(exception& e) {
  56                 errorOut(e, "PreClusterCommand", "PreClusterCommand");
  57                 exit(1);
  58         }
  59 }
  60
  61 //**********************************************************************************************************************
  62 PreClusterCommand::~PreClusterCommand(){}
  63 //**********************************************************************************************************************
  64
  65 void PreClusterCommand::help(){
  66         try {
  67                 mothurOut("The pre.cluster command groups sequences that are within a given number of base mismatches.\n");
  68                 mothurOut("The pre.cluster command outputs a new fasta and name file.\n");
  69                 mothurOut("The pre.cluster command parameters are fasta, names and diffs. The fasta parameter is required. \n");
  70                 mothurOut("The names parameter allows you to give a list of seqs that are identical. This file is 2 columns, first column is name or representative sequence, second column is a list of its identical sequences separated by commas.\n");
  71                 mothurOut("The diffs parameter allows you to specify maximum number of mismatched bases allowed between sequences in a grouping. The default is 1.\n");
  72                 mothurOut("The pre.cluster command should be in the following format: \n");
  73                 mothurOut("pre.cluster(fasta=yourFastaFile, names=yourNamesFile, diffs=yourMaxDiffs) \n");
  74                 mothurOut("Example pre.cluster(fasta=amazon.fasta, diffs=2).\n");
  75                 mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n");
  76         }
  77         catch(exception& e) {
  78                 errorOut(e, "PreClusterCommand", "help");
  79                 exit(1);
  80         }
  81 }
  82 //**********************************************************************************************************************
  83
  84 int PreClusterCommand::execute(){
  85         try {
  86
  87                 if (abort == true) { return 0; }
  88
  89                 //reads fasta file and return number of seqs
  90                 int numSeqs = readSeqs(); //fills alignSeqs and makes all seqs active
  91
  92                 if (numSeqs == 0) { mothurOut("Error reading fasta file...please correct."); mothurOutEndLine(); return 0;  }
  93                 if (diffs > length) { mothurOut("Error: diffs is greater than your sequence length."); mothurOutEndLine(); return 0;  }
  94
  95                 //clear sizes since you only needed this info to build the alignSeqs seqPNode structs
  96                 sizes.clear();
  97
  98                 //sort seqs by number of identical seqs
  99                 sort(alignSeqs.begin(), alignSeqs.end(), comparePriority);
 100
 101                 //go through active list and cluster everthing you can, until all nodes are inactive
 102                 //taking advantage of the fact that maps are already sorted
 103                 map<string, bool>::iterator itActive;
 104                 map<string, bool>::iterator it2Active;
 105                 int count = 0;
 106
 107                 for (int i = 0; i < alignSeqs.size(); i++) {
 108
 109                         //are you active
 110                         itActive = active.find(alignSeqs[i].seq.getName());
 111
 112                         if (itActive != active.end()) {  //this sequence has not been merged yet
 113
 114                                 //try to merge it with all smaller seqs
 115                                 for (int j = i; j < alignSeqs.size(); j++) {
 116
 117                                         if (i != j) {
 118                                                 //are you active
 119                                                 it2Active = active.find(alignSeqs[j].seq.getName());
 120                                                 if (it2Active != active.end()) {  //this sequence has not been merged yet
 121                                                         //are you within "diff" bases
 122                                                         int mismatch = calcMisMatches(alignSeqs[i].seq.getAligned(), alignSeqs[j].seq.getAligned());
 123
 124                                                         if (mismatch <= diffs) {
 125                                                                 //merge
 126                                                                 names[alignSeqs[i].seq.getName()] += "," + names[alignSeqs[j].seq.getName()];
 127
 128                                                                 //remove from active list
 129                                                                 active.erase(it2Active);
 130
 131                                                                 //set numIdentical to 0, so you only print the representative seqs in the fasta file
 132                                                                 alignSeqs[j].numIdentical = 0;
 133                                                                 count++;
 134                                                         }
 135                                                 }//end if j active
 136                                         }//end if i != j
 137                                 }//end for loop
 138
 139                                 //remove from active list
 140                                 active.erase(itActive);
 141                         }//end if active i
 142                 }
 143
 144                 string newFastaFile = getRootName(fastafile) + "precluster" + getExtension(fastafile);
 145                 string newNamesFile = getRootName(fastafile) + "precluster.names";
 146
 147                 printData(newFastaFile, newNamesFile);
 148
 149                 mothurOut("Total number of sequences before precluster was " + toString(alignSeqs.size()) + "."); mothurOutEndLine();
 150                 mothurOut("pre.cluster removed " + toString(count) + " sequences."); mothurOutEndLine();
 151
 152                 return 0;
 153
 154         }
 155         catch(exception& e) {
 156                 errorOut(e, "PreClusterCommand", "execute");
 157                 exit(1);
 158         }
 159 }
 160 /**************************************************************************************************/
 161 int PreClusterCommand::readSeqs(){
 162         try {
 163                 ifstream inFasta;
 164                 openInputFile(fastafile, inFasta);
 165                 length = 0;
 166                 map<string, string>::iterator it;
 167
 168                 while (!inFasta.eof()) {
 169                         Sequence temp(inFasta);  //read seq
 170
 171                         if (temp.getName() != "") {
 172                                 if (namefile != "") {
 173                                         //make sure fasta and name files match
 174                                         it = names.find(temp.getName());
 175                                         if (it == names.end()) { mothurOut(temp.getName() + " is not in your names file, please correct."); mothurOutEndLine(); exit(1); }
 176                                 }else { sizes[temp.getName()] = 1; }
 177
 178                                 seqPNode tempNode(sizes[temp.getName()], temp);
 179                                 alignSeqs.push_back(tempNode);
 180                                 active[temp.getName()] = true;
 181                         }
 182                         gobble(inFasta);
 183                 }
 184                 inFasta.close();
 185
 186                 if (alignSeqs.size() != 0) {  length = alignSeqs[0].seq.getAligned().length();  }
 187
 188                 return alignSeqs.size();
 189         }
 190         catch(exception& e) {
 191                 errorOut(e, "PreClusterCommand", "readSeqs");
 192                 exit(1);
 193         }
 194 }
 195 /**************************************************************************************************/
 196 void PreClusterCommand::readNameFile(){
 197         try {
 198                 ifstream in;
 199                 openInputFile(namefile, in);
 200                 string firstCol, secondCol;
 201
 202                 while (!in.eof()) {
 203                         in >> firstCol >> secondCol; gobble(in);
 204                         names[firstCol] = secondCol;
 205                         int size = 1;
 206                         while (secondCol.find_first_of(',') != -1) {
 207                                 size++;
 208                                 secondCol = secondCol.substr(secondCol.find_first_of(',')+1, secondCol.length());
 209                         }
 210                         sizes[firstCol] = size;
 211                 }
 212                 in.close();
 213         }
 214         catch(exception& e) {
 215                 errorOut(e, "PreClusterCommand", "readNameFile");
 216                 exit(1);
 217         }
 218 }
 219 /**************************************************************************************************/
 220 int PreClusterCommand::calcMisMatches(string seq1, string seq2){
 221         try {
 222                 int numBad = 0;
 223
 224                 for (int i = 0; i < seq1.length(); i++) {
 225                         //do they match
 226                         if (seq1[i] != seq2[i]) { numBad++; }
 227                         if (numBad > diffs) { return length;  } //to far to cluster
 228                 }
 229
 230                 return numBad;
 231         }
 232         catch(exception& e) {
 233                 errorOut(e, "PreClusterCommand", "calcMisMatches");
 234                 exit(1);
 235         }
 236 }
 237 /**************************************************************************************************/
 238 void PreClusterCommand::printData(string newfasta, string newname){
 239         try {
 240                 ofstream outFasta;
 241                 ofstream outNames;
 242                 openOutputFile(newfasta, outFasta);
 243                 openOutputFile(newname, outNames);
 244
 245                 map<string, string>::iterator itNames;
 246
 247                 for (int i = 0; i < alignSeqs.size(); i++) {
 248                         if (alignSeqs[i].numIdentical != 0) {
 249                                 alignSeqs[i].seq.printSequence(outFasta);
 250
 251                                 itNames = names.find(alignSeqs[i].seq.getName());
 252
 253                                 outNames << itNames->first << '\t' << itNames->second << endl;
 254                         }
 255                 }
 256
 257                 outFasta.close();
 258                 outNames.close();
 259
 260         }
 261         catch(exception& e) {
 262                 errorOut(e, "PreClusterCommand", "printData");
 263                 exit(1);
 264         }
 265 }
 266
 267 /**************************************************************************************************/
 268
 269