chimeracheckrdp.cpp

   1 /*
   2  *  chimeracheckrdp.cpp
   3  *  Mothur
   4  *
   5  *  Created by westcott on 9/8/09.
   6  *  Copyright 2009 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "chimeracheckrdp.h"
  11
  12 //***************************************************************************************************************
  13 ChimeraCheckRDP::ChimeraCheckRDP(string filename,  string o) {  fastafile = filename;  outputDir = o;  }
  14 //***************************************************************************************************************
  15
  16 ChimeraCheckRDP::~ChimeraCheckRDP() {
  17         try {
  18                 delete templateDB;
  19                 delete kmer;
  20         }
  21         catch(exception& e) {
  22                 errorOut(e, "ChimeraCheckRDP", "~AlignSim");
  23                 exit(1);
  24         }
  25 }
  26 //***************************************************************************************************************
  27 void ChimeraCheckRDP::print(ostream& out) {
  28         try {
  29
  30                 mothurOut("Processing: " + querySeq->getName()); mothurOutEndLine();
  31
  32                 out << querySeq->getName() << endl;
  33                 out << "IS scores: " << '\t';
  34
  35                 for (int k = 0; k < IS.size(); k++) {
  36                         out << IS[k].score << '\t';
  37                 }
  38                 out << endl;
  39
  40                 if (svg) {
  41                         if (name != "") { //if user has specific names
  42                                 map<string, string>::iterator it = names.find(querySeq->getName());
  43
  44                                 if (it != names.end()) { //user wants pic of this
  45                                         makeSVGpic(IS);  //zeros out negative results
  46                                 }
  47                         }else{//output them all
  48                                 makeSVGpic(IS);  //zeros out negative results
  49                         }
  50                 }
  51         }
  52         catch(exception& e) {
  53                 errorOut(e, "ChimeraCheckRDP", "print");
  54                 exit(1);
  55         }
  56 }
  57 //***************************************************************************************************************
  58 void ChimeraCheckRDP::doPrep() {
  59         try {
  60                 templateDB = new AlignmentDB(templateFileName, "kmer", kmerSize, 0.0,0.0,0.0,0.0);
  61                 mothurOutEndLine();
  62
  63                 kmer = new Kmer(kmerSize);
  64
  65                 if (name != "") {
  66                         readName(name);  //fills name map with names of seqs the user wants to have .svg for.
  67                 }
  68         }
  69         catch(exception& e) {
  70                 errorOut(e, "ChimeraCheckRDP", "doPrep");
  71                 exit(1);
  72         }
  73 }
  74 //***************************************************************************************************************
  75 int ChimeraCheckRDP::getChimeras(Sequence* query) {
  76         try {
  77
  78                 IS.clear();
  79
  80                 querySeq = query;
  81
  82                 closest = templateDB->findClosestSequence(query);
  83
  84                 IS = findIS();
  85
  86                 //determine chimera report cutoff - window score above 95%
  87                 //getCutoff();  - not very acurate predictor
  88
  89                 return 0;
  90         }
  91         catch(exception& e) {
  92                 errorOut(e, "ChimeraCheckRDP", "getChimeras");
  93                 exit(1);
  94         }
  95 }
  96 //***************************************************************************************************************
  97 vector<sim> ChimeraCheckRDP::findIS() {
  98         try {
  99
 100
 101                 vector< map<int, int> > queryKmerInfo;  //vector of maps - each entry in the vector is a map of the kmers up to that spot in the unaligned seq
 102                                                                                                 //example:  seqKmerInfo[50] = map containing the kmers found in the first 50 + kmersize characters of ecoli.
 103                                                                                                 //i chose to store the kmers numbers in a map so you wouldn't have to check for dupilcate entries and could easily find the
 104                                                                                                 //kmers 2 seqs had in common.  There may be a better way to do this thats why I am leaving so many comments...
 105                 vector< map<int, int> > subjectKmerInfo;
 106
 107                 vector<sim>  isValues;
 108                 string queryName = querySeq->getName();
 109                 string seq = querySeq->getUnaligned();
 110
 111                 queryKmerInfo = kmer->getKmerCounts(seq);
 112                 subjectKmerInfo = kmer->getKmerCounts(closest.getUnaligned());
 113
 114                 //find total kmers you have in common with closest[query] by looking at the last entry in the vector of maps for each
 115                 int nTotal = calcKmers(queryKmerInfo[(queryKmerInfo.size()-1)], subjectKmerInfo[(subjectKmerInfo.size()-1)]);
 116
 117                 //you don't want the starting point to be virtually at hte end so move it in 10%
 118                 int start = seq.length() / 10;
 119
 120                 //for each window
 121                 for (int m = start; m < (seq.length() - start); m+=increment) {
 122
 123                         if ((m - kmerSize) < 0)  { mothurOut("Your sequence is too short for your kmerSize."); mothurOutEndLine(); exit(1); }
 124
 125                         sim temp;
 126
 127                         string fragLeft = seq.substr(0, m);  //left side of breakpoint
 128                         string fragRight = seq.substr(m);  //right side of breakpoint
 129
 130                         //make a sequence of the left side and right side
 131                         Sequence* left = new Sequence(queryName, fragLeft);
 132                         Sequence* right = new Sequence(queryName, fragRight);
 133
 134                         //find seqs closest to each fragment
 135                         Sequence closestLeft = templateDB->findClosestSequence(left);
 136
 137                         Sequence closestRight = templateDB->findClosestSequence(right);
 138
 139                         //get kmerinfo for the closest left
 140                         vector< map<int, int> > closeLeftKmerInfo = kmer->getKmerCounts(closestLeft.getUnaligned());
 141
 142                         //get kmerinfo for the closest right
 143                         vector< map<int, int> > closeRightKmerInfo = kmer->getKmerCounts(closestRight.getUnaligned());
 144
 145                         //right side is tricky - since the counts grow on eachother to find the correct counts of only the right side you must subtract the counts of the left side
 146                         //iterate through left sides map to subtract the number of times you saw things before you got the the right side
 147                         map<int, int> rightside = queryKmerInfo[queryKmerInfo.size()-1];
 148                         for (map<int, int>::iterator itleft = queryKmerInfo[m-kmerSize].begin(); itleft != queryKmerInfo[m-kmerSize].end(); itleft++) {
 149                                 int howManyTotal = queryKmerInfo[queryKmerInfo.size()-1][itleft->first];   //times that kmer was seen in total
 150
 151                                 //itleft->second is times it was seen in left side, so howmanytotal - leftside should give you right side
 152                                 int howmanyright = howManyTotal - itleft->second;
 153
 154                                 //if any were seen just on the left erase
 155                                 if (howmanyright == 0) {
 156                                         rightside.erase(itleft->first);
 157                                 }
 158                         }
 159
 160                         map<int, int> closerightside = closeRightKmerInfo[closeRightKmerInfo.size()-1];
 161                         for (map<int, int>::iterator itright = closeRightKmerInfo[m-kmerSize].begin(); itright != closeRightKmerInfo[m-kmerSize].end(); itright++) {
 162                                 int howManyTotal = closeRightKmerInfo[(closeRightKmerInfo.size()-1)][itright->first];   //times that kmer was seen in total
 163
 164                                 //itleft->second is times it was seen in left side, so howmanytotal - leftside should give you right side
 165                                 int howmanyright = howManyTotal - itright->second;
 166
 167                                 //if any were seen just on the left erase
 168                                 if (howmanyright == 0) {
 169                                         closerightside.erase(itright->first);
 170                                 }
 171                         }
 172
 173
 174                         int nLeft = calcKmers(closeLeftKmerInfo[m-kmerSize], queryKmerInfo[m-kmerSize]);
 175
 176                         int nRight = calcKmers(closerightside, rightside);
 177
 178                         int is = nLeft + nRight - nTotal;
 179
 180                         //save IS, leftparent, rightparent, breakpoint
 181                         temp.leftParent = closestLeft.getName();
 182                         temp.rightParent = closestRight.getName();
 183                         temp.score = is;
 184                         temp.midpoint = m;
 185
 186                         isValues.push_back(temp);
 187
 188                         delete left;
 189                         delete right;
 190                 }
 191
 192                 return isValues;
 193
 194         }
 195         catch(exception& e) {
 196                 errorOut(e, "ChimeraCheckRDP", "findIS");
 197                 exit(1);
 198         }
 199 }
 200 //***************************************************************************************************************
 201 void ChimeraCheckRDP::readName(string namefile) {
 202         try{
 203                 ifstream in;
 204                 openInputFile(namefile, in);
 205                 string name;
 206
 207                 while (!in.eof()) {
 208
 209                         in >> name;
 210
 211                         names[name] = name;
 212
 213                         gobble(in);
 214                 }
 215
 216         }
 217         catch(exception& e) {
 218                 errorOut(e, "ChimeraCheckRDP", "readName");
 219                 exit(1);
 220         }
 221 }
 222
 223 //***************************************************************************************************************
 224 //find the smaller map and iterate through it and count kmers in common
 225 int ChimeraCheckRDP::calcKmers(map<int, int> query, map<int, int> subject) {
 226         try{
 227
 228                 int common = 0;
 229                 map<int, int>::iterator small;
 230                 map<int, int>::iterator large;
 231
 232                 if (query.size() < subject.size()) {
 233
 234                         for (small = query.begin(); small != query.end(); small++) {
 235                                 large = subject.find(small->first);
 236
 237                                 //if you found it they have that kmer in common
 238                                 if (large != subject.end()) {   common++;       }
 239                         }
 240
 241                 }else {
 242
 243                         for (small = subject.begin(); small != subject.end(); small++) {
 244                                 large = query.find(small->first);
 245
 246                                 //if you found it they have that kmer in common
 247                                 if (large != query.end()) {             common++;        }
 248                         }
 249                 }
 250
 251                 return common;
 252
 253         }
 254         catch(exception& e) {
 255                 errorOut(e, "ChimeraCheckRDP", "calcKmers");
 256                 exit(1);
 257         }
 258 }
 259
 260 //***************************************************************************************************************
 261 void ChimeraCheckRDP::makeSVGpic(vector<sim> info) {
 262         try{
 263
 264                 string file = outputDir + querySeq->getName() + ".chimeracheck.svg";
 265                 ofstream outsvg;
 266                 openOutputFile(file, outsvg);
 267
 268                 int width = (info.size()*5) + 150;
 269
 270                 outsvg << "<svg xmlns:svg=\"http://www.w3.org/2000/svg\" xmlns=\"http://www.w3.org/2000/svg\" width=\"100%\" height=\"100%\" viewBox=\"0 0 700 " + toString(width) + "\">\n";
 271                 outsvg << "<g>\n";
 272                 outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString((width / 2) - 150) + "\" y=\"25\">Plotted IS values for " + querySeq->getName() + "</text>\n";
 273
 274                 outsvg <<  "<line x1=\"75\" y1=\"600\" x2=\"" + toString((info.size()*5) + 75) + "\" y2=\"600\" stroke=\"black\" stroke-width=\"2\"/>\n";
 275                 outsvg <<  "<line x1=\"75\" y1=\"600\" x2=\"75\" y2=\"125\" stroke=\"black\" stroke-width=\"2\"/>\n";
 276
 277                 outsvg << "<text fill=\"black\" class=\"seri\" x=\"80\" y=\"620\">" + toString(info[0].midpoint) + "</text>\n";
 278                 outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString((info.size()*5) + 75) + "\" y=\"620\">" + toString(info[info.size()-1].midpoint) + "</text>\n";
 279                 outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString((width / 2) - 150) + "\" y=\"650\">Base Positions</text>\n";
 280
 281                 outsvg << "<text fill=\"black\" class=\"seri\" x=\"50\" y=\"580\">0</text>\n";
 282
 283                 outsvg << "<text fill=\"black\" class=\"seri\" x=\"50\" y=\"350\">IS</text>\n";
 284
 285
 286                 //find max is score
 287                 float biggest = 0.0;
 288                 for (int i = 0; i < info.size(); i++) {
 289                         if (info[i].score > biggest)  {
 290                                 biggest = info[i].score;
 291                         }
 292                 }
 293
 294                 outsvg << "<text fill=\"black\" class=\"seri\" x=\"50\" y=\"135\">" + toString(biggest) + "</text>\n";
 295
 296                 int scaler2 = 500 / biggest;
 297
 298
 299                 outsvg << "<polyline fill=\"none\" stroke=\"red\" stroke-width=\"2\" points=\"";
 300                 //160,200 180,230 200,210 234,220\"/> ";
 301                 for (int i = 0; i < info.size(); i++) {
 302                         if(info[i].score < 0) { info[i].score = 0; }
 303                         outsvg << ((i*5) + 75) << "," << (600 - (info[i].score * scaler2)) << " ";
 304                 }
 305
 306                 outsvg << "\"/> ";
 307                 outsvg << "</g>\n</svg>\n";
 308
 309                 outsvg.close();
 310
 311         }
 312         catch(exception& e) {
 313                 errorOut(e, "ChimeraCheckRDP", "makeSVGpic");
 314                 exit(1);
 315         }
 316 }
 317 //***************************************************************************************************************
 318
 319