screenseqscommand.h

   1 #ifndef SCREENSEQSCOMMAND_H
   2 #define SCREENSEQSCOMMAND_H
   3
   4 /*
   5  *  screenseqscommand.h
   6  *  Mothur
   7  *
   8  *  Created by Pat Schloss on 6/3/09.
   9  *  Copyright 2009 Patrick D. Schloss. All rights reserved.
  10  *
  11  */
  12 #include "mothur.h"
  13 #include "command.hpp"
  14 #include "sequence.hpp"
  15
  16 class ScreenSeqsCommand : public Command {
  17
  18 public:
  19         ScreenSeqsCommand(string);
  20         ScreenSeqsCommand();
  21         ~ScreenSeqsCommand() {}
  22
  23         vector<string> setParameters();
  24         string getCommandName()                 { return "screen.seqs";                         }
  25         string getCommandCategory()             { return "Sequence Processing";         }
  26         string getHelpString();
  27         string getCitation() { return "http://www.mothur.org/wiki/Screen.seqs"; }
  28         string getDescription()         { return "enables you to keep sequences that fulfill certain user defined criteria"; }
  29
  30         int execute();
  31         void help() { m->mothurOut(getHelpString()); }
  32
  33
  34 private:
  35
  36         struct linePair {
  37                 unsigned long long start;
  38                 unsigned long long end;
  39                 linePair(unsigned long long i, unsigned long long j) : start(i), end(j) {}
  40         };
  41
  42         vector<linePair> lines;
  43
  44         int screenNameGroupFile(set<string>);
  45         int screenGroupFile(set<string>);
  46         int screenAlignReport(set<string>);
  47         int screenQual(set<string>);
  48         int screenTaxonomy(set<string>);
  49
  50         int driver(linePair, string, string, string, set<string>&);
  51         int createProcesses(string, string, string, set<string>&);
  52
  53         #ifdef USE_MPI
  54         int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, vector<unsigned long long>&, set<string>&);
  55         #endif
  56
  57         bool abort;
  58         string fastafile, namefile, groupfile, alignreport, outputDir, qualfile, taxonomy;
  59         int startPos, endPos, maxAmbig, maxHomoP, minLength, maxLength, processors, criteria;
  60         vector<string> outputNames;
  61         vector<string> optimize;
  62         map<string, int> nameMap;
  63
  64         int getSummary(vector<unsigned long long>&);
  65         int createProcessesCreateSummary(vector<int>&, vector<int>&, vector<int>&, vector<int>&, vector<int>&, string);
  66         int driverCreateSummary(vector<int>&, vector<int>&, vector<int>&, vector<int>&, vector<int>&, string, linePair);
  67 };
  68
  69 /**************************************************************************************************/
  70 //custom data structure for threads to use.
  71 // This is passed by void pointer so it can be any data type
  72 // that can be passed using a single void pointer (LPVOID).
  73 struct sumData {
  74         vector<int> startPosition;
  75         vector<int> endPosition;
  76         vector<int> seqLength;
  77         vector<int> ambigBases;
  78         vector<int> longHomoPolymer;
  79         string filename, namefile;
  80         unsigned long long start;
  81         unsigned long long end;
  82         int count;
  83         MothurOut* m;
  84         map<string, int> nameMap;
  85
  86
  87         sumData(){}
  88         sumData(string f, MothurOut* mout, unsigned long long st, unsigned long long en, string nf, map<string, int> nam) {
  89                 filename = f;
  90         namefile = nf;
  91                 m = mout;
  92                 start = st;
  93                 end = en;
  94                 nameMap = nam;
  95                 count = 0;
  96         }
  97 };
  98 /**************************************************************************************************/
  99 //custom data structure for threads to use.
 100 // This is passed by void pointer so it can be any data type
 101 // that can be passed using a single void pointer (LPVOID).
 102 struct sumScreenData {
 103     int startPos, endPos, maxAmbig, maxHomoP, minLength, maxLength;
 104         unsigned long long start;
 105         unsigned long long end;
 106         int count;
 107         MothurOut* m;
 108         string goodFName, badAccnosFName, filename;
 109     set<string> badSeqNames;
 110
 111
 112         sumScreenData(){}
 113         sumScreenData(int s, int e, int a, int h, int minl, int maxl, string f, MothurOut* mout, unsigned long long st, unsigned long long en, string gf, string bf) {
 114                 startPos = s;
 115                 endPos = e;
 116                 minLength = minl;
 117         maxLength = maxl;
 118                 maxAmbig = a;
 119                 maxHomoP = h;
 120                 filename = f;
 121         goodFName = gf;
 122         badAccnosFName = bf;
 123                 m = mout;
 124                 start = st;
 125                 end = en;
 126                 count = 0;
 127         }
 128 };
 129
 130
 131 /**************************************************************************************************/
 132 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 133 #else
 134 static DWORD WINAPI MySumThreadFunction(LPVOID lpParam){
 135         sumData* pDataArray;
 136         pDataArray = (sumData*)lpParam;
 137
 138         try {
 139                 ifstream in;
 140                 pDataArray->m->openInputFile(pDataArray->filename, in);
 141
 142                 //print header if you are process 0
 143                 if ((pDataArray->start == 0) || (pDataArray->start == 1)) {
 144                         in.seekg(0);
 145                 }else { //this accounts for the difference in line endings.
 146                         in.seekg(pDataArray->start-1); pDataArray->m->gobble(in);
 147                 }
 148
 149                 pDataArray->count = pDataArray->end;
 150                 for(int i = 0; i < pDataArray->end; i++){ //end is the number of sequences to process
 151
 152                         if (pDataArray->m->control_pressed) { in.close();  pDataArray->count = 1; return 1; }
 153
 154                         Sequence current(in); pDataArray->m->gobble(in);
 155
 156                         if (current.getName() != "") {
 157
 158                                 int num = 1;
 159                                 if (pDataArray->namefile != "") {
 160                                         //make sure this sequence is in the namefile, else error
 161                                         map<string, int>::iterator it = pDataArray->nameMap.find(current.getName());
 162
 163                                         if (it == pDataArray->nameMap.end()) { pDataArray->m->mothurOut("[ERROR]: " + current.getName() + " is not in your namefile, please correct."); pDataArray->m->mothurOutEndLine(); pDataArray->m->control_pressed = true; }
 164                                         else { num = it->second; }
 165                                 }
 166
 167                                 //for each sequence this sequence represents
 168                                 for (int i = 0; i < num; i++) {
 169                                         pDataArray->startPosition.push_back(current.getStartPos());
 170                                         pDataArray->endPosition.push_back(current.getEndPos());
 171                                         pDataArray->seqLength.push_back(current.getNumBases());
 172                                         pDataArray->ambigBases.push_back(current.getAmbigBases());
 173                                         pDataArray->longHomoPolymer.push_back(current.getLongHomoPolymer());
 174                                 }
 175             }
 176                 }
 177
 178                 in.close();
 179
 180                 return 0;
 181
 182         }
 183         catch(exception& e) {
 184                 pDataArray->m->errorOut(e, "ScreenSeqsCommand", "MySumThreadFunction");
 185                 exit(1);
 186         }
 187 }
 188
 189 /**************************************************************************************************/
 190
 191 static DWORD WINAPI MySumScreenThreadFunction(LPVOID lpParam){
 192         sumScreenData* pDataArray;
 193         pDataArray = (sumScreenData*)lpParam;
 194
 195         try {
 196
 197         ofstream goodFile;
 198                 pDataArray->m->openOutputFile(pDataArray->goodFName, goodFile);
 199
 200                 ofstream badAccnosFile;
 201                 pDataArray->m->openOutputFile(pDataArray->badAccnosFName, badAccnosFile);
 202
 203                 ifstream in;
 204                 pDataArray->m->openInputFile(pDataArray->filename, in);
 205
 206                 //print header if you are process 0
 207                 if ((pDataArray->start == 0) || (pDataArray->start == 1)) {
 208                         in.seekg(0);
 209                 }else { //this accounts for the difference in line endings.
 210                         in.seekg(pDataArray->start-1); pDataArray->m->gobble(in);
 211                 }
 212
 213                 pDataArray->count = pDataArray->end;
 214                 for(int i = 0; i < pDataArray->end; i++){ //end is the number of sequences to process
 215
 216                         if (pDataArray->m->control_pressed) { in.close(); badAccnosFile.close(); goodFile.close(); pDataArray->count = 1; return 1; }
 217
 218                         Sequence currSeq(in); pDataArray->m->gobble(in);
 219
 220                         if (currSeq.getName() != "") {
 221                                 bool goodSeq = 1;               //      innocent until proven guilty
 222                                 if(goodSeq == 1 && pDataArray->startPos != -1 && pDataArray->startPos < currSeq.getStartPos())                  {       goodSeq = 0;    }
 223                                 if(goodSeq == 1 && pDataArray->endPos != -1 && pDataArray->endPos > currSeq.getEndPos())                                {       goodSeq = 0;    }
 224                                 if(goodSeq == 1 && pDataArray->maxAmbig != -1 && pDataArray->maxAmbig < currSeq.getAmbigBases())                {       goodSeq = 0;    }
 225                                 if(goodSeq == 1 && pDataArray->maxHomoP != -1 && pDataArray->maxHomoP < currSeq.getLongHomoPolymer())   {       goodSeq = 0;    }
 226                                 if(goodSeq == 1 && pDataArray->minLength != -1 && pDataArray->minLength > currSeq.getNumBases())                {       goodSeq = 0;    }
 227                                 if(goodSeq == 1 && pDataArray->maxLength != -1 && pDataArray->maxLength < currSeq.getNumBases())                {       goodSeq = 0;    }
 228
 229                                 if(goodSeq == 1){
 230                                         currSeq.printSequence(goodFile);
 231                                 }
 232                                 else{
 233                                         badAccnosFile << currSeq.getName() << endl;
 234                                         pDataArray->badSeqNames.insert(currSeq.getName());
 235                                 }
 236
 237                         }
 238             //report progress
 239                         if((i+1) % 100 == 0){   pDataArray->m->mothurOut("Processing sequence: " + toString(i+1)); pDataArray->m->mothurOutEndLine();           }
 240                 }
 241                 //report progress
 242                 if((pDataArray->count) % 100 != 0){     pDataArray->m->mothurOut("Processing sequence: " + toString(pDataArray->count)); pDataArray->m->mothurOutEndLine();             }
 243
 244
 245
 246                 in.close();
 247         goodFile.close();
 248         badAccnosFile.close();
 249
 250                 return 0;
 251
 252         }
 253         catch(exception& e) {
 254                 pDataArray->m->errorOut(e, "ScreenSeqsCommand", "MySumScreenThreadFunction");
 255                 exit(1);
 256         }
 257 }
 258
 259 #endif
 260
 261 /**************************************************************************************************/
 262
 263
 264
 265 #endif