metastatscommand.h

   1 #ifndef METASTATSCOMMAND_H
   2 #define METASTATSCOMMAND_H
   3
   4 /*
   5  *  metastatscommand.h
   6  *  Mothur
   7  *
   8  *  Created by westcott on 9/16/10.
   9  *  Copyright 2010 Schloss Lab. All rights reserved.
  10  *
  11  */
  12
  13 #include "command.hpp"
  14 #include "inputdata.h"
  15 #include "sharedrabundvector.h"
  16 #include "mothurmetastats.h"
  17
  18 class MetaStatsCommand : public Command {
  19
  20 public:
  21         MetaStatsCommand(string);
  22         MetaStatsCommand();
  23         ~MetaStatsCommand() {}
  24
  25         vector<string> setParameters();
  26         string getCommandName()                 { return "metastats";                           }
  27         string getCommandCategory()             { return "OTU-Based Approaches";        }
  28         string getHelpString();
  29         string getCitation() { return "White JR, Nagarajan N, Pop M (2009). Statistical methods for detecting differentially abundant features in clinical metagenomic samples. PLoS Comput Biol 5: e1000352. \nhttp://www.mothur.org/wiki/Metastats"; }
  30         string getDescription()         { return "detects differentially abundant features in clinical metagenomic samples"; }
  31
  32         int execute();
  33         void help() { m->mothurOut(getHelpString()); }
  34
  35 private:
  36         struct linePair {
  37                 int start;
  38                 int num;
  39                 linePair(int i, int j) : start(i), num(j) {}
  40         };
  41         vector<linePair> lines;
  42
  43         GroupMap* designMap;
  44         InputData* input;
  45         vector<SharedRAbundVector*> lookup;
  46
  47         bool abort, allLines, pickedGroups;
  48         set<string> labels; //holds labels to be used
  49         string groups, label, outputDir, inputDir, designfile, sets, sharedfile;
  50         vector<string> Groups, outputNames, Sets;
  51         vector< vector<string> > namesOfGroupCombos;
  52         int iters, processors;
  53         float threshold;
  54
  55         int process(vector<SharedRAbundVector*>&);
  56         int driver(int, int, vector<SharedRAbundVector*>&);
  57 };
  58
  59 /**************************************************************************************************/
  60 //custom data structure for threads to use.
  61 // This is passed by void pointer so it can be any data type
  62 // that can be passed using a single void pointer (LPVOID).
  63 struct metastatsData {
  64     vector<SharedRAbundVector*> thisLookUp;
  65     vector< vector<string> > namesOfGroupCombos;
  66     vector<string> designMapGroups;
  67     vector<string> outputNames;
  68         int start;
  69         int num, iters;
  70         float threshold;
  71         MothurOut* m;
  72         string sharedfile;
  73     string outputDir;
  74
  75         metastatsData(){}
  76         metastatsData(string sf, string oDir, MothurOut* mout, int st, int en, vector< vector<string> > ns, vector<SharedRAbundVector*> lu, vector<string> dg, int i, float thr) {
  77                 sharedfile = sf;
  78         outputDir = oDir;
  79                 m = mout;
  80                 start = st;
  81                 num = en;
  82         namesOfGroupCombos = ns;
  83         thisLookUp = lu;
  84         designMapGroups = dg;
  85         iters = i;
  86         threshold = thr;
  87         }
  88 };
  89 /**************************************************************************************************/
  90 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
  91 #else
  92 static DWORD WINAPI MyMetastatsThreadFunction(LPVOID lpParam){
  93         metastatsData* pDataArray;
  94         pDataArray = (metastatsData*)lpParam;
  95
  96         try {
  97
  98         //for each combo
  99                 for (int c = pDataArray->start; c < (pDataArray->start+pDataArray->num); c++) {
 100
 101                         //get set names
 102                         string setA = pDataArray->namesOfGroupCombos[c][0];
 103                         string setB = pDataArray->namesOfGroupCombos[c][1];
 104
 105                         //get filename
 106                         string outputFileName = pDataArray->outputDir +  pDataArray->m->getRootName(pDataArray->m->getSimpleName(pDataArray->sharedfile)) + pDataArray->thisLookUp[0]->getLabel() + "." + setA + "-" + setB + ".metastats";
 107                         pDataArray->outputNames.push_back(outputFileName);
 108
 109                         vector< vector<double> > data2; data2.resize(pDataArray->thisLookUp[0]->getNumBins());
 110
 111                         vector<SharedRAbundVector*> subset;
 112                         int setACount = 0;
 113                         int setBCount = 0;
 114                         for (int i = 0; i < pDataArray->thisLookUp.size(); i++) {
 115                                 //is this group for a set we want to compare??
 116                                 //sorting the sets by putting setB at the back and setA in the front
 117                                 if (pDataArray->designMapGroups[i] == setB) {
 118                                         subset.push_back(pDataArray->thisLookUp[i]);
 119                                         setBCount++;
 120                                 }else if (pDataArray->designMapGroups[i] == setA) {
 121                                         subset.insert(subset.begin()+setACount, pDataArray->thisLookUp[i]);
 122                                         setACount++;
 123                                 }
 124                         }
 125
 126                         if ((setACount == 0) || (setBCount == 0))  {
 127                                 pDataArray->m->mothurOut("Missing shared info for " + setA + " or " + setB + ". Skipping comparison."); pDataArray->m->mothurOutEndLine();
 128                                 pDataArray->outputNames.pop_back();
 129                         }else {
 130                                 //fill data
 131                                 for (int j = 0; j < pDataArray->thisLookUp[0]->getNumBins(); j++) {
 132                                         data2[j].resize(subset.size(), 0.0);
 133                                         for (int i = 0; i < subset.size(); i++) {
 134                                                 data2[j][i] = (subset[i]->getAbundance(j));
 135                                         }
 136                                 }
 137
 138                                 pDataArray->m->mothurOut("Comparing " + setA + " and " + setB + "..."); pDataArray->m->mothurOutEndLine();
 139
 140                                 pDataArray->m->mothurOutEndLine();
 141                                 MothurMetastats mothurMeta(pDataArray->threshold, pDataArray->iters);
 142                                 mothurMeta.runMetastats(outputFileName, data2, setACount);
 143                                 pDataArray->m->mothurOutEndLine();
 144                                 pDataArray->m->mothurOutEndLine();
 145                         }
 146         }
 147
 148                 return 0;
 149
 150         }
 151         catch(exception& e) {
 152                 pDataArray->m->errorOut(e, "MetaStatsCommand", "MyMetastatsThreadFunction");
 153                 exit(1);
 154         }
 155 }
 156 #endif
 157
 158
 159
 160 #endif
 161