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
  29         string getHelpString();
  30     string getOutputPattern(string);
  31         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"; }
  32         string getDescription()         { return "detects differentially abundant features in clinical metagenomic samples"; }
  33
  34         int execute();
  35         void help() { m->mothurOut(getHelpString()); }
  36
  37 private:
  38         struct linePair {
  39                 int start;
  40                 int num;
  41                 linePair(int i, int j) : start(i), num(j) {}
  42         };
  43         vector<linePair> lines;
  44
  45         GroupMap* designMap;
  46         InputData* input;
  47         vector<SharedRAbundVector*> lookup;
  48
  49         bool abort, allLines, pickedGroups;
  50         set<string> labels; //holds labels to be used
  51         string groups, label, outputDir, inputDir, designfile, sets, sharedfile;
  52         vector<string> Groups, outputNames, Sets;
  53         vector< vector<string> > namesOfGroupCombos;
  54         int iters, processors;
  55         float threshold;
  56
  57         int process(vector<SharedRAbundVector*>&);
  58         int driver(int, int, vector<SharedRAbundVector*>&);
  59     int convertToShared(string filename);
  60     int convertToInput(vector<SharedRAbundVector*>&, string);
  61     bool convertSharedToInput;
  62 };
  63
  64 /**************************************************************************************************/
  65 //custom data structure for threads to use.
  66 // This is passed by void pointer so it can be any data type
  67 // that can be passed using a single void pointer (LPVOID).
  68 struct metastatsData {
  69     vector<SharedRAbundVector*> thisLookUp;
  70     vector< vector<string> > namesOfGroupCombos;
  71     vector<string> designMapGroups;
  72     vector<string> outputNames;
  73         int start;
  74         int num, iters, count;
  75         float threshold;
  76         MothurOut* m;
  77         string sharedfile;
  78     string outputDir;
  79
  80         metastatsData(){}
  81         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) {
  82                 sharedfile = sf;
  83         outputDir = oDir;
  84                 m = mout;
  85                 start = st;
  86                 num = en;
  87         namesOfGroupCombos = ns;
  88         thisLookUp = lu;
  89         designMapGroups = dg;
  90         iters = i;
  91         threshold = thr;
  92         count=0;
  93         }
  94 };
  95 /**************************************************************************************************/
  96 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
  97 #else
  98 static DWORD WINAPI MyMetastatsThreadFunction(LPVOID lpParam){
  99         metastatsData* pDataArray;
 100         pDataArray = (metastatsData*)lpParam;
 101
 102         try {
 103
 104         //for each combo
 105                 for (int c = pDataArray->start; c < (pDataArray->start+pDataArray->num); c++) {
 106                         pDataArray->count++;
 107                         //get set names
 108                         string setA = pDataArray->namesOfGroupCombos[c][0];
 109                         string setB = pDataArray->namesOfGroupCombos[c][1];
 110
 111                         //get filename
 112                         string outputFileName = pDataArray->outputDir +  pDataArray->m->getRootName(pDataArray->m->getSimpleName(pDataArray->sharedfile)) + pDataArray->thisLookUp[0]->getLabel() + "." + setA + "-" + setB + ".metastats";
 113                         pDataArray->outputNames.push_back(outputFileName);
 114
 115                         vector< vector<double> > data2; data2.resize(pDataArray->thisLookUp[0]->getNumBins());
 116
 117                         vector<SharedRAbundVector*> subset;
 118                         int setACount = 0;
 119                         int setBCount = 0;
 120                         for (int i = 0; i < pDataArray->thisLookUp.size(); i++) {
 121                                 //is this group for a set we want to compare??
 122                                 //sorting the sets by putting setB at the back and setA in the front
 123                                 if (pDataArray->designMapGroups[i] == setB) {
 124                                         subset.push_back(pDataArray->thisLookUp[i]);
 125                                         setBCount++;
 126                                 }else if (pDataArray->designMapGroups[i] == setA) {
 127                                         subset.insert(subset.begin()+setACount, pDataArray->thisLookUp[i]);
 128                                         setACount++;
 129                                 }
 130                         }
 131
 132                         if ((setACount == 0) || (setBCount == 0))  {
 133                                 pDataArray->m->mothurOut("Missing shared info for " + setA + " or " + setB + ". Skipping comparison."); pDataArray->m->mothurOutEndLine();
 134                                 pDataArray->outputNames.pop_back();
 135                         }else {
 136                                 //fill data
 137                                 for (int j = 0; j < pDataArray->thisLookUp[0]->getNumBins(); j++) {
 138                                         data2[j].resize(subset.size(), 0.0);
 139                                         for (int i = 0; i < subset.size(); i++) {
 140                                                 data2[j][i] = (subset[i]->getAbundance(j));
 141                                         }
 142                                 }
 143
 144                                 pDataArray->m->mothurOut("Comparing " + setA + " and " + setB + "..."); pDataArray->m->mothurOutEndLine();
 145
 146                                 pDataArray->m->mothurOutEndLine();
 147                                 MothurMetastats mothurMeta(pDataArray->threshold, pDataArray->iters);
 148                                 mothurMeta.runMetastats(outputFileName, data2, setACount);
 149                                 pDataArray->m->mothurOutEndLine();
 150                                 pDataArray->m->mothurOutEndLine();
 151                         }
 152         }
 153
 154                 return 0;
 155
 156         }
 157         catch(exception& e) {
 158                 pDataArray->m->errorOut(e, "MetaStatsCommand", "MyMetastatsThreadFunction");
 159                 exit(1);
 160         }
 161 }
 162 #endif
 163
 164
 165
 166 #endif
 167