#include "command.hpp"
#include "inputdata.h"
-#include "readotu.h"
#include "sharedrabundvector.h"
-
-class GlobalData;
+#include "mothurmetastats.h"
class MetaStatsCommand : public Command {
public:
MetaStatsCommand(string);
- ~MetaStatsCommand();
- int execute();
- void help();
+ MetaStatsCommand();
+ ~MetaStatsCommand() {}
+
+ vector<string> setParameters();
+ string getCommandName() { return "metastats"; }
+ string getCommandCategory() { return "OTU-Based Approaches"; }
+
+ string getHelpString();
+ string getOutputPattern(string);
+ 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"; }
+ string getDescription() { return "detects differentially abundant features in clinical metagenomic samples"; }
+
+ int execute();
+ void help() { m->mothurOut(getHelpString()); }
private:
- GlobalData* globaldata;
+ struct linePair {
+ int start;
+ int num;
+ linePair(int i, int j) : start(i), num(j) {}
+ };
+ vector<linePair> lines;
+
GroupMap* designMap;
- ReadOTUFile* read;
InputData* input;
vector<SharedRAbundVector*> lookup;
-
+
bool abort, allLines, pickedGroups;
set<string> labels; //holds labels to be used
- string groups, label, outputDir, inputDir, designfile;
- vector<string> Groups, outputNames;
- int iters, g;
+ string groups, label, outputDir, inputDir, designfile, sets, sharedfile;
+ vector<string> Groups, outputNames, Sets;
+ vector< vector<string> > namesOfGroupCombos;
+ int iters, processors;
float threshold;
int process(vector<SharedRAbundVector*>&);
- int eliminateZeroOTUS(vector<SharedRAbundVector*>&);
+ int driver(int, int, vector<SharedRAbundVector*>&);
+ int convertToShared(string filename);
+ int convertToInput(vector<SharedRAbundVector*>&, string);
+ bool convertSharedToInput;
+};
+
+/**************************************************************************************************/
+//custom data structure for threads to use.
+// This is passed by void pointer so it can be any data type
+// that can be passed using a single void pointer (LPVOID).
+struct metastatsData {
+ vector<SharedRAbundVector*> thisLookUp;
+ vector< vector<string> > namesOfGroupCombos;
+ vector<string> designMapGroups;
+ vector<string> outputNames;
+ int start;
+ int num, iters, count;
+ float threshold;
+ MothurOut* m;
+ string sharedfile;
+ string outputDir;
+
+ metastatsData(){}
+ 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) {
+ sharedfile = sf;
+ outputDir = oDir;
+ m = mout;
+ start = st;
+ num = en;
+ namesOfGroupCombos = ns;
+ thisLookUp = lu;
+ designMapGroups = dg;
+ iters = i;
+ threshold = thr;
+ count=0;
+ }
};
+/**************************************************************************************************/
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+#else
+static DWORD WINAPI MyMetastatsThreadFunction(LPVOID lpParam){
+ metastatsData* pDataArray;
+ pDataArray = (metastatsData*)lpParam;
+
+ try {
+
+ //for each combo
+ for (int c = pDataArray->start; c < (pDataArray->start+pDataArray->num); c++) {
+ pDataArray->count++;
+ //get set names
+ string setA = pDataArray->namesOfGroupCombos[c][0];
+ string setB = pDataArray->namesOfGroupCombos[c][1];
+
+ //get filename
+ string outputFileName = pDataArray->outputDir + pDataArray->m->getRootName(pDataArray->m->getSimpleName(pDataArray->sharedfile)) + pDataArray->thisLookUp[0]->getLabel() + "." + setA + "-" + setB + ".metastats";
+ pDataArray->outputNames.push_back(outputFileName);
+
+ vector< vector<double> > data2; data2.resize(pDataArray->thisLookUp[0]->getNumBins());
+
+ vector<SharedRAbundVector*> subset;
+ int setACount = 0;
+ int setBCount = 0;
+ for (int i = 0; i < pDataArray->thisLookUp.size(); i++) {
+ //is this group for a set we want to compare??
+ //sorting the sets by putting setB at the back and setA in the front
+ if (pDataArray->designMapGroups[i] == setB) {
+ subset.push_back(pDataArray->thisLookUp[i]);
+ setBCount++;
+ }else if (pDataArray->designMapGroups[i] == setA) {
+ subset.insert(subset.begin()+setACount, pDataArray->thisLookUp[i]);
+ setACount++;
+ }
+ }
+
+ if ((setACount == 0) || (setBCount == 0)) {
+ pDataArray->m->mothurOut("Missing shared info for " + setA + " or " + setB + ". Skipping comparison."); pDataArray->m->mothurOutEndLine();
+ pDataArray->outputNames.pop_back();
+ }else {
+ //fill data
+ for (int j = 0; j < pDataArray->thisLookUp[0]->getNumBins(); j++) {
+ data2[j].resize(subset.size(), 0.0);
+ for (int i = 0; i < subset.size(); i++) {
+ data2[j][i] = (subset[i]->getAbundance(j));
+ }
+ }
+
+ pDataArray->m->mothurOut("Comparing " + setA + " and " + setB + "..."); pDataArray->m->mothurOutEndLine();
+
+ pDataArray->m->mothurOutEndLine();
+ MothurMetastats mothurMeta(pDataArray->threshold, pDataArray->iters);
+ mothurMeta.runMetastats(outputFileName, data2, setACount);
+ pDataArray->m->mothurOutEndLine();
+ pDataArray->m->mothurOutEndLine();
+ }
+ }
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ pDataArray->m->errorOut(e, "MetaStatsCommand", "MyMetastatsThreadFunction");
+ exit(1);
+ }
+}
+#endif
+
+
#endif
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