*/
#include "metastatscommand.h"
-#include "metastats.h"
#include "sharedutilities.h"
//**********************************************************************************************************************
vector<string> MetaStatsCommand::setParameters(){
try {
- CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pshared);
- CommandParameter pdesign("design", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pdesign);
- CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
- CommandParameter piters("iters", "Number", "", "1000", "", "", "",false,false); parameters.push_back(piters);
- CommandParameter pthreshold("threshold", "Number", "", "0.05", "", "", "",false,false); parameters.push_back(pthreshold);
- CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
- CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
- CommandParameter psets("sets", "String", "", "", "", "", "",false,false); parameters.push_back(psets);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none","metastats",false,true,true); parameters.push_back(pshared);
+ CommandParameter pdesign("design", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(pdesign);
+ CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
+ CommandParameter piters("iters", "Number", "", "1000", "", "", "","",false,false); parameters.push_back(piters);
+ CommandParameter pthreshold("threshold", "Number", "", "0.05", "", "", "","",false,false); parameters.push_back(pthreshold);
+ CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+ CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
+ CommandParameter psets("sets", "String", "", "", "", "", "","",false,false); parameters.push_back(psets);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
+string MetaStatsCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
+
+ if (type == "metastats") { pattern = "[filename],[distance],[group],metastats"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "MetaStatsCommand", "getOutputPattern");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
MetaStatsCommand::MetaStatsCommand(){
try {
abort = true; calledHelp = true;
//only 1 combo
if (numGroups == 2) { processors = 1; }
else if (numGroups < 2) { m->mothurOut("Not enough sets, I need at least 2 valid sets. Unable to complete command."); m->mothurOutEndLine(); m->control_pressed = true; }
-
-// #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
- if(processors != 1){
- int numPairs = namesOfGroupCombos.size();
- int numPairsPerProcessor = numPairs / processors;
+
+ if(processors != 1){
+ int numPairs = namesOfGroupCombos.size();
+ int numPairsPerProcessor = numPairs / processors;
- for (int i = 0; i < processors; i++) {
- int startPos = i * numPairsPerProcessor;
- if(i == processors - 1){
- numPairsPerProcessor = numPairs - i * numPairsPerProcessor;
- }
- lines.push_back(linePair(startPos, numPairsPerProcessor));
- }
- }
-// #endif
+ for (int i = 0; i < processors; i++) {
+ int startPos = i * numPairsPerProcessor;
+ if(i == processors - 1){
+ numPairsPerProcessor = numPairs - i * numPairsPerProcessor;
+ }
+ lines.push_back(linePair(startPos, numPairsPerProcessor));
+ }
+ }
//as long as you are not at the end of the file or done wih the lines you want
while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
}else{
int process = 1;
vector<int> processIDS;
- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
//loop through and create all the processes you want
while (process != processors) {
int pid = fork();
//Close all thread handles and free memory allocations.
for(int i=0; i < pDataArray.size(); i++){
+ if (pDataArray[i]->count != (pDataArray[i]->num)) {
+ m->mothurOut("[ERROR]: process " + toString(i) + " only processed " + toString(pDataArray[i]->count) + " of " + toString(pDataArray[i]->num) + " groups assigned to it, quitting. \n"); m->control_pressed = true;
+ }
for (int j = 0; j < pDataArray[i]->thisLookUp.size(); j++) { delete pDataArray[i]->thisLookUp[j]; }
for (int j = 0; j < pDataArray[i]->outputNames.size(); j++) {
outputNames.push_back(pDataArray[i]->outputNames[j]);
string setB = namesOfGroupCombos[c][1];
//get filename
- string outputFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + thisLookUp[0]->getLabel() + "." + setA + "-" + setB + ".metastats";
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(sharedfile));
+ variables["[distance]"] = thisLookUp[0]->getLabel();
+ variables["[group]"] = setA + "-" + setB;
+ string outputFileName = getOutputFileName("metastats",variables);
outputNames.push_back(outputFileName); outputTypes["metastats"].push_back(outputFileName);
//int nameLength = outputFileName.length();
//char * output = new char[nameLength];
m->mothurOut("Missing shared info for " + setA + " or " + setB + ". Skipping comparison."); m->mothurOutEndLine();
outputNames.pop_back();
}else {
+
//fill data
for (int j = 0; j < thisLookUp[0]->getNumBins(); j++) {
//data[j] = new double[subset.size()];
data2[j].resize(subset.size(), 0.0);
+
for (int i = 0; i < subset.size(); i++) {
- //data[j][i] = (subset[i]->getAbundance(j));
data2[j][i] = (subset[i]->getAbundance(j));
}
}
MothurMetastats mothurMeta(threshold, iters);
mothurMeta.runMetastats(outputFileName , data2, setACount);
m->mothurOutEndLine();
-
m->mothurOutEndLine();
}