#include "metastatscommand.h"
#include "metastats.h"
+#include "sharedutilities.h"
//**********************************************************************************************************************
else {
//valid paramters for this command
- string AlignArray[] = {"groups","label","outputdir","iters","threshold","g","design","inputdir"};
+ string AlignArray[] = {"groups","label","outputdir","iters","threshold","g","design","sets","processors","inputdir"};
vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
OptionParser parser(option);
globaldata->Groups = Groups;
}
+ sets = validParameter.validFile(parameters, "sets", false);
+ if (sets == "not found") { sets = ""; }
+ else {
+ m->splitAtDash(sets, Sets);
+ }
+
+
string temp = validParameter.validFile(parameters, "iters", false); if (temp == "not found") { temp = "1000"; }
convert(temp, iters);
temp = validParameter.validFile(parameters, "threshold", false); if (temp == "not found") { temp = "0.05"; }
convert(temp, threshold);
- //temp = validParameter.validFile(parameters, "g", false); if (temp == "not found") { temp = "0"; }
- //convert(temp, g);
+ temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = "1"; }
+ convert(temp, processors);
}
}
void MetaStatsCommand::help(){
try {
- m->mothurOut("Paper reference goes here....\n");
+ m->mothurOut("This command is based on the Metastats program, White, J.R., Nagarajan, N. & Pop, M. Statistical methods for detecting differentially abundant features in clinical metagenomic samples. PLoS Comput Biol 5, e1000352 (2009).\n");
m->mothurOut("The metastats command can only be executed after a successful read.otu command of a list and group or shared file.\n");
- m->mothurOut("The metastats command outputs a .... file. \n");
- m->mothurOut("The metastats command parameters are iters, threshold, groups, design and label. No parameters are required.\n");
+ m->mothurOut("The metastats command outputs a .metastats file. \n");
+ m->mothurOut("The metastats command parameters are iters, threshold, groups, label, design, sets and processors. The design parameter is required.\n");
m->mothurOut("The design parameter allows you to assign your groups to sets when you are running metastat. mothur will run all pairwise comparisons of the sets. It is required. \n");
m->mothurOut("The design file looks like the group file. It is a 2 column tab delimited file, where the first column is the group name and the second column is the set the group belongs to.\n");
- m->mothurOut("The iters parameter ...\n");
- m->mothurOut("The threshold parameter ...\n");
+ m->mothurOut("The sets parameter allows you to specify which of the sets in your designfile you would like to analyze. The set names are separated by dashes. THe default is all sets in the designfile.\n");
+ m->mothurOut("The iters parameter allows you to set number of bootstrap permutations for estimating null distribution of t statistic. The default is 1000. \n");
+ m->mothurOut("The threshold parameter allows you to set the significance level to reject null hypotheses (default 0.05).\n");
m->mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like included. The group names are separated by dashes.\n");
m->mothurOut("The label parameter allows you to select what distance levels you would like, and are also separated by dashes.\n");
- m->mothurOut("The metastats command should be in the following format: metastats(groups=yourGroups, label=yourLabels).\n");
- m->mothurOut("Example metastats(groups=A-B-C).\n");
+ m->mothurOut("The processors parameter allows you to specify how many processors you would like to use. The default is 1. \n");
+ m->mothurOut("The metastats command should be in the following format: metastats(design=yourDesignFile).\n");
+ m->mothurOut("Example metastats(design=temp.design, groups=A-B-C).\n");
m->mothurOut("The default value for groups is all the groups in your groupfile, and all labels in your inputfile will be used.\n");
m->mothurOut("Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n");
//if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
set<string> processedLabels;
set<string> userLabels = labels;
-
+
+ //setup the pairwise comparions of sets for metastats
+ //calculate number of comparisons i.e. with groups A,B,C = AB, AC, BC = 3;
+ //make sure sets are all in designMap
+ SharedUtil* util = new SharedUtil();
+ util->setGroups(Sets, designMap->namesOfGroups);
+ delete util;
+
+ int numGroups = Sets.size();
+ for (int a=0; a<numGroups; a++) {
+ for (int l = a+1; l < numGroups; l++) {
+ vector<string> groups; groups.push_back(Sets[a]); groups.push_back(Sets[l]);
+ namesOfGroupCombos.push_back(groups);
+ }
+ }
+
+
+ //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;
+
+ 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
+
//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))) {
- if (m->control_pressed) { for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } globaldata->Groups.clear(); delete read; for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+ if (m->control_pressed) { for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } globaldata->Groups.clear(); delete read; delete designMap; for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
//prevent memory leak
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; lookup[i] = NULL; }
- if (m->control_pressed) { globaldata->Groups.clear(); delete read; for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+ if (m->control_pressed) { globaldata->Groups.clear(); delete read; delete designMap; for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
//get next line to process
lookup = input->getSharedRAbundVectors();
}
- if (m->control_pressed) { globaldata->Groups.clear(); delete read; for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+ if (m->control_pressed) { globaldata->Groups.clear(); delete read; delete designMap; for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
//output error messages about any remaining user labels
set<string>::iterator it;
globaldata->Groups.clear();
delete input; globaldata->ginput = NULL;
delete read;
+ delete designMap;
if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0;}
try {
if (pickedGroups) { eliminateZeroOTUS(thisLookUp); }
- string outputFileName = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + thisLookUp[0]->getLabel() + ".metastats";
- outputNames.push_back(outputFileName);
- int nameLength = outputFileName.length();
- char * output = new char[nameLength];
- strcpy(output, outputFileName.c_str());
-
- //build matrix from shared rabunds
- double** data;
- data = new double*[thisLookUp[0]->getNumBins()];
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ if(processors == 1){
+ driver(0, namesOfGroupCombos.size(), thisLookUp);
+ }else{
+ int process = 1;
+ vector<int> processIDS;
+
+ //loop through and create all the processes you want
+ while (process != processors) {
+ int pid = fork();
+
+ if (pid > 0) {
+ processIDS.push_back(pid); //create map from line number to pid so you can append files in correct order later
+ process++;
+ }else if (pid == 0){
+ driver(lines[process].start, lines[process].num, thisLookUp);
+ exit(0);
+ }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
+ }
+
+ //do my part
+ driver(lines[0].start, lines[0].num, thisLookUp);
+
+ //force parent to wait until all the processes are done
+ for (int i=0;i<(processors-1);i++) {
+ int temp = processIDS[i];
+ wait(&temp);
+ }
+ }
+ #else
+ driver(0, namesOfGroupCombos.size(), thisLookUp);
+ #endif
+
+ return 0;
- for (int j = 0; j < thisLookUp[0]->getNumBins(); j++) {
- data[j] = new double[thisLookUp.size()];
+ }
+ catch(exception& e) {
+ m->errorOut(e, "MetaStatsCommand", "process");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int MetaStatsCommand::driver(int start, int num, vector<SharedRAbundVector*>& thisLookUp) {
+ try {
+
+ //for each combo
+ for (int c = start; c < (start+num); c++) {
+
+ //get set names
+ string setA = namesOfGroupCombos[c][0];
+ string setB = namesOfGroupCombos[c][1];
+
+ //get filename
+ string outputFileName = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + thisLookUp[0]->getLabel() + "." + setA + "-" + setB + ".metastats";
+ outputNames.push_back(outputFileName);
+ int nameLength = outputFileName.length();
+ char * output = new char[nameLength];
+ strcpy(output, outputFileName.c_str());
+
+ //build matrix from shared rabunds
+ double** data;
+ data = new double*[thisLookUp[0]->getNumBins()];
+
+ vector<SharedRAbundVector*> subset;
+ int setACount = 0;
+ int setBCount = 0;
for (int i = 0; i < thisLookUp.size(); i++) {
- data[j][i] = (thisLookUp[i]->getAbundance(j));
+ string thisGroup = thisLookUp[i]->getGroup();
+
+ //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 ((designMap->getGroup(thisGroup) == setB)) {
+ subset.push_back(thisLookUp[i]);
+ setBCount++;
+ }else if ((designMap->getGroup(thisGroup) == setA)) {
+ subset.insert(subset.begin()+setACount, thisLookUp[i]);
+ setACount++;
+ }
}
+
+ if ((setACount == 0) || (setBCount == 0)) {
+ 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()];
+ for (int i = 0; i < subset.size(); i++) {
+ data[j][i] = (subset[i]->getAbundance(j));
+ }
+ }
+
+ m->mothurOut("Comparing " + setA + " and " + setB + "..."); m->mothurOutEndLine();
+
+ metastat_main(output, thisLookUp[0]->getNumBins(), subset.size(), threshold, iters, data, setACount);
+
+ m->mothurOutEndLine();
+ }
+
+ //free memory
+ delete output;
+ for(int i = 0; i < thisLookUp[0]->getNumBins(); i++) { delete[] data[i]; }
+ delete[] data;
}
-
- if (g == 0) { g = thisLookUp.size() / 2; }
- metastat_main(output, thisLookUp[0]->getNumBins(), thisLookUp.size(), threshold, iters, data, g);
-
return 0;
+
}
catch(exception& e) {
- m->errorOut(e, "MetaStatsCommand", "normalize");
+ m->errorOut(e, "MetaStatsCommand", "driver");
exit(1);
}
}
projects / mothur.git / blobdiff