*/
#include "summarysharedcommand.h"
-#include "sharedsobscollectsummary.h"
-#include "sharedchao1.h"
-#include "sharedace.h"
-#include "sharednseqs.h"
-#include "sharedjabund.h"
-#include "sharedsorabund.h"
-#include "sharedjclass.h"
-#include "sharedsorclass.h"
-#include "sharedjest.h"
-#include "sharedsorest.h"
-#include "sharedthetayc.h"
-#include "sharedthetan.h"
-#include "sharedkstest.h"
-#include "whittaker.h"
-#include "sharedochiai.h"
-#include "sharedanderbergs.h"
-#include "sharedkulczynski.h"
-#include "sharedkulczynskicody.h"
-#include "sharedlennon.h"
-#include "sharedmorisitahorn.h"
-#include "sharedbraycurtis.h"
-#include "sharedjackknife.h"
-#include "whittaker.h"
-#include "odum.h"
-#include "canberra.h"
-#include "structeuclidean.h"
-#include "structchord.h"
-#include "hellinger.h"
-#include "manhattan.h"
-#include "structpearson.h"
-#include "soergel.h"
-#include "spearman.h"
-#include "structkulczynski.h"
-#include "structchi2.h"
-#include "speciesprofile.h"
-#include "hamming.h"
-#include "gower.h"
-#include "memchi2.h"
-#include "memchord.h"
-#include "memeuclidean.h"
-#include "mempearson.h"
+#include "subsample.h"
//**********************************************************************************************************************
vector<string> SummarySharedCommand::setParameters(){
try {
- CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pshared);
- CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
- CommandParameter pdistance("distance", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pdistance);
- CommandParameter pcalc("calc", "Multiple", "sharedchao-sharedsobs-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan-kstest-whittaker-sharednseqs-ochiai-anderberg-kulczynski-kulczynskicody-lennon-morisitahorn-braycurtis-odum-canberra-structeuclidean-structchord-hellinger-manhattan-structpearson-soergel-spearman-structkulczynski-speciesprofile-structchi2-hamming-gower-memchi2-memchord-memeuclidean-mempearson", "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan", "", "", "",true,false); parameters.push_back(pcalc);
- CommandParameter pall("all", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pall);
- CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
- CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
- 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","summary",false,true,true); parameters.push_back(pshared);
+ CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+ CommandParameter psubsample("subsample", "String", "", "", "", "", "","phylip",false,false); parameters.push_back(psubsample);
+ CommandParameter pdistance("distance", "Boolean", "", "F", "", "", "","phylip",false,false); parameters.push_back(pdistance);
+ CommandParameter pcalc("calc", "Multiple", "sharedchao-sharedsobs-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan-kstest-whittaker-sharednseqs-ochiai-anderberg-kulczynski-kulczynskicody-lennon-morisitahorn-braycurtis-odum-canberra-structeuclidean-structchord-hellinger-manhattan-structpearson-soergel-spearman-structkulczynski-speciesprofile-structchi2-hamming-gower-memchi2-memchord-memeuclidean-mempearson-jsd-rjsd", "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan", "", "", "","",true,false,true); parameters.push_back(pcalc);
+ CommandParameter poutput("output", "Multiple", "lt-square", "lt", "", "", "","",false,false); parameters.push_back(poutput);
+ CommandParameter pall("all", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pall);
+ CommandParameter piters("iters", "Number", "", "1000", "", "", "","",false,false); parameters.push_back(piters);
+ CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
+ CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
+ 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); }
try {
string helpString = "";
ValidCalculators validCalculator;
- helpString += "The summary.shared command parameters are shared, label, calc, distance, processors and all. shared is required if there is no current sharedfile.\n";
+ helpString += "The summary.shared command parameters are shared, label, calc, distance, processors, subsample, iters and all. shared is required if there is no current sharedfile.\n";
helpString += "The summary.shared command should be in the following format: \n";
helpString += "summary.shared(label=yourLabel, calc=yourEstimators, groups=yourGroups).\n";
helpString += "Example summary.shared(label=unique-.01-.03, groups=B-C, calc=sharedchao-sharedace-jabund-sorensonabund-jclass-sorclass-jest-sorest-thetayc-thetan).\n";
helpString += validCalculator.printCalc("sharedsummary");
+ helpString += "The iters parameter allows you to choose the number of times you would like to run the subsample.\n";
+ helpString += "The subsample parameter allows you to enter the size pergroup of the sample or you can set subsample=T and mothur will use the size of your smallest group.\n";
+ helpString += "The output parameter allows you to specify format of your distance matrix. Options are lt, and square. The default is lt.\n";
helpString += "The default value for calc is sharedsobs-sharedchao-sharedace-jabund-sorensonabund-jclass-sorclass-jest-sorest-thetayc-thetan\n";
helpString += "The default value for groups is all the groups in your groupfile.\n";
helpString += "The distance parameter allows you to indicate you would like a distance file created for each calculator for each label, default=f.\n";
}
}
//**********************************************************************************************************************
+string SummarySharedCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
+
+ if (type == "summary") { pattern = "[filename],summary-[filename],[tag],summary"; }
+ else if (type == "phylip") { pattern = "[filename],[calc],[distance],[outputtag],[tag2],dist"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SummarySharedCommand", "getOutputPattern");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
SummarySharedCommand::SummarySharedCommand(){
try {
abort = true; calledHelp = true;
setParameters();
vector<string> tempOutNames;
outputTypes["summary"] = tempOutNames;
+ outputTypes["phylip"] = tempOutNames;
}
catch(exception& e) {
m->errorOut(e, "SummarySharedCommand", "SummarySharedCommand");
//initialize outputTypes
vector<string> tempOutNames;
outputTypes["summary"] = tempOutNames;
+ outputTypes["phylip"] = tempOutNames;
//if the user changes the input directory command factory will send this info to us in the output parameter
string inputDir = validParameter.validFile(parameters, "inputdir", false);
if (groups == "not found") { groups = ""; }
else {
m->splitAtDash(groups, Groups);
- m->Groups = Groups;
+ m->setGroups(Groups);
}
string temp = validParameter.validFile(parameters, "all", false); if (temp == "not found") { temp = "false"; }
all = m->isTrue(temp);
- temp = validParameter.validFile(parameters, "distance", false); if (temp == "not found") { temp = "false"; }
+ temp = validParameter.validFile(parameters, "iters", false); if (temp == "not found") { temp = "1000"; }
+ m->mothurConvert(temp, iters);
+
+ output = validParameter.validFile(parameters, "output", false);
+ if(output == "not found"){ output = "lt"; }
+ else { createPhylip = true; }
+ if ((output != "lt") && (output != "square")) { m->mothurOut(output + " is not a valid output form. Options are lt and square. I will use lt."); m->mothurOutEndLine(); output = "lt"; }
+
+ temp = validParameter.validFile(parameters, "subsample", false); if (temp == "not found") { temp = "F"; }
+ if (m->isNumeric1(temp)) { m->mothurConvert(temp, subsampleSize); subsample = true; }
+ else {
+ if (m->isTrue(temp)) { subsample = true; subsampleSize = -1; } //we will set it to smallest group later
+ else { subsample = false; }
+ }
+
+ if (subsample == false) { iters = 0; }
+
+ temp = validParameter.validFile(parameters, "distance", false); if (temp == "not found") { temp = "false"; }
createPhylip = m->isTrue(temp);
-
+ if (subsample) { createPhylip = true; }
+
temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
m->setProcessors(temp);
- convert(temp, processors);
+ m->mothurConvert(temp, processors);
if (abort == false) {
sumCalculators.push_back(new MemEuclidean());
}else if (Estimators[i] == "mempearson") {
sumCalculators.push_back(new MemPearson());
+ }else if (Estimators[i] == "jsd") {
+ sumCalculators.push_back(new JSD());
+ }else if (Estimators[i] == "rjsd") {
+ sumCalculators.push_back(new RJSD());
}
}
}
if (abort == true) { if (calledHelp) { return 0; } return 2; }
ofstream outputFileHandle, outAll;
- string outputFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + "shared.summary";
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(sharedfile));
+ string outputFileName = getOutputFileName("summary",variables);
//if the users entered no valid calculators don't execute command
if (sumCalculators.size() == 0) { return 0; }
outputFileHandle.close();
//create file and put column headers for multiple groups file
- string outAllFileName = ((m->getRootName(sharedfile)) + "sharedmultiple.summary");
+ variables["[tag]"]= "multiple";
+ string outAllFileName = getOutputFileName("summary",variables);
if (mult == true) {
m->openOutputFile(outAllFileName, outAll);
outputNames.push_back(outAllFileName);
delete input;
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
for(int i=0;i<sumCalculators.size();i++){ delete sumCalculators[i]; }
- m->Groups.clear();
+ m->clearGroups();
return 0;
}
/******************************************************/
-
+ if (subsample) {
+ if (subsampleSize == -1) { //user has not set size, set size = smallest samples size
+ subsampleSize = lookup[0]->getNumSeqs();
+ for (int i = 1; i < lookup.size(); i++) {
+ int thisSize = lookup[i]->getNumSeqs();
+
+ if (thisSize < subsampleSize) { subsampleSize = thisSize; }
+ }
+ }else {
+ m->clearGroups();
+ Groups.clear();
+ vector<SharedRAbundVector*> temp;
+ for (int i = 0; i < lookup.size(); i++) {
+ if (lookup[i]->getNumSeqs() < subsampleSize) {
+ m->mothurOut(lookup[i]->getGroup() + " contains " + toString(lookup[i]->getNumSeqs()) + ". Eliminating."); m->mothurOutEndLine();
+ delete lookup[i];
+ }else {
+ Groups.push_back(lookup[i]->getGroup());
+ temp.push_back(lookup[i]);
+ }
+ }
+ lookup = temp;
+ m->setGroups(Groups);
+ }
+
+ if (lookup.size() < 2) { m->mothurOut("You have not provided enough valid groups. I cannot run the command."); m->mothurOutEndLine(); m->control_pressed = true; delete input; return 0; }
+ }
+
/******************************************************/
//comparison breakup to be used by different processes later
- numGroups = m->Groups.size();
+ numGroups = lookup.size();
lines.resize(processors);
for (int i = 0; i < processors; i++) {
lines[i].start = int (sqrt(float(i)/float(processors)) * numGroups);
delete input;
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
for(int i=0;i<sumCalculators.size();i++){ delete sumCalculators[i]; }
- m->Groups.clear();
+ m->clearGroups();
return 0;
}
m->mothurRemove(outputFileName);
delete input;
for(int i=0;i<sumCalculators.size();i++){ delete sumCalculators[i]; }
- m->Groups.clear();
+ m->clearGroups();
return 0;
}
//reset groups parameter
- m->Groups.clear();
+ m->clearGroups();
for(int i=0;i<sumCalculators.size();i++){ delete sumCalculators[i]; }
delete input;
exit(1);
}
}
-
/***********************************************************/
-int SummarySharedCommand::process(vector<SharedRAbundVector*> thisLookup, string sumFileName, string sumAllFileName) {
+int SummarySharedCommand::printSims(ostream& out, vector< vector<double> >& simMatrix) {
try {
- vector< vector<seqDist> > calcDists; //vector containing vectors that contains the summary results for each group compare
- calcDists.resize(sumCalculators.size()); //one for each calc, this will be used to make .dist files
-
- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
- if(processors == 1){
- driver(thisLookup, 0, numGroups, sumFileName+".temp", sumAllFileName+".temp", calcDists);
- m->appendFiles((sumFileName + ".temp"), sumFileName);
- m->mothurRemove((sumFileName + ".temp"));
- if (mult) {
- m->appendFiles((sumAllFileName + ".temp"), sumAllFileName);
- m->mothurRemove((sumAllFileName + ".temp"));
- }
- }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);
- process++;
- }else if (pid == 0){
- driver(thisLookup, lines[process].start, lines[process].end, sumFileName + toString(getpid()) + ".temp", sumAllFileName + toString(getpid()) + ".temp", calcDists);
-
- //only do this if you want a distance file
- if (createPhylip) {
- string tempdistFileName = m->getRootName(m->getSimpleName(sumFileName)) + toString(getpid()) + ".dist";
- ofstream outtemp;
- m->openOutputFile(tempdistFileName, outtemp);
-
- for (int i = 0; i < calcDists.size(); i++) {
- outtemp << calcDists[i].size() << endl;
-
- for (int j = 0; j < calcDists[i].size(); j++) {
- outtemp << calcDists[i][j].seq1 << '\t' << calcDists[i][j].seq2 << '\t' << calcDists[i][j].dist << endl;
- }
- }
- outtemp.close();
- }
-
- exit(0);
- }else {
- m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
- for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
- exit(0);
- }
- }
-
- //parent do your part
- driver(thisLookup, lines[0].start, lines[0].end, sumFileName + toString(getpid()) + ".temp", sumAllFileName + toString(getpid()) + ".temp", calcDists);
- m->appendFiles((sumFileName + toString(getpid()) + ".temp"), sumFileName);
- m->mothurRemove((sumFileName + toString(getpid()) + ".temp"));
- if (mult) { m->appendFiles((sumAllFileName + toString(getpid()) + ".temp"), sumAllFileName); }
-
- //force parent to wait until all the processes are done
- for (int i = 0; i < processIDS.size(); i++) {
- int temp = processIDS[i];
- wait(&temp);
- }
-
- for (int i = 0; i < processIDS.size(); i++) {
- m->appendFiles((sumFileName + toString(processIDS[i]) + ".temp"), sumFileName);
- m->mothurRemove((sumFileName + toString(processIDS[i]) + ".temp"));
- if (mult) { m->mothurRemove((sumAllFileName + toString(processIDS[i]) + ".temp")); }
-
- if (createPhylip) {
- string tempdistFileName = m->getRootName(m->getSimpleName(sumFileName)) + toString(processIDS[i]) + ".dist";
- ifstream intemp;
- m->openInputFile(tempdistFileName, intemp);
-
- for (int k = 0; k < calcDists.size(); k++) {
- int size = 0;
- intemp >> size; m->gobble(intemp);
-
- for (int j = 0; j < size; j++) {
- int seq1 = 0;
- int seq2 = 0;
- float dist = 1.0;
-
- intemp >> seq1 >> seq2 >> dist; m->gobble(intemp);
-
- seqDist tempDist(seq1, seq2, dist);
- calcDists[k].push_back(tempDist);
- }
- }
- intemp.close();
- m->mothurRemove(tempdistFileName);
- }
- }
-
- }
- #else
- driver(thisLookup, 0, numGroups, (sumFileName + ".temp"), (sumAllFileName + ".temp"), calcDists);
- m->appendFiles((sumFileName + ".temp"), sumFileName);
- m->mothurRemove((sumFileName + ".temp"));
- if (mult) {
- m->appendFiles((sumAllFileName + ".temp"), sumAllFileName);
- m->mothurRemove((sumAllFileName + ".temp"));
+ out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
+
+ //output num seqs
+ out << simMatrix.size() << endl;
+
+ if (output == "lt") {
+ for (int b = 0; b < simMatrix.size(); b++) {
+ out << lookup[b]->getGroup() << '\t';
+ for (int n = 0; n < b; n++) {
+ if (m->control_pressed) { return 0; }
+ out << simMatrix[b][n] << '\t';
}
- #endif
-
- if (createPhylip) {
- for (int i = 0; i < calcDists.size(); i++) {
- if (m->control_pressed) { break; }
-
- string distFileName = outputDir + m->getRootName(m->getSimpleName(sumFileName)) + sumCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + ".dist";
- outputNames.push_back(distFileName);
- ofstream outDist;
- m->openOutputFile(distFileName, outDist);
- outDist.setf(ios::fixed, ios::floatfield); outDist.setf(ios::showpoint);
-
- //initialize matrix
- vector< vector<float> > matrix; //square matrix to represent the distance
- matrix.resize(thisLookup.size());
- for (int k = 0; k < thisLookup.size(); k++) { matrix[k].resize(thisLookup.size(), 0.0); }
-
-
- for (int j = 0; j < calcDists[i].size(); j++) {
- int row = calcDists[i][j].seq1;
- int column = calcDists[i][j].seq2;
- float dist = calcDists[i][j].dist;
-
- matrix[row][column] = dist;
- matrix[column][row] = dist;
- }
-
- //output to file
- outDist << thisLookup.size() << endl;
- for (int r=0; r<thisLookup.size(); r++) {
- //output name
- string name = thisLookup[r]->getGroup();
- if (name.length() < 10) { //pad with spaces to make compatible
- while (name.length() < 10) { name += " "; }
- }
- outDist << name << '\t';
-
- //output distances
- for (int l = 0; l < r; l++) { outDist << matrix[r][l] << '\t'; }
- outDist << endl;
- }
-
- outDist.close();
+ out << endl;
+ }
+ }else{
+ for (int b = 0; b < simMatrix.size(); m++) {
+ out << lookup[b]->getGroup() << '\t';
+ for (int n = 0; n < simMatrix[b].size(); n++) {
+ if (m->control_pressed) { return 0; }
+ out << simMatrix[b][n] << '\t';
}
+ out << endl;
}
- return 0;
+ }
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SummarySharedCommand", "printSims");
+ exit(1);
+ }
+}
+/***********************************************************/
+int SummarySharedCommand::process(vector<SharedRAbundVector*> thisLookup, string sumFileName, string sumAllFileName) {
+ try {
+ vector< vector< vector<seqDist> > > calcDistsTotals; //each iter, one for each calc, then each groupCombos dists. this will be used to make .dist files
+ vector< vector<seqDist> > calcDists; calcDists.resize(sumCalculators.size());
+
+ for (int thisIter = 0; thisIter < iters+1; thisIter++) {
+
+ vector<SharedRAbundVector*> thisItersLookup = thisLookup;
+
+ if (subsample && (thisIter != 0)) { //we want the summary results for the whole dataset, then the subsampling
+ SubSample sample;
+ vector<string> tempLabels; //dont need since we arent printing the sampled sharedRabunds
+
+ //make copy of lookup so we don't get access violations
+ vector<SharedRAbundVector*> newLookup;
+ for (int k = 0; k < thisItersLookup.size(); k++) {
+ SharedRAbundVector* temp = new SharedRAbundVector();
+ temp->setLabel(thisItersLookup[k]->getLabel());
+ temp->setGroup(thisItersLookup[k]->getGroup());
+ newLookup.push_back(temp);
+ }
+
+ //for each bin
+ for (int k = 0; k < thisItersLookup[0]->getNumBins(); k++) {
+ if (m->control_pressed) { for (int j = 0; j < newLookup.size(); j++) { delete newLookup[j]; } return 0; }
+ for (int j = 0; j < thisItersLookup.size(); j++) { newLookup[j]->push_back(thisItersLookup[j]->getAbundance(k), thisItersLookup[j]->getGroup()); }
+ }
+
+ tempLabels = sample.getSample(newLookup, subsampleSize);
+ thisItersLookup = newLookup;
+ }
+
+
+ if(processors == 1){
+ driver(thisLookup, 0, numGroups, sumFileName+".temp", sumAllFileName+".temp", calcDists);
+ m->appendFiles((sumFileName + ".temp"), sumFileName);
+ m->mothurRemove((sumFileName + ".temp"));
+ if (mult) {
+ m->appendFiles((sumAllFileName + ".temp"), sumAllFileName);
+ m->mothurRemove((sumAllFileName + ".temp"));
+ }
+ }else{
+
+ int process = 1;
+ vector<int> processIDS;
+
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+ //loop through and create all the processes you want
+ while (process != processors) {
+ int pid = fork();
+
+ if (pid > 0) {
+ processIDS.push_back(pid);
+ process++;
+ }else if (pid == 0){
+ driver(thisLookup, lines[process].start, lines[process].end, sumFileName + toString(getpid()) + ".temp", sumAllFileName + toString(getpid()) + ".temp", calcDists);
+
+ //only do this if you want a distance file
+ if (createPhylip) {
+ string tempdistFileName = m->getRootName(m->getSimpleName(sumFileName)) + toString(getpid()) + ".dist";
+ ofstream outtemp;
+ m->openOutputFile(tempdistFileName, outtemp);
+
+ for (int i = 0; i < calcDists.size(); i++) {
+ outtemp << calcDists[i].size() << endl;
+
+ for (int j = 0; j < calcDists[i].size(); j++) {
+ outtemp << calcDists[i][j].seq1 << '\t' << calcDists[i][j].seq2 << '\t' << calcDists[i][j].dist << endl;
+ }
+ }
+ outtemp.close();
+ }
+
+ exit(0);
+ }else {
+ m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
+ for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
+ exit(0);
+ }
+ }
+
+ //parent do your part
+ driver(thisLookup, lines[0].start, lines[0].end, sumFileName + toString(getpid()) + ".temp", sumAllFileName + toString(getpid()) + ".temp", calcDists);
+ m->appendFiles((sumFileName + toString(getpid()) + ".temp"), sumFileName);
+ m->mothurRemove((sumFileName + toString(getpid()) + ".temp"));
+ if (mult) { m->appendFiles((sumAllFileName + toString(getpid()) + ".temp"), sumAllFileName); }
+
+ //force parent to wait until all the processes are done
+ for (int i = 0; i < processIDS.size(); i++) {
+ int temp = processIDS[i];
+ wait(&temp);
+ }
+
+ for (int i = 0; i < processIDS.size(); i++) {
+ m->appendFiles((sumFileName + toString(processIDS[i]) + ".temp"), sumFileName);
+ m->mothurRemove((sumFileName + toString(processIDS[i]) + ".temp"));
+ if (mult) { m->mothurRemove((sumAllFileName + toString(processIDS[i]) + ".temp")); }
+
+ if (createPhylip) {
+ string tempdistFileName = m->getRootName(m->getSimpleName(sumFileName)) + toString(processIDS[i]) + ".dist";
+ ifstream intemp;
+ m->openInputFile(tempdistFileName, intemp);
+
+ for (int k = 0; k < calcDists.size(); k++) {
+ int size = 0;
+ intemp >> size; m->gobble(intemp);
+
+ for (int j = 0; j < size; j++) {
+ int seq1 = 0;
+ int seq2 = 0;
+ float dist = 1.0;
+
+ intemp >> seq1 >> seq2 >> dist; m->gobble(intemp);
+
+ seqDist tempDist(seq1, seq2, dist);
+ calcDists[k].push_back(tempDist);
+ }
+ }
+ intemp.close();
+ m->mothurRemove(tempdistFileName);
+ }
+ }
+#else
+ //////////////////////////////////////////////////////////////////////////////////////////////////////
+ //Windows version shared memory, so be careful when passing variables through the summarySharedData struct.
+ //Above fork() will clone, so memory is separate, but that's not the case with windows,
+ //Taking advantage of shared memory to pass results vectors.
+ //////////////////////////////////////////////////////////////////////////////////////////////////////
+
+ vector<summarySharedData*> pDataArray;
+ DWORD dwThreadIdArray[processors-1];
+ HANDLE hThreadArray[processors-1];
+
+ //Create processor worker threads.
+ for( int i=1; i<processors; i++ ){
+
+ //make copy of lookup so we don't get access violations
+ vector<SharedRAbundVector*> newLookup;
+ for (int k = 0; k < thisLookup.size(); k++) {
+ SharedRAbundVector* temp = new SharedRAbundVector();
+ temp->setLabel(thisLookup[k]->getLabel());
+ temp->setGroup(thisLookup[k]->getGroup());
+ newLookup.push_back(temp);
+ }
+
+
+ //for each bin
+ for (int k = 0; k < thisLookup[0]->getNumBins(); k++) {
+ if (m->control_pressed) { for (int j = 0; j < newLookup.size(); j++) { delete newLookup[j]; } return 0; }
+ for (int j = 0; j < thisLookup.size(); j++) { newLookup[j]->push_back(thisLookup[j]->getAbundance(k), thisLookup[j]->getGroup()); }
+ }
+
+ // Allocate memory for thread data.
+ summarySharedData* tempSum = new summarySharedData((sumFileName+toString(i)+".temp"), m, lines[i].start, lines[i].end, Estimators, newLookup);
+ pDataArray.push_back(tempSum);
+ processIDS.push_back(i);
+
+ hThreadArray[i-1] = CreateThread(NULL, 0, MySummarySharedThreadFunction, pDataArray[i-1], 0, &dwThreadIdArray[i-1]);
+ }
+
+ //parent do your part
+ driver(thisLookup, lines[0].start, lines[0].end, sumFileName +"0.temp", sumAllFileName + "0.temp", calcDists);
+ m->appendFiles((sumFileName + "0.temp"), sumFileName);
+ m->mothurRemove((sumFileName + "0.temp"));
+ if (mult) { m->appendFiles((sumAllFileName + "0.temp"), sumAllFileName); }
+
+ //Wait until all threads have terminated.
+ WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
+
+ //Close all thread handles and free memory allocations.
+ for(int i=0; i < pDataArray.size(); i++){
+ if (pDataArray[i]->count != (pDataArray[i]->end-pDataArray[i]->start)) {
+ m->mothurOut("[ERROR]: process " + toString(i) + " only processed " + toString(pDataArray[i]->count) + " of " + toString(pDataArray[i]->end-pDataArray[i]->start) + " groups assigned to it, quitting. \n"); m->control_pressed = true;
+ }
+ m->appendFiles((sumFileName + toString(processIDS[i]) + ".temp"), sumFileName);
+ m->mothurRemove((sumFileName + toString(processIDS[i]) + ".temp"));
+
+ for (int j = 0; j < pDataArray[i]->thisLookup.size(); j++) { delete pDataArray[i]->thisLookup[j]; }
+
+ if (createPhylip) {
+ for (int k = 0; k < calcDists.size(); k++) {
+ int size = pDataArray[i]->calcDists[k].size();
+ for (int j = 0; j < size; j++) { calcDists[k].push_back(pDataArray[i]->calcDists[k][j]); }
+ }
+ }
+
+ CloseHandle(hThreadArray[i]);
+ delete pDataArray[i];
+ }
+
+#endif
+ }
+
+ if (subsample && (thisIter != 0)) { //we want the summary results for the whole dataset, then the subsampling
+
+ calcDistsTotals.push_back(calcDists);
+ //clean up memory
+ for (int i = 0; i < thisItersLookup.size(); i++) { delete thisItersLookup[i]; }
+ thisItersLookup.clear();
+ }else {
+ if (createPhylip) {
+ for (int i = 0; i < calcDists.size(); i++) {
+ if (m->control_pressed) { break; }
+
+ //initialize matrix
+ vector< vector<double> > matrix; //square matrix to represent the distance
+ matrix.resize(thisLookup.size());
+ for (int k = 0; k < thisLookup.size(); k++) { matrix[k].resize(thisLookup.size(), 0.0); }
+
+ for (int j = 0; j < calcDists[i].size(); j++) {
+ int row = calcDists[i][j].seq1;
+ int column = calcDists[i][j].seq2;
+ double dist = calcDists[i][j].dist;
+
+ matrix[row][column] = dist;
+ matrix[column][row] = dist;
+ }
+
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(sharedfile));
+ variables["[calc]"] = sumCalculators[i]->getName();
+ variables["[distance]"] = thisLookup[0]->getLabel();
+ variables["[outputtag]"] = output;
+ variables["[tag2]"] = "";
+ string distFileName = getOutputFileName("phylip",variables);
+ outputNames.push_back(distFileName); outputTypes["phylip"].push_back(distFileName);
+ ofstream outDist;
+ m->openOutputFile(distFileName, outDist);
+ outDist.setf(ios::fixed, ios::floatfield); outDist.setf(ios::showpoint);
+
+ printSims(outDist, matrix);
+
+ outDist.close();
+ }
+ }
+ }
+ for (int i = 0; i < calcDists.size(); i++) { calcDists[i].clear(); }
+ }
+
+ if (iters != 0) {
+ //we need to find the average distance and standard deviation for each groups distance
+ vector< vector<seqDist> > calcAverages = m->getAverages(calcDistsTotals);
+
+ //find standard deviation
+ vector< vector<seqDist> > stdDev = m->getStandardDeviation(calcDistsTotals, calcAverages);
+
+ //print results
+ for (int i = 0; i < calcDists.size(); i++) {
+ vector< vector<double> > matrix; //square matrix to represent the distance
+ matrix.resize(thisLookup.size());
+ for (int k = 0; k < thisLookup.size(); k++) { matrix[k].resize(thisLookup.size(), 0.0); }
+
+ vector< vector<double> > stdmatrix; //square matrix to represent the stdDev
+ stdmatrix.resize(thisLookup.size());
+ for (int k = 0; k < thisLookup.size(); k++) { stdmatrix[k].resize(thisLookup.size(), 0.0); }
+
+
+ for (int j = 0; j < calcAverages[i].size(); j++) {
+ int row = calcAverages[i][j].seq1;
+ int column = calcAverages[i][j].seq2;
+ float dist = calcAverages[i][j].dist;
+ float stdDist = stdDev[i][j].dist;
+
+ matrix[row][column] = dist;
+ matrix[column][row] = dist;
+ stdmatrix[row][column] = stdDist;
+ stdmatrix[column][row] = stdDist;
+ }
+
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(sharedfile));
+ variables["[calc]"] = sumCalculators[i]->getName();
+ variables["[distance]"] = thisLookup[0]->getLabel();
+ variables["[outputtag]"] = output;
+ variables["[tag2]"] = "ave";
+ string distFileName = getOutputFileName("phylip",variables);
+ outputNames.push_back(distFileName); outputTypes["phylip"].push_back(distFileName);
+ ofstream outAve;
+ m->openOutputFile(distFileName, outAve);
+ outAve.setf(ios::fixed, ios::floatfield); outAve.setf(ios::showpoint);
+
+ printSims(outAve, matrix);
+
+ outAve.close();
+
+ variables["[tag2]"] = "std";
+ distFileName = getOutputFileName("phylip",variables);
+ outputNames.push_back(distFileName); outputTypes["phylip"].push_back(distFileName);
+ ofstream outSTD;
+ m->openOutputFile(distFileName, outSTD);
+ outSTD.setf(ios::fixed, ios::floatfield); outSTD.setf(ios::showpoint);
+
+ printSims(outSTD, stdmatrix);
+
+ outSTD.close();
+
+ }
+ }
+
+ return 0;
}
catch(exception& e) {
m->errorOut(e, "SummarySharedCommand", "process");
projects / mothur.git / blobdiff