#include "unifracweightedcommand.h"
+//**********************************************************************************************************************
+vector<string> UnifracWeightedCommand::getValidParameters(){
+ try {
+ string Array[] = {"groups","iters","distance","random","processors","outputdir","inputdir"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "UnifracWeightedCommand", "getValidParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+UnifracWeightedCommand::UnifracWeightedCommand(){
+ try {
+ abort = true;
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["weighted"] = tempOutNames;
+ outputTypes["wsummary"] = tempOutNames;
+ outputTypes["phylip"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "UnifracWeightedCommand", "UnifracWeightedCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> UnifracWeightedCommand::getRequiredParameters(){
+ try {
+ vector<string> myArray;
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "UnifracWeightedCommand", "getRequiredParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> UnifracWeightedCommand::getRequiredFiles(){
+ try {
+ string Array[] = {"tree","group"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "UnifracWeightedCommand", "getRequiredFiles");
+ exit(1);
+ }
+}
/***********************************************************/
UnifracWeightedCommand::UnifracWeightedCommand(string option) {
try {
else {
//valid paramters for this command
- string Array[] = {"groups","iters","distance","random","outputdir","inputdir"};
+ string Array[] = {"groups","iters","distance","random","processors","outputdir","inputdir"};
vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
OptionParser parser(option);
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["weighted"] = tempOutNames;
+ outputTypes["wsummary"] = tempOutNames;
+ outputTypes["phylip"] = tempOutNames;
+
if (globaldata->gTree.size() == 0) {//no trees were read
m->mothurOut("You must execute the read.tree command, before you may execute the unifrac.weighted command."); m->mothurOutEndLine(); abort = true; }
string temp = validParameter.validFile(parameters, "distance", false); if (temp == "not found") { temp = "false"; }
phylip = m->isTrue(temp);
- temp = validParameter.validFile(parameters, "random", false); if (temp == "not found") { temp = "true"; }
+ temp = validParameter.validFile(parameters, "random", false); if (temp == "not found") { temp = "F"; }
random = m->isTrue(temp);
+ temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = "1"; }
+ convert(temp, processors);
+
if (!random) { iters = 0; } //turn off random calcs
tmap = globaldata->gTreemap;
sumFile = outputDir + m->getSimpleName(globaldata->getTreeFile()) + ".wsummary";
m->openOutputFile(sumFile, outSum);
- outputNames.push_back(sumFile);
+ outputNames.push_back(sumFile); outputTypes["wsummary"].push_back(sumFile);
util = new SharedUtil();
string s; //to make work with setgroups
void UnifracWeightedCommand::help(){
try {
m->mothurOut("The unifrac.weighted command can only be executed after a successful read.tree command.\n");
- m->mothurOut("The unifrac.weighted command parameters are groups, iters, distance and random. No parameters are required.\n");
+ m->mothurOut("The unifrac.weighted command parameters are groups, iters, distance, processors and random. No parameters are required.\n");
m->mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like analyzed. You must enter at least 2 valid groups.\n");
m->mothurOut("The group names are separated by dashes. The iters parameter allows you to specify how many random trees you would like compared to your tree.\n");
m->mothurOut("The distance parameter allows you to create a distance file from the results. The default is false.\n");
- m->mothurOut("The random parameter allows you to shut off the comparison to random trees. The default is true, meaning compare your trees with randomly generated trees.\n");
+ m->mothurOut("The random parameter allows you to shut off the comparison to random trees. The default is false, meaning don't compare your trees with randomly generated trees.\n");
+ m->mothurOut("The processors parameter allows you to specify the number of processors to use. The default is 1.\n");
m->mothurOut("The unifrac.weighted command should be in the following format: unifrac.weighted(groups=yourGroups, iters=yourIters).\n");
m->mothurOut("Example unifrac.weighted(groups=A-B-C, iters=500).\n");
m->mothurOut("The default value for groups is all the groups in your groupfile, and iters is 1000.\n");
if (abort == true) { return 0; }
- Progress* reading;
- if (random) { reading = new Progress("Comparing to random:", iters); }
+ int start = time(NULL);
//get weighted for users tree
userData.resize(numComp,0); //data[0] = weightedscore AB, data[1] = weightedscore AC...
randomData.resize(numComp,0); //data[0] = weightedscore AB, data[1] = weightedscore AC...
- //create new tree with same num nodes and leaves as users
- randT = new Tree();
-
//get weighted scores for users trees
for (int i = 0; i < T.size(); i++) {
- if (m->control_pressed) {
- delete randT;
- if (random) { delete reading; }
- outSum.close();
- for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
- return 0;
- }
+ if (m->control_pressed) { outSum.close(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
counter = 0;
rScores.resize(numComp); //data[0] = weightedscore AB, data[1] = weightedscore AC...
if (random) {
output = new ColumnFile(outputDir + m->getSimpleName(globaldata->getTreeFile()) + toString(i+1) + ".weighted", itersString);
outputNames.push_back(outputDir + m->getSimpleName(globaldata->getTreeFile()) + toString(i+1) + ".weighted");
+ outputTypes["weighted"].push_back(outputDir + m->getSimpleName(globaldata->getTreeFile()) + toString(i+1) + ".weighted");
}
- userData = weighted->getValues(T[i]); //userData[0] = weightedscore
+ userData = weighted->getValues(T[i], processors, outputDir); //userData[0] = weightedscore
- if (m->control_pressed) {
- delete randT;
- if (random) { delete reading; delete output; }
- outSum.close();
- for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
- return 0;
- }
-
+ if (m->control_pressed) { if (random) { delete output; } outSum.close(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
//save users score
for (int s=0; s<numComp; s++) {
utreeScores.push_back(userData[s]);
}
- //get scores for random trees
- for (int j = 0; j < iters; j++) {
- int count = 0;
- for (int r=0; r<numGroups; r++) {
- for (int l = r+1; l < numGroups; l++) {
- //copy T[i]'s info.
- randT->getCopy(T[i]);
-
- //create a random tree with same topology as T[i], but different labels
- randT->assembleRandomUnifracTree(globaldata->Groups[r], globaldata->Groups[l]);
-
- if (m->control_pressed) {
- delete randT;
- if (random) { delete reading; delete output; }
- outSum.close();
- for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
- return 0;
- }
-
-
- //get wscore of random tree
- randomData = weighted->getValues(randT, globaldata->Groups[r], globaldata->Groups[l]);
-
- if (m->control_pressed) {
- delete randT;
- if (random) { delete reading; delete output; }
- outSum.close();
- for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
- return 0;
- }
-
- //save scores
- rScores[count].push_back(randomData[0]);
- count++;
+ if (random) {
+
+ //calculate number of comparisons i.e. with groups A,B,C = AB, AC, BC = 3;
+ vector< vector<string> > namesOfGroupCombos;
+ for (int a=0; a<numGroups; a++) {
+ for (int l = 0; l < a; l++) {
+ vector<string> groups; groups.push_back(globaldata->Groups[a]); groups.push_back(globaldata->Groups[l]);
+ namesOfGroupCombos.push_back(groups);
}
}
- //update progress bar
- reading->update(j);
-
- }
+ lines.clear();
+
+ #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
- //removeValidScoresDuplicates();
- //find the signifigance of the score for summary file
- if (random) {
+
+ //get scores for random trees
+ for (int j = 0; j < iters; j++) {
+
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ if(processors == 1){
+ driver(T[i], namesOfGroupCombos, 0, namesOfGroupCombos.size(), rScores);
+ }else{
+ createProcesses(T[i], namesOfGroupCombos, rScores);
+ }
+ #else
+ driver(T[i], namesOfGroupCombos, 0, namesOfGroupCombos.size(), rScores);
+ #endif
+
+ if (m->control_pressed) { delete output; outSum.close(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+
+ //report progress
+ m->mothurOut("Iter: " + toString(j+1)); m->mothurOutEndLine();
+ }
+ lines.clear();
+
+ //find the signifigance of the score for summary file
for (int f = 0; f < numComp; f++) {
//sort random scores
sort(rScores[f].begin(), rScores[f].end());
printWeightedFile();
delete output;
+
}
//clear data
}
- if (m->control_pressed) {
- delete randT;
- if (random) { delete reading; }
- outSum.close();
- for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
- return 0;
- }
-
- //finish progress bar
- if (random) { reading->finish(); delete reading; }
+ if (m->control_pressed) { outSum.close(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
printWSummaryFile();
//clear out users groups
globaldata->Groups.clear();
- delete randT;
if (m->control_pressed) {
for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
return 0;
}
+ m->mothurOut("It took " + toString(time(NULL) - start) + " secs to run unifrac.weighted."); m->mothurOutEndLine();
+
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
exit(1);
}
}
+/**************************************************************************************************/
+
+int UnifracWeightedCommand::createProcesses(Tree* t, vector< vector<string> > namesOfGroupCombos, vector< vector<double> >& scores) {
+ try {
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ int process = 1;
+ int num = 0;
+ vector<int> processIDS;
+
+ EstOutput results;
+
+ //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(t, namesOfGroupCombos, lines[process].start, lines[process].num, scores);
+
+ //pass numSeqs to parent
+ ofstream out;
+ string tempFile = outputDir + toString(getpid()) + ".weightedcommand.results.temp";
+ m->openOutputFile(tempFile, out);
+ for (int i = lines[process].start; i < (lines[process].start + lines[process].num); i++) { out << scores[i][(scores[i].size()-1)] << '\t'; } out << endl;
+ out.close();
+
+ exit(0);
+ }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
+ }
+
+ driver(t, namesOfGroupCombos, lines[0].start, lines[0].num, scores);
+
+ //force parent to wait until all the processes are done
+ for (int i=0;i<(processors-1);i++) {
+ int temp = processIDS[i];
+ wait(&temp);
+ }
+
+ //get data created by processes
+ for (int i=0;i<(processors-1);i++) {
+
+ ifstream in;
+ string s = outputDir + toString(processIDS[i]) + ".weightedcommand.results.temp";
+ m->openInputFile(s, in);
+
+ double tempScore;
+ for (int j = lines[(i+1)].start; j < (lines[(i+1)].start + lines[(i+1)].num); j++) { in >> tempScore; scores[j].push_back(tempScore); }
+ in.close();
+ remove(s.c_str());
+ }
+
+ return 0;
+#endif
+ }
+ catch(exception& e) {
+ m->errorOut(e, "UnifracWeightedCommand", "createProcesses");
+ exit(1);
+ }
+}
+
+/**************************************************************************************************/
+int UnifracWeightedCommand::driver(Tree* t, vector< vector<string> > namesOfGroupCombos, int start, int num, vector< vector<double> >& scores) {
+ try {
+ Tree* randT = new Tree();
+
+ for (int h = start; h < (start+num); h++) {
+
+ if (m->control_pressed) { return 0; }
+
+ //initialize weighted score
+ string groupA = namesOfGroupCombos[h][0];
+ string groupB = namesOfGroupCombos[h][1];
+
+ //copy T[i]'s info.
+ randT->getCopy(t);
+
+ //create a random tree with same topology as T[i], but different labels
+ randT->assembleRandomUnifracTree(groupA, groupB);
+
+ if (m->control_pressed) { delete randT; return 0; }
+
+ //get wscore of random tree
+ EstOutput randomData = weighted->getValues(randT, groupA, groupB);
+
+ if (m->control_pressed) { delete randT; return 0; }
+
+ //save scores
+ scores[h].push_back(randomData[0]);
+ }
+
+ delete randT;
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "UnifracWeightedCommand", "driver");
+ exit(1);
+ }
+}
/***********************************************************/
void UnifracWeightedCommand::printWeightedFile() {
try {
if (WScoreSig[count] > (1/(float)iters)) {
outSum << setprecision(6) << i+1 << '\t' << groupComb[j] << '\t' << utreeScores[count] << '\t' << setprecision(itersString.length()) << WScoreSig[count] << endl;
cout << setprecision(6) << i+1 << '\t' << groupComb[j] << '\t' << utreeScores[count] << '\t' << setprecision(itersString.length()) << WScoreSig[count] << endl;
- m->mothurOutJustToLog(toString(i+1) +"\t" + groupComb[j] +"\t" + toString(utreeScores[count]) +"\t" + toString(WScoreSig[count])); m->mothurOutEndLine();
+ m->mothurOutJustToLog(toString(i+1) +"\t" + groupComb[j] +"\t" + toString(utreeScores[count]) +"\t" + toString(WScoreSig[count]) + "\n");
}else{
outSum << setprecision(6) << i+1 << '\t' << groupComb[j] << '\t' << utreeScores[count] << '\t' << setprecision(itersString.length()) << "<" << (1/float(iters)) << endl;
cout << setprecision(6) << i+1 << '\t' << groupComb[j] << '\t' << utreeScores[count] << '\t' << setprecision(itersString.length()) << "<" << (1/float(iters)) << endl;
- m->mothurOutJustToLog(toString(i+1) +"\t" + groupComb[j] +"\t" + toString(utreeScores[count]) +"\t<" + toString((1/float(iters)))); m->mothurOutEndLine();
+ m->mothurOutJustToLog(toString(i+1) +"\t" + groupComb[j] +"\t" + toString(utreeScores[count]) +"\t<" + toString((1/float(iters))) + "\n");
}
}else{
outSum << setprecision(6) << i+1 << '\t' << groupComb[j] << '\t' << utreeScores[count] << '\t' << "0.00" << endl;
cout << setprecision(6) << i+1 << '\t' << groupComb[j] << '\t' << utreeScores[count] << '\t' << "0.00" << endl;
- m->mothurOutJustToLog(toString(i+1) +"\t" + groupComb[j] +"\t" + toString(utreeScores[count]) +"\t0.00"); m->mothurOutEndLine();
+ m->mothurOutJustToLog(toString(i+1) +"\t" + groupComb[j] +"\t" + toString(utreeScores[count]) +"\t0.00\n");
}
count++;
}
string phylipFileName = outputDir + m->getSimpleName(globaldata->getTreeFile()) + toString(i+1) + ".weighted.dist";
outputNames.push_back(phylipFileName);
+ outputTypes["phylip"].push_back(phylipFileName);
ofstream out;
m->openOutputFile(phylipFileName, out);
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