#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"
-
+//**********************************************************************************************************************
+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-skulczynski-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);
+
+ vector<string> myArray;
+ for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SummarySharedCommand", "setParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string SummarySharedCommand::getHelpString(){
+ 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 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 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";
+ helpString += "The label parameter is used to analyze specific labels in your input.\n";
+ helpString += "The all parameter is used to specify if you want the estimate of all your groups together. This estimate can only be made for sharedsobs and sharedchao calculators. The default is false.\n";
+ helpString += "If you use sharedchao and run into memory issues, set all to false. \n";
+ helpString += "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";
+ helpString += "Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabel).\n";
+ return helpString;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SummarySharedCommand", "getHelpString");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+SummarySharedCommand::SummarySharedCommand(){
+ try {
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["summary"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SummarySharedCommand", "SummarySharedCommand");
+ exit(1);
+ }
+}
//**********************************************************************************************************************
-SummarySharedCommand::SummarySharedCommand(string option){
+SummarySharedCommand::SummarySharedCommand(string option) {
try {
- globaldata = GlobalData::getInstance();
- abort = false;
+ abort = false; calledHelp = false;
allLines = 1;
- lines.clear();
- labels.clear();
- Estimators.clear();
-
+
//allow user to run help
- if(option == "help") { validCalculator = new ValidCalculators(); help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else {
- //valid paramters for this command
- string Array[] = {"line","label","calc","groups"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ vector<string> myArray = setParameters();
OptionParser parser(option);
map<string, string> parameters = parser.getParameters();
+ map<string, string>::iterator it;
ValidParameters validParameter;
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
- //make sure the user has already run the read.otu command
- if (globaldata->getSharedFile() == "") {
- mothurOut("You must read a list and a group, or a shared before you can use the summary.shared command."); mothurOutEndLine(); abort = true;
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["summary"] = 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 (inputDir == "not found"){ inputDir = ""; }
+ else {
+ string path;
+ it = parameters.find("shared");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["shared"] = inputDir + it->second; }
+ }
}
- //check for optional parameter and set defaults
- // ...at some point should added some additional type checking...
- line = validParameter.validFile(parameters, "line", false);
- if (line == "not found") { line = ""; }
- else {
- if(line != "all") { splitAtDash(line, lines); allLines = 0; }
- else { allLines = 1; }
+ //get shared file
+ sharedfile = validParameter.validFile(parameters, "shared", true);
+ if (sharedfile == "not open") { sharedfile = ""; abort = true; }
+ else if (sharedfile == "not found") {
+ //if there is a current shared file, use it
+ sharedfile = m->getSharedFile();
+ if (sharedfile != "") { m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
+ else { m->mothurOut("You have no current sharedfile and the shared parameter is required."); m->mothurOutEndLine(); abort = true; }
}
+
+ //if the user changes the output directory command factory will send this info to us in the output parameter
+ outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = m->hasPath(sharedfile); }
+
+
+ //check for optional parameter and set defaults
+ // ...at some point should added some additional type checking...
label = validParameter.validFile(parameters, "label", false);
if (label == "not found") { label = ""; }
else {
- if(label != "all") { splitAtDash(label, labels); allLines = 0; }
+ if(label != "all") { m->splitAtDash(label, labels); allLines = 0; }
else { allLines = 1; }
}
- //make sure user did not use both the line and label parameters
- if ((line != "") && (label != "")) { mothurOut("You cannot use both the line and label parameters at the same time. "); mothurOutEndLine(); abort = true; }
- //if the user has not specified any line or labels use the ones from read.otu
- else if((line == "") && (label == "")) {
- allLines = globaldata->allLines;
- labels = globaldata->labels;
- lines = globaldata->lines;
- }
-
+
calc = validParameter.validFile(parameters, "calc", false);
if (calc == "not found") { calc = "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan"; }
else {
if (calc == "default") { calc = "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan"; }
}
- splitAtDash(calc, Estimators);
+ m->splitAtDash(calc, Estimators);
+ if (m->inUsersGroups("citation", Estimators)) {
+ ValidCalculators validCalc; validCalc.printCitations(Estimators);
+ //remove citation from list of calcs
+ for (int i = 0; i < Estimators.size(); i++) { if (Estimators[i] == "citation") { Estimators.erase(Estimators.begin()+i); break; } }
+ }
groups = validParameter.validFile(parameters, "groups", false);
if (groups == "not found") { groups = ""; }
else {
- splitAtDash(groups, Groups);
- globaldata->Groups = Groups;
+ m->splitAtDash(groups, Groups);
+ m->Groups = 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"; }
+ createPhylip = m->isTrue(temp);
+
+ temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
+ m->setProcessors(temp);
+ convert(temp, processors);
+
if (abort == false) {
- validCalculator = new ValidCalculators();
+ ValidCalculators validCalculator;
int i;
for (i=0; i<Estimators.size(); i++) {
- if (validCalculator->isValidCalculator("sharedsummary", Estimators[i]) == true) {
+ if (validCalculator.isValidCalculator("sharedsummary", Estimators[i]) == true) {
if (Estimators[i] == "sharedsobs") {
sumCalculators.push_back(new SharedSobsCS());
}else if (Estimators[i] == "sharedchao") {
sumCalculators.push_back(new BrayCurtis());
}else if (Estimators[i] == "whittaker") {
sumCalculators.push_back(new Whittaker());
+ }else if (Estimators[i] == "odum") {
+ sumCalculators.push_back(new Odum());
+ }else if (Estimators[i] == "canberra") {
+ sumCalculators.push_back(new Canberra());
+ }else if (Estimators[i] == "structeuclidean") {
+ sumCalculators.push_back(new StructEuclidean());
+ }else if (Estimators[i] == "structchord") {
+ sumCalculators.push_back(new StructChord());
+ }else if (Estimators[i] == "hellinger") {
+ sumCalculators.push_back(new Hellinger());
+ }else if (Estimators[i] == "manhattan") {
+ sumCalculators.push_back(new Manhattan());
+ }else if (Estimators[i] == "structpearson") {
+ sumCalculators.push_back(new StructPearson());
+ }else if (Estimators[i] == "soergel") {
+ sumCalculators.push_back(new Soergel());
+ }else if (Estimators[i] == "spearman") {
+ sumCalculators.push_back(new Spearman());
+ }else if (Estimators[i] == "structkulczynski") {
+ sumCalculators.push_back(new StructKulczynski());
+ }else if (Estimators[i] == "speciesprofile") {
+ sumCalculators.push_back(new SpeciesProfile());
+ }else if (Estimators[i] == "hamming") {
+ sumCalculators.push_back(new Hamming());
+ }else if (Estimators[i] == "structchi2") {
+ sumCalculators.push_back(new StructChi2());
+ }else if (Estimators[i] == "gower") {
+ sumCalculators.push_back(new Gower());
+ }else if (Estimators[i] == "memchi2") {
+ sumCalculators.push_back(new MemChi2());
+ }else if (Estimators[i] == "memchord") {
+ sumCalculators.push_back(new MemChord());
+ }else if (Estimators[i] == "memeuclidean") {
+ sumCalculators.push_back(new MemEuclidean());
+ }else if (Estimators[i] == "mempearson") {
+ sumCalculators.push_back(new MemPearson());
}
}
}
- outputFileName = ((getRootName(globaldata->inputFileName)) + "shared.summary");
- openOutputFile(outputFileName, outputFileHandle);
mult = false;
}
}
}
catch(exception& e) {
- errorOut(e, "SummarySharedCommand", "SummarySharedCommand");
- exit(1);
- }
-}
-
-//**********************************************************************************************************************
-
-void SummarySharedCommand::help(){
- try {
- mothurOut("The summary.shared command can only be executed after a successful read.otu command.\n");
- mothurOut("The summary.shared command parameters are label, line and calc. No parameters are required, but you may not use \n");
- mothurOut("both the line and label parameters at the same time. The summary.shared command should be in the following format: \n");
- mothurOut("summary.shared(label=yourLabel, line=yourLines, calc=yourEstimators, groups=yourGroups).\n");
- mothurOut("Example summary.shared(label=unique-.01-.03, line=0,5,10, groups=B-C, calc=sharedchao-sharedace-jabund-sorensonabund-jclass-sorclass-jest-sorest-thetayc-thetan).\n");
- validCalculator->printCalc("sharedsummary", cout);
- mothurOut("The default value for calc is sharedsobs-sharedchao-sharedace-jabund-sorensonabund-jclass-sorclass-jest-sorest-thetayc-thetan\n");
- mothurOut("The default value for groups is all the groups in your groupfile.\n");
- mothurOut("The label and line parameters are used to analyze specific lines in your input.\n");
- 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");
- mothurOut("Note: No spaces between parameter labels (i.e. line), '=' and parameters (i.e.yourLines).\n\n");
- }
- catch(exception& e) {
- errorOut(e, "SummarySharedCommand", "help");
+ m->errorOut(e, "SummarySharedCommand", "SummarySharedCommand");
exit(1);
}
}
-
-//**********************************************************************************************************************
-
-SummarySharedCommand::~SummarySharedCommand(){
- if (abort == false) {
- delete read;
- delete validCalculator;
- }
-}
-
//**********************************************************************************************************************
int SummarySharedCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
+
+ ofstream outputFileHandle, outAll;
+ string outputFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + "shared.summary";
- int count = 1;
-
//if the users entered no valid calculators don't execute command
if (sumCalculators.size() == 0) { return 0; }
//check if any calcs can do multiples
else{
- for (int i = 0; i < sumCalculators.size(); i++) {
- if (sumCalculators[i]->getMultiple() == true) { mult = true; }
+ if (all){
+ for (int i = 0; i < sumCalculators.size(); i++) {
+ if (sumCalculators[i]->getMultiple() == true) { mult = true; }
+ }
}
}
-
- //read first line
- read = new ReadOTUFile(globaldata->inputFileName);
- read->read(&*globaldata);
- input = globaldata->ginput;
+ input = new InputData(sharedfile, "sharedfile");
lookup = input->getSharedRAbundVectors();
string lastLabel = lookup[0]->getLabel();
-
+
+ /******************************************************/
+ //output headings for files
+ /******************************************************/
//output estimator names as column headers
+ m->openOutputFile(outputFileName, outputFileHandle);
outputFileHandle << "label" <<'\t' << "comparison" << '\t';
for(int i=0;i<sumCalculators.size();i++){
outputFileHandle << '\t' << sumCalculators[i]->getName();
+ if (sumCalculators[i]->getCols() == 3) { outputFileHandle << "\t" << sumCalculators[i]->getName() << "_lci\t" << sumCalculators[i]->getName() << "_hci"; }
}
outputFileHandle << endl;
+ outputFileHandle.close();
//create file and put column headers for multiple groups file
+ string outAllFileName = ((m->getRootName(sharedfile)) + "sharedmultiple.summary");
if (mult == true) {
- outAllFileName = ((getRootName(globaldata->inputFileName)) + "sharedmultiple.summary");
- openOutputFile(outAllFileName, outAll);
+ m->openOutputFile(outAllFileName, outAll);
+ outputNames.push_back(outAllFileName);
outAll << "label" <<'\t' << "comparison" << '\t';
for(int i=0;i<sumCalculators.size();i++){
}
}
outAll << endl;
+ outAll.close();
}
if (lookup.size() < 2) {
- mothurOut("I cannot run the command without at least 2 valid groups.");
+ m->mothurOut("I cannot run the command without at least 2 valid groups.");
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
//close files and clean up
- outputFileHandle.close(); remove(outputFileName.c_str());
- if (mult == true) { outAll.close(); remove(outAllFileName.c_str()); }
+ remove(outputFileName.c_str());
+ if (mult == true) { remove(outAllFileName.c_str()); }
return 0;
//if you only have 2 groups you don't need a .sharedmultiple file
}else if ((lookup.size() == 2) && (mult == true)) {
mult = false;
- outAll.close();
remove(outAllFileName.c_str());
+ outputNames.pop_back();
}
-
+
+ if (m->control_pressed) {
+ if (mult) { remove(outAllFileName.c_str()); }
+ remove(outputFileName.c_str());
+ 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();
+ return 0;
+ }
+ /******************************************************/
+
+
+ /******************************************************/
+ //comparison breakup to be used by different processes later
+ numGroups = m->Groups.size();
+ lines.resize(processors);
+ for (int i = 0; i < processors; i++) {
+ lines[i].start = int (sqrt(float(i)/float(processors)) * numGroups);
+ lines[i].end = int (sqrt(float(i+1)/float(processors)) * numGroups);
+ }
+ /******************************************************/
+
//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;
- set<int> userLines = lines;
-
+
//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) || (userLines.size() != 0))) {
+ while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
+ if (m->control_pressed) {
+ if (mult) { remove(outAllFileName.c_str()); }
+ remove(outputFileName.c_str());
+ 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();
+ return 0;
+ }
+
- if(allLines == 1 || lines.count(count) == 1 || labels.count(lookup[0]->getLabel()) == 1){
- mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
- process(lookup);
+ if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
+ m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
+ process(lookup, outputFileName, outAllFileName);
processedLabels.insert(lookup[0]->getLabel());
userLabels.erase(lookup[0]->getLabel());
- userLines.erase(count);
}
- if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ string saveLabel = lookup[0]->getLabel();
+
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
lookup = input->getSharedRAbundVectors(lastLabel);
- mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
- process(lookup);
+ m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
+ process(lookup, outputFileName, outAllFileName);
processedLabels.insert(lookup[0]->getLabel());
userLabels.erase(lookup[0]->getLabel());
+
+ //restore real lastlabel to save below
+ lookup[0]->setLabel(saveLabel);
}
-
-
lastLabel = lookup[0]->getLabel();
//prevent memory leak
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
lookup = input->getSharedRAbundVectors();
- count++;
}
+ if (m->control_pressed) {
+ if (mult) { remove(outAllFileName.c_str()); }
+ remove(outputFileName.c_str());
+ delete input;
+ for(int i=0;i<sumCalculators.size();i++){ delete sumCalculators[i]; }
+ m->Groups.clear();
+ return 0;
+ }
+
//output error messages about any remaining user labels
set<string>::iterator it;
bool needToRun = false;
for (it = userLabels.begin(); it != userLabels.end(); it++) {
- mothurOut("Your file does not include the label " + *it);
+ m->mothurOut("Your file does not include the label " + *it);
if (processedLabels.count(lastLabel) != 1) {
- mothurOut(". I will use " + lastLabel + "."); mothurOutEndLine();
+ m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
needToRun = true;
}else {
- mothurOut(". Please refer to " + lastLabel + "."); mothurOutEndLine();
+ m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
}
}
- //run last line if you need to
+ //run last label if you need to
if (needToRun == true) {
- for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+ for (int i = 0; i < lookup.size(); i++) { if (lookup[i] != NULL) { delete lookup[i]; } }
lookup = input->getSharedRAbundVectors(lastLabel);
- mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
- process(lookup);
+ m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
+ process(lookup, outputFileName, outAllFileName);
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
}
-
+
//reset groups parameter
- globaldata->Groups.clear();
-
- //close files
- outputFileHandle.close();
- if (mult == true) { outAll.close(); }
+ m->Groups.clear();
for(int i=0;i<sumCalculators.size();i++){ delete sumCalculators[i]; }
+ delete input;
+
+ if (m->control_pressed) {
+ remove(outAllFileName.c_str());
+ remove(outputFileName.c_str());
+ return 0;
+ }
- delete input; globaldata->ginput = NULL;
+ m->mothurOutEndLine();
+ m->mothurOut("Output File Names: "); m->mothurOutEndLine();
+ m->mothurOut(outputFileName); m->mothurOutEndLine();
+ if (mult) { m->mothurOut(outAllFileName); m->mothurOutEndLine(); outputTypes["summary"].push_back(outAllFileName); }
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); } outputTypes["summary"].push_back(outputFileName);
+ m->mothurOutEndLine();
return 0;
}
catch(exception& e) {
- errorOut(e, "SummarySharedCommand", "execute");
+ m->errorOut(e, "SummarySharedCommand", "execute");
exit(1);
}
}
/***********************************************************/
-void SummarySharedCommand::process(vector<SharedRAbundVector*> thisLookup) {
+int SummarySharedCommand::process(vector<SharedRAbundVector*> thisLookup, string sumFileName, string sumAllFileName) {
try {
- //loop through calculators and add to file all for all calcs that can do mutiple groups
- if (mult == true) {
- //output label
- outAll << thisLookup[0]->getLabel() << '\t';
+ 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);
+ remove((sumFileName + ".temp").c_str());
+ if (mult) {
+ m->appendFiles((sumAllFileName + ".temp"), sumAllFileName);
+ remove((sumAllFileName + ".temp").c_str());
+ }
+ }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);
+ }
+ }
- //output groups names
- string outNames = "";
- for (int j = 0; j < thisLookup.size(); j++) {
- outNames += thisLookup[j]->getGroup() + "-";
+ //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);
+ remove((sumFileName + toString(getpid()) + ".temp").c_str());
+ 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);
}
- outNames = outNames.substr(0, outNames.length()-1); //rip off extra '-';
- outAll << outNames << '\t';
- for(int i=0;i<sumCalculators.size();i++){
- if (sumCalculators[i]->getMultiple() == true) {
- sumCalculators[i]->getValues(thisLookup);
- outAll << '\t';
- sumCalculators[i]->print(outAll);
+ for (int i = 0; i < processIDS.size(); i++) {
+ m->appendFiles((sumFileName + toString(processIDS[i]) + ".temp"), sumFileName);
+ remove((sumFileName + toString(processIDS[i]) + ".temp").c_str());
+ if (mult) { remove((sumAllFileName + toString(processIDS[i]) + ".temp").c_str()); }
+
+ if (createPhylip) {
+ string tempdistFileName = m->getRootName(m->getSimpleName(sumFileName)) + toString(processIDS[i]) + ".dist";
+ ifstream intemp;
+ m->openInputFile(tempdistFileName, intemp);
+
+ for (int i = 0; i < calcDists.size(); i++) {
+ 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[i].push_back(tempDist);
+ }
+ }
+ intemp.close();
+ remove(tempdistFileName.c_str());
}
}
- outAll << endl;
+
}
-
- int n = 1;
- vector<SharedRAbundVector*> subset;
- for (int k = 0; k < (thisLookup.size() - 1); k++) { // pass cdd each set of groups to commpare
- for (int l = n; l < thisLookup.size(); l++) {
-
- outputFileHandle << thisLookup[0]->getLabel() << '\t';
-
- subset.clear(); //clear out old pair of sharedrabunds
- //add new pair of sharedrabunds
- subset.push_back(thisLookup[k]); subset.push_back(thisLookup[l]);
+ #else
+ driver(thisLookup, 0, numGroups, (sumFileName + ".temp"), (sumAllFileName + ".temp"), calcDists);
+ m->appendFiles((sumFileName + ".temp"), sumFileName);
+ remove((sumFileName + ".temp").c_str());
+ if (mult) {
+ m->appendFiles((sumAllFileName + ".temp"), sumAllFileName);
+ remove((sumAllFileName + ".temp").c_str());
+ }
+ #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;
- //sort groups to be alphanumeric
- if (thisLookup[k]->getGroup() > thisLookup[l]->getGroup()) {
- outputFileHandle << (thisLookup[l]->getGroup() +'\t' + thisLookup[k]->getGroup()) << '\t'; //print out groups
- }else{
- outputFileHandle << (thisLookup[k]->getGroup() +'\t' + thisLookup[l]->getGroup()) << '\t'; //print out groups
+ 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 += " "; }
}
-
- for(int i=0;i<sumCalculators.size();i++) {
+ outDist << name << '\t';
+
+ //output distances
+ for (int l = 0; l < r; l++) { outDist << matrix[r][l] << '\t'; }
+ outDist << endl;
+ }
+
+ outDist.close();
+ }
+ }
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SummarySharedCommand", "process");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+int SummarySharedCommand::driver(vector<SharedRAbundVector*> thisLookup, int start, int end, string sumFile, string sumAllFile, vector< vector<seqDist> >& calcDists) {
+ try {
+
+ //loop through calculators and add to file all for all calcs that can do mutiple groups
+ if (mult == true) {
+ ofstream outAll;
+ m->openOutputFile(sumAllFile, outAll);
+
+ //output label
+ outAll << thisLookup[0]->getLabel() << '\t';
+
+ //output groups names
+ string outNames = "";
+ for (int j = 0; j < thisLookup.size(); j++) {
+ outNames += thisLookup[j]->getGroup() + "-";
+ }
+ outNames = outNames.substr(0, outNames.length()-1); //rip off extra '-';
+ outAll << outNames << '\t';
+
+ for(int i=0;i<sumCalculators.size();i++){
+ if (sumCalculators[i]->getMultiple() == true) {
+ sumCalculators[i]->getValues(thisLookup);
+
+ if (m->control_pressed) { outAll.close(); return 1; }
+
+ outAll << '\t';
+ sumCalculators[i]->print(outAll);
+ }
+ }
+ outAll << endl;
+ outAll.close();
+ }
+
+ ofstream outputFileHandle;
+ m->openOutputFile(sumFile, outputFileHandle);
+
+ vector<SharedRAbundVector*> subset;
+ for (int k = start; k < end; k++) { // pass cdd each set of groups to compare
- sumCalculators[i]->getValues(subset); //saves the calculator outputs
- outputFileHandle << '\t';
- sumCalculators[i]->print(outputFileHandle);
+ for (int l = 0; l < k; l++) {
+
+ outputFileHandle << thisLookup[0]->getLabel() << '\t';
+
+ subset.clear(); //clear out old pair of sharedrabunds
+ //add new pair of sharedrabunds
+ subset.push_back(thisLookup[k]); subset.push_back(thisLookup[l]);
+
+ //sort groups to be alphanumeric
+ if (thisLookup[k]->getGroup() > thisLookup[l]->getGroup()) {
+ outputFileHandle << (thisLookup[l]->getGroup() +'\t' + thisLookup[k]->getGroup()) << '\t'; //print out groups
+ }else{
+ outputFileHandle << (thisLookup[k]->getGroup() +'\t' + thisLookup[l]->getGroup()) << '\t'; //print out groups
+ }
+
+ for(int i=0;i<sumCalculators.size();i++) {
+
+ //if this calc needs all groups to calculate the pair load all groups
+ if (sumCalculators[i]->getNeedsAll()) {
+ //load subset with rest of lookup for those calcs that need everyone to calc for a pair
+ for (int w = 0; w < thisLookup.size(); w++) {
+ if ((w != k) && (w != l)) { subset.push_back(thisLookup[w]); }
}
- outputFileHandle << endl;
}
- n++;
+
+ vector<double> tempdata = sumCalculators[i]->getValues(subset); //saves the calculator outputs
+
+ if (m->control_pressed) { outputFileHandle.close(); return 1; }
+
+ outputFileHandle << '\t';
+ sumCalculators[i]->print(outputFileHandle);
+
+ seqDist temp(l, k, (1.0 - tempdata[0]));
+ calcDists[i].push_back(temp);
}
-
+ outputFileHandle << endl;
+ }
+ }
+
+ outputFileHandle.close();
+
+ return 0;
}
catch(exception& e) {
- errorOut(e, "SummarySharedCommand", "process");
+ m->errorOut(e, "SummarySharedCommand", "driver");
exit(1);
}
}
+/**************************************************************************************************/
+
-/***********************************************************/
projects / mothur.git / blobdiff