#include "memchord.h"
#include "memeuclidean.h"
#include "mempearson.h"
+
//**********************************************************************************************************************
-vector<string> MatrixOutputCommand::getValidParameters(){
+vector<string> MatrixOutputCommand::setParameters(){
try {
- string Array[] = {"label","calc","groups","outputdir","inputdir", "output"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pshared);
+ CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
+ CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
+ CommandParameter pcalc("calc", "Multiple", "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan-kstest-sharednseqs-ochiai-anderberg-kulczynski-kulczynskicody-lennon-morisitahorn-braycurtis-whittaker-odum-canberra-structeuclidean-structchord-hellinger-manhattan-structpearson-soergel-spearman-structkulczynski-speciesprofile-hamming-structchi2-gower-memchi2-memchord-memeuclidean-mempearson", "jclass-thetayc", "", "", "",true,false); parameters.push_back(pcalc);
+ CommandParameter poutput("output", "Multiple", "lt-square", "lt", "", "", "",false,false); parameters.push_back(poutput);
+ CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
+ 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, "MatrixOutputCommand", "getValidParameters");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-MatrixOutputCommand::MatrixOutputCommand(){
- try {
- abort = true; calledHelp = true;
- vector<string> tempOutNames;
- outputTypes["phylip"] = tempOutNames;
- }
- catch(exception& e) {
- m->errorOut(e, "MatrixOutputCommand", "MatrixOutputCommand");
+ m->errorOut(e, "MatrixOutputCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
-vector<string> MatrixOutputCommand::getRequiredParameters(){
+string MatrixOutputCommand::getHelpString(){
try {
- vector<string> myArray;
- return myArray;
+ string helpString = "";
+ ValidCalculators validCalculator;
+ helpString += "The dist.shared command parameters are shared, groups, calc, output, processors and label. shared is a required, unless you have a valid current file.\n";
+ helpString += "The groups parameter allows you to specify which of the groups in your groupfile you would like included used.\n";
+ helpString += "The group names are separated by dashes. The label parameter allows you to select what distance levels you would like distance matrices created for, and is also separated by dashes.\n";
+ helpString += "The dist.shared command should be in the following format: dist.shared(groups=yourGroups, calc=yourCalcs, label=yourLabels).\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 += "Example dist.shared(groups=A-B-C, calc=jabund-sorabund).\n";
+ helpString += "The default value for groups is all the groups in your groupfile.\n";
+ helpString += "The default value for calc is jclass and thetayc.\n";
+ helpString += validCalculator.printCalc("matrix");
+ helpString += "The dist.shared command outputs a .dist file for each calculator you specify at each distance you choose.\n";
+ helpString += "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n";
+ return helpString;
}
catch(exception& e) {
- m->errorOut(e, "MatrixOutputCommand", "getRequiredParameters");
+ m->errorOut(e, "MatrixOutputCommand", "getHelpString");
exit(1);
}
}
//**********************************************************************************************************************
-vector<string> MatrixOutputCommand::getRequiredFiles(){
+MatrixOutputCommand::MatrixOutputCommand(){
try {
- string Array[] = {"shared"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
- return myArray;
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["phylip"] = tempOutNames;
}
catch(exception& e) {
- m->errorOut(e, "MatrixOutputCommand", "getRequiredFiles");
+ m->errorOut(e, "MatrixOutputCommand", "MatrixOutputCommand");
exit(1);
}
}
MatrixOutputCommand::MatrixOutputCommand(string option) {
try {
- globaldata = GlobalData::getInstance();
abort = false; calledHelp = false;
allLines = 1;
- labels.clear();
- Groups.clear();
- Estimators.clear();
-
+
//allow user to run help
- if(option == "help") { validCalculator = new ValidCalculators(); help(); abort = true; calledHelp = 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[] = {"label","calc","groups","outputdir","inputdir", "output"};
- 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;
//check to make sure all parameters are valid for command
- for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
+ for (it = parameters.begin(); it != parameters.end(); it++) {
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
vector<string> 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 (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; }
+ }
+ }
+
+ sharedfile = validParameter.validFile(parameters, "shared", true);
+ 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; }
+ }else if (sharedfile == "not open") { sharedfile = ""; abort = true; }
+ else { m->setSharedFile(sharedfile); }
+
//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 = "";
- outputDir += m->hasPath(globaldata->inputFileName); //if user entered a file with a path then preserve it
- }
-
- //make sure the user has already run the read.otu command
- if (globaldata->getSharedFile() == "") {
- if (globaldata->getListFile() == "") { m->mothurOut("You must read a list and a group, or a shared before you can use the dist.shared command."); m->mothurOutEndLine(); abort = true; }
- else if (globaldata->getGroupFile() == "") { m->mothurOut("You must read a list and a group, or a shared before you can use the dist.shared command."); m->mothurOutEndLine(); abort = true; }
+ outputDir += m->hasPath(sharedfile); //if user entered a file with a path then preserve it
}
//check for optional parameter and set defaults
output = validParameter.validFile(parameters, "output", false); if(output == "not found"){ output = "lt"; }
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"; }
- //if the user has not specified any labels use the ones from read.otu
- if (label == "") {
- allLines = globaldata->allLines;
- labels = globaldata->labels;
- }
-
groups = validParameter.validFile(parameters, "groups", false);
if (groups == "not found") { groups = ""; }
else {
m->splitAtDash(groups, Groups);
- globaldata->Groups = Groups;
+ m->Groups = Groups;
}
+
+ string temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
+ m->setProcessors(temp);
+ convert(temp, processors);
calc = validParameter.validFile(parameters, "calc", false);
if (calc == "not found") { calc = "jclass-thetayc"; }
if (calc == "default") { calc = "jclass-thetayc"; }
}
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; } }
+ }
if (abort == false) {
- validCalculator = new ValidCalculators();
+ ValidCalculators validCalculator;
int i;
for (i=0; i<Estimators.size(); i++) {
- if (validCalculator->isValidCalculator("matrix", Estimators[i]) == true) {
+ if (validCalculator.isValidCalculator("matrix", Estimators[i]) == true) {
if (Estimators[i] == "sharedsobs") {
matrixCalculators.push_back(new SharedSobsCS());
}else if (Estimators[i] == "sharedchao") {
//**********************************************************************************************************************
-void MatrixOutputCommand::help(){
- try {
- m->mothurOut("The dist.shared command can only be executed after a successful read.otu command.\n");
- m->mothurOut("The dist.shared command parameters are groups, calc, output and label. No parameters are required.\n");
- m->mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like included used.\n");
- m->mothurOut("The group names are separated by dashes. The label parameter allows you to select what distance levels you would like distance matrices created for, and is also separated by dashes.\n");
- m->mothurOut("The dist.shared command should be in the following format: dist.shared(groups=yourGroups, calc=yourCalcs, label=yourLabels).\n");
- m->mothurOut("The output parameter allows you to specify format of your distance matrix. Options are lt, and square. The default is lt.\n");
- m->mothurOut("Example dist.shared(groups=A-B-C, calc=jabund-sorabund).\n");
- m->mothurOut("The default value for groups is all the groups in your groupfile.\n");
- m->mothurOut("The default value for calc is jclass and thetayc.\n");
- validCalculator->printCalc("matrix", cout);
- m->mothurOut("The dist.shared command outputs a .dist file for each calculator you specify at each distance you choose.\n");
- m->mothurOut("Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n");
- }
- catch(exception& e) {
- m->errorOut(e, "MatrixOutputCommand", "help");
- exit(1);
- }
-}
-
-
-//**********************************************************************************************************************
-
-MatrixOutputCommand::~MatrixOutputCommand(){
- if (abort == false) {
- delete input; globaldata->ginput = NULL;
- delete read;
- delete validCalculator;
- }
-}
+MatrixOutputCommand::~MatrixOutputCommand(){}
//**********************************************************************************************************************
//if the users entered no valid calculators don't execute command
if (matrixCalculators.size() == 0) { m->mothurOut("No valid calculators."); m->mothurOutEndLine(); return 0; }
-
- //you have groups
- read = new ReadOTUFile(globaldata->inputFileName);
- read->read(&*globaldata);
- input = globaldata->ginput;
+ input = new InputData(sharedfile, "sharedfile");
lookup = input->getSharedRAbundVectors();
string lastLabel = lookup[0]->getLabel();
set<string> processedLabels;
set<string> userLabels = labels;
- if (lookup.size() < 2) { m->mothurOut("You have not provided enough valid groups. I cannot run the command."); m->mothurOutEndLine(); return 0;}
+ if (lookup.size() < 2) { m->mothurOut("You have not provided enough valid groups. I cannot run the command."); m->mothurOutEndLine(); delete input; for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } return 0;}
numGroups = lookup.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 (m->control_pressed) { delete read; delete input; globaldata->ginput = NULL; for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } globaldata->Groups.clear(); return 0; }
+ if (m->control_pressed) { delete input; for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } m->Groups.clear(); return 0; }
//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) { outputTypes.clear(); delete read; delete input; globaldata->ginput = NULL; for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } globaldata->Groups.clear(); return 0; }
+ if (m->control_pressed) { outputTypes.clear(); delete input; for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } m->Groups.clear(); return 0; }
if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
lookup = input->getSharedRAbundVectors();
}
- if (m->control_pressed) { outputTypes.clear(); delete read; delete input; globaldata->ginput = NULL; for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } globaldata->Groups.clear(); return 0; }
+ if (m->control_pressed) { outputTypes.clear(); delete input; for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } m->Groups.clear(); return 0; }
//output error messages about any remaining user labels
set<string>::iterator it;
}
}
- if (m->control_pressed) { outputTypes.clear(); delete read; delete input; globaldata->ginput = NULL; for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } globaldata->Groups.clear(); return 0; }
+ if (m->control_pressed) { outputTypes.clear(); delete input; for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } m->Groups.clear(); return 0; }
//run last label if you need to
if (needToRun == true) {
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
}
- if (m->control_pressed) { outputTypes.clear(); delete read; delete input; globaldata->ginput = NULL; for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } globaldata->Groups.clear(); return 0; }
+ if (m->control_pressed) { outputTypes.clear(); delete input; for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } m->Groups.clear(); return 0; }
//reset groups parameter
- globaldata->Groups.clear();
+ m->Groups.clear();
+
+ //set phylip file as new current phylipfile
+ string current = "";
+ itTypes = outputTypes.find("phylip");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setPhylipFile(current); }
+ }
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
}
}
/***********************************************************/
-void MatrixOutputCommand::printSims(ostream& out) {
+void MatrixOutputCommand::printSims(ostream& out, vector< vector<float> >& simMatrix) {
try {
out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
/***********************************************************/
int MatrixOutputCommand::process(vector<SharedRAbundVector*> thisLookup){
try {
-
- EstOutput data;
- vector<SharedRAbundVector*> subset;
-
- //for each calculator
- for(int i = 0 ; i < matrixCalculators.size(); i++) {
+ EstOutput data;
+ vector<SharedRAbundVector*> subset;
+ vector< vector<seqDist> > calcDists; calcDists.resize(matrixCalculators.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, calcDists);
+ }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, calcDists);
- //initialize simMatrix
- simMatrix.clear();
- simMatrix.resize(numGroups);
- for (int p = 0; p < simMatrix.size(); p++) {
- for (int j = 0; j < simMatrix.size(); j++) {
- simMatrix[p].push_back(0.0);
+ string tempdistFileName = m->getRootName(m->getSimpleName(sharedfile)) + 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, calcDists);
+
+ //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++) {
+ string tempdistFileName = m->getRootName(m->getSimpleName(sharedfile)) + 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, calcDists);
+#endif
+
+ for (int i = 0; i < calcDists.size(); i++) {
+ if (m->control_pressed) { break; }
+
+ //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 k = 0; k < thisLookup.size(); k++) {
- for (int l = k; l < thisLookup.size(); l++) {
- if (k != l) { //we dont need to similiarity of a groups to itself
- //get estimated similarity between 2 groups
-
- if (m->control_pressed) { return 0; }
-
- subset.clear(); //clear out old pair of sharedrabunds
- //add new pair of sharedrabunds
- subset.push_back(thisLookup[k]); subset.push_back(thisLookup[l]);
-
- //if this calc needs all groups to calculate the pair load all groups
- if (matrixCalculators[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]); }
- }
- }
-
- data = matrixCalculators[i]->getValues(subset); //saves the calculator outputs
- //save values in similarity matrix
- simMatrix[k][l] = 1.0 - data[0]; //convert similiarity to distance
- simMatrix[l][k] = 1.0 - data[0]; //convert similiarity to distance
+ 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;
+ }
+
+ string distFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + matrixCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + "." + output + ".dist";
+ 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();
+ }
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "MatrixOutputCommand", "process");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+int MatrixOutputCommand::driver(vector<SharedRAbundVector*> thisLookup, int start, int end, vector< vector<seqDist> >& calcDists) {
+ try {
+
+ vector<SharedRAbundVector*> subset;
+ for (int k = start; k < end; k++) { // pass cdd each set of groups to compare
+
+ for (int l = 0; l < k; l++) {
+
+ if (k != l) { //we dont need to similiarity of a groups to itself
+ subset.clear(); //clear out old pair of sharedrabunds
+ //add new pair of sharedrabunds
+ subset.push_back(thisLookup[k]); subset.push_back(thisLookup[l]);
+
+ for(int i=0;i<matrixCalculators.size();i++) {
+
+ //if this calc needs all groups to calculate the pair load all groups
+ if (matrixCalculators[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]); }
}
}
+
+ vector<double> tempdata = matrixCalculators[i]->getValues(subset); //saves the calculator outputs
+
+ if (m->control_pressed) { return 1; }
+
+ seqDist temp(l, k, tempdata[0]);
+ calcDists[i].push_back(temp);
}
-
- exportFileName = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + matrixCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + "." + output + ".dist";
- m->openOutputFile(exportFileName, out);
- outputNames.push_back(exportFileName); outputTypes["phylip"].push_back(exportFileName);
-
- printSims(out);
- out.close();
-
}
-
- return 0;
+ }
+ }
+ return 0;
}
catch(exception& e) {
- m->errorOut(e, "MatrixOutputCommand", "process");
+ m->errorOut(e, "MatrixOutputCommand", "driver");
exit(1);
}
}
projects / mothur.git / blobdiff