*
*/
-#include "libshuffcommand.h"
+/* This class is designed to implement an integral form of the Cramer-von Mises statistic.
+ you may refer to the "Integration of Microbial Ecology and Statistics: A Test To Compare Gene Libraries"
+ paper in Applied and Environmental Microbiology, Sept. 2004, p. 5485-5492 0099-2240/04/$8.00+0
+ DOI: 10.1128/AEM.70.9.5485-5492.2004 Copyright 2004 American Society for Microbiology for more information. */
-//**********************************************************************************************************************
+#include "libshuffcommand.h"
+#include "libshuff.h"
+#include "slibshuff.h"
+#include "dlibshuff.h"
-LibShuffCommand::LibShuffCommand(){
- try {
- globaldata = GlobalData::getInstance();
- convert(globaldata->getCutOff(), cutOff);
- convert(globaldata->getIters(), iters);
- convert(globaldata->getStep(), step);
- form = globaldata->getForm();
- matrix = globaldata->gMatrix;
- coverageFile = getRootName(globaldata->getPhylipFile()) + "coverage";
- summaryFile = getRootName(globaldata->getPhylipFile()) + "slsummary";
- openOutputFile(coverageFile, out);
- openOutputFile(summaryFile, outSum);
-
- //set the groups to be analyzed
- setGroups();
- //file headers for coverage file
- out << "D" << '\t';
- for (int i = 0; i < groupComb.size(); i++) {
- out << "C" + groupComb[i] << '\t';
- }
-
- for (int i = 0; i < numGroups; i++) {
- for (int j = 0; j < numGroups; j++) {
- //don't output AA to AA
- if (i != j) {
- out << "Delta" + globaldata->Groups[i] + "-" + globaldata->Groups[j] << '\t';
- }
- }
- }
- out << endl;
- numComp = numGroups*numGroups;
-
- coverage = new Coverage();
+//**********************************************************************************************************************
+vector<string> LibShuffCommand::setParameters(){
+ try {
+ CommandParameter pphylip("phylip", "InputTypes", "", "", "none", "none", "none","coverage-libshuffsummary",false,true,true); parameters.push_back(pphylip);
+ CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(pgroup);
+ CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
+ CommandParameter piters("iters", "Number", "", "10000", "", "", "","",false,false); parameters.push_back(piters);
+ CommandParameter pstep("step", "Number", "", "0.01", "", "", "","",false,false); parameters.push_back(pstep);
+ CommandParameter pcutoff("cutoff", "Number", "", "1.0", "", "", "","",false,false); parameters.push_back(pcutoff);
+ CommandParameter pform("form", "Multiple", "discrete-integral", "integral", "", "", "","",false,false); parameters.push_back(pform);
+ CommandParameter psim("sim", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(psim);
+ 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) {
- cout << "Standard Error: " << e.what() << " has occurred in the LibShuffCommand class Function LibShuffCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "LibShuffCommand", "setParameters");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the LibShuffCommand class function LibShuffCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+}
+//**********************************************************************************************************************
+string LibShuffCommand::getHelpString(){
+ try {
+ string helpString = "";
+ helpString += "The libshuff command parameters are phylip, group, sim, groups, iters, step, form and cutoff. phylip and group parameters are required, unless you have valid current files.\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 += "The group names are separated by dashes. The iters parameter allows you to specify how many random matrices you would like compared to your matrix.\n";
+ helpString += "The step parameter allows you to specify change in distance you would like between each output if you are using the discrete form.\n";
+ helpString += "The form parameter allows you to specify if you would like to analyze your matrix using the discrete or integral form. Your options are integral or discrete.\n";
+ helpString += "The libshuff command should be in the following format: libshuff(groups=yourGroups, iters=yourIters, cutOff=yourCutOff, form=yourForm, step=yourStep).\n";
+ helpString += "Example libshuff(groups=A-B-C, iters=500, form=discrete, step=0.01, cutOff=2.0).\n";
+ helpString += "The default value for groups is all the groups in your groupfile, iters is 10000, cutoff is 1.0, form is integral and step is 0.01.\n";
+ helpString += "The libshuff command output two files: .coverage and .slsummary their descriptions are in the manual.\n";
+ helpString += "Note: No spaces between parameter labels (i.e. iters), '=' and parameters (i.e.yourIters).\n";
+ return helpString;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "LibShuffCommand", "getHelpString");
exit(1);
- }
-
+ }
}
-
//**********************************************************************************************************************
-
-LibShuffCommand::~LibShuffCommand(){
- delete coverage;
+string LibShuffCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
+
+ if (type == "coverage") { pattern = "[filename],libshuff.coverage"; }
+ else if (type == "libshuffsummary") { pattern = "[filename],libshuff.summary"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "LibShuffCommand", "getOutputPattern");
+ exit(1);
+ }
}
-
//**********************************************************************************************************************
+LibShuffCommand::LibShuffCommand(){
+ try {
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["coverage"] = tempOutNames;
+ outputTypes["libshuffsummary"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "LibShuffCommand", "LibShuffCommand");
+ exit(1);
+ }
+}
-int LibShuffCommand::execute(){
+//**********************************************************************************************************************
+LibShuffCommand::LibShuffCommand(string option) {
try {
- //deltaValues[0] = scores for the difference between AA and AB.
- //cValues[0][0][0] = AA at distance 0.0, cValues[0][0][1] = AB at distance 0.0, cValues[0][0][2] = AC at distance 0.0, cValues[0][1][0] = BA at distance 0.0, cValues[0][1][1] = BB...
- Progress* reading;
- reading = new Progress("Comparing to random:", iters);
-
- sumDelta.resize(numComp-numGroups, 0.0);
+ abort = false; calledHelp = false;
- matrix->setBounds();
+ //allow user to run help
+ if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
- //load distances
- if (form != "discrete") { matrix->getDist(dist); }
else {
- float f = 0.0;
- while (f <= cutOff) {
- dist.push_back(f);
- f += step;
+ 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 (it = parameters.begin(); it != parameters.end(); it++) {
+ if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
- }
-
- /*****************************/
- //get values for users matrix
- /*****************************/
- //clear out old Values
- deltaValues.clear();
- deltaValues.resize(dist.size());
-
- coverage->getValues(matrix, cValues, dist, "user");
-
- //loop through each distance and load rsumdelta
- for (int p = 0; p < cValues.size(); p++) {
- //find delta values
- int count = 0;
- for (int i = 0; i < numGroups; i++) {
- for (int j = 0; j < numGroups; j++) {
- //don't save AA to AA
- if (i != j) {
- //(Caa - Cab)^2
- deltaValues[p].push_back( (abs(cValues[p][i][i]-cValues[p][i][j]) * abs(cValues[p][i][i]-cValues[p][i][j])) );
- sumDelta[count] += deltaValues[p][count];
- count++;
- }
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["coverage"] = tempOutNames;
+ outputTypes["libshuffsummary"] = tempOutNames;
+
+ string inputDir = validParameter.validFile(parameters, "inputdir", false);
+ if (inputDir == "not found"){ inputDir = ""; }
+ else {
+ string path;
+ it = parameters.find("phylip");
+ //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["phylip"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("group");
+ //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["group"] = inputDir + it->second; }
}
}
- }
- printCoverageFile();
+ //check for required parameters
+ phylipfile = validParameter.validFile(parameters, "phylip", true);
+ if (phylipfile == "not open") { phylipfile = ""; abort = true; }
+ else if (phylipfile == "not found") {
+ phylipfile = m->getPhylipFile();
+ if (phylipfile != "") { m->mothurOut("Using " + phylipfile + " as input file for the phylip parameter."); m->mothurOutEndLine(); }
+ else {
+ m->mothurOut("You must provide a phylip file."); m->mothurOutEndLine();
+ abort = true;
+ }
+ }else { m->setPhylipFile(phylipfile); }
- /*******************************************************************************/
- //create and score random matrixes finding the sumDelta values for summary file
- /******************************************************************************/
-
- //initialize rsumDelta
- rsumDelta.resize(numComp-numGroups);
- for (int l = 0; l < rsumDelta.size(); l++) {
- for (int w = 0; w < iters; w++) {
- rsumDelta[l].push_back(0.0);
+ //check for required parameters
+ groupfile = validParameter.validFile(parameters, "group", true);
+ if (groupfile == "not open") { groupfile = ""; abort = true; }
+ else if (groupfile == "not found") {
+ groupfile = m->getGroupFile();
+ if (groupfile != "") { m->mothurOut("Using " + groupfile + " as input file for the group parameter."); m->mothurOutEndLine(); }
+ else {
+ m->mothurOut("You must provide a group file."); m->mothurOutEndLine();
+ abort = true;
+ }
+ }else { m->setGroupFile(groupfile); }
+
+ //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(phylipfile); //if user entered a file with a path then preserve it
}
+
+ //check for optional parameter and set defaults
+ // ...at some point should added some additional type checking...
+ groups = validParameter.validFile(parameters, "groups", false);
+ if (groups == "not found") { groups = ""; savegroups = groups; }
+ else {
+ savegroups = groups;
+ m->splitAtDash(groups, Groups);
+ m->setGroups(Groups);
+ }
+
+ string temp;
+ temp = validParameter.validFile(parameters, "iters", false); if (temp == "not found") { temp = "10000"; }
+ m->mothurConvert(temp, iters);
+
+ temp = validParameter.validFile(parameters, "cutoff", false); if (temp == "not found") { temp = "1.0"; }
+ m->mothurConvert(temp, cutOff);
+
+ temp = validParameter.validFile(parameters, "step", false); if (temp == "not found") { temp = "0.01"; }
+ m->mothurConvert(temp, step);
+
+ temp = validParameter.validFile(parameters, "sim", false); if (temp == "not found") { temp = "F"; }
+ sim = m->isTrue(temp);
+
+ userform = validParameter.validFile(parameters, "form", false); if (userform == "not found") { userform = "integral"; }
+
}
+ }
+ catch(exception& e) {
+ m->errorOut(e, "LibShuffCommand", "LibShuffCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+int LibShuffCommand::execute(){
+ try {
+
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
+
+ //read files
+ groupMap = new GroupMap(groupfile);
+ int error = groupMap->readMap();
+ if (error == 1) { delete groupMap; return 0; }
- for (int m = 0; m < iters; m++) {
- //generate random matrix in getValues
- //values for random matrix
+ ifstream in;
+ m->openInputFile(phylipfile, in);
+ matrix = new FullMatrix(in, groupMap, sim); //reads the matrix file
+ in.close();
- coverage->getValues(matrix, cValues, dist, "random");
+ if (m->control_pressed) { delete groupMap; delete matrix; return 0; }
+
+ //if files don't match...
+ if (matrix->getNumSeqs() < groupMap->getNumSeqs()) {
+ m->mothurOut("Your distance file contains " + toString(matrix->getNumSeqs()) + " sequences, and your group file contains " + toString(groupMap->getNumSeqs()) + " sequences."); m->mothurOutEndLine();
+ //create new group file
+ if(outputDir == "") { outputDir += m->hasPath(groupfile); }
- //loop through each distance and load rsumdelta
- for (int p = 0; p < cValues.size(); p++) {
- //find delta values
- int count = 0;
- for (int i = 0; i < numGroups; i++) {
- for (int j = 0; j < numGroups; j++) {
- //don't save AA to AA
- if (i != j) {
- //(Caa - Cab)^2
- rsumDelta[count][m] += ((abs(cValues[p][i][i]-cValues[p][i][j]) * abs(cValues[p][i][i]-cValues[p][i][j])));
- count++;
- }
- }
- }
+ string newGroupFile = outputDir + m->getRootName(m->getSimpleName(groupfile)) + "editted.groups";
+ outputNames.push_back(newGroupFile);
+ ofstream outGroups;
+ m->openOutputFile(newGroupFile, outGroups);
+
+ for (int i = 0; i < matrix->getNumSeqs(); i++) {
+ if (m->control_pressed) { delete groupMap; delete matrix; outGroups.close(); m->mothurRemove(newGroupFile); return 0; }
+ Names temp = matrix->getRowInfo(i);
+ outGroups << temp.seqName << '\t' << temp.groupName << endl;
}
-//cout << "iter " << m << endl;
- //clear out old Values
- reading->update(m);
- cValues.clear();
+ outGroups.close();
-//cout << "random sum delta for iter " << m << endl;
-//for (int i = 0; i < rsumDelta.size(); i++) {
-// cout << setprecision(6) << rsumDelta[i][m] << '\t';
-//}
-//cout << endl;
-
+ m->mothurOut(newGroupFile + " is a new group file containing only the sequence that are in your distance file. I will read this file instead."); m->mothurOutEndLine();
+
+ //read new groupfile
+ delete groupMap;
+ groupfile = newGroupFile;
+
+ groupMap = new GroupMap(groupfile);
+ groupMap->readMap();
+
+ if (m->control_pressed) { delete groupMap; delete matrix; m->mothurRemove(newGroupFile); return 0; }
}
- reading->finish();
- delete reading;
-
- /**********************************************************/
- //find the signifigance of the user matrix' sumdelta values
- /**********************************************************/
+
+ setGroups(); //set the groups to be analyzed and sorts them
+
+ if (numGroups < 2) { m->mothurOut("[ERROR]: libshuff requires at least 2 groups, you only have " + toString(numGroups) + ", aborting."); m->mothurOutEndLine(); m->control_pressed = true; }
- for (int t = 0; t < rsumDelta.size(); t++) {
- //sort rsumDelta t
- sort(rsumDelta[t].begin(), rsumDelta[t].end());
+ if (m->control_pressed) { delete groupMap; delete matrix; return 0; }
+
+ /********************************************************************************************/
+ //this is needed because when we read the matrix we sort it into groups in alphabetical order
+ //the rest of the command and the classes used in this command assume specific order
+ /********************************************************************************************/
+ matrix->setGroups(groupMap->getNamesOfGroups());
+ vector<int> sizes;
+ for (int i = 0; i < (groupMap->getNamesOfGroups()).size(); i++) { sizes.push_back(groupMap->getNumSeqs((groupMap->getNamesOfGroups())[i])); }
+ matrix->setSizes(sizes);
- //the index of the score higher than yours is returned
- //so if you have 1000 random matrices the index returned is 100
- //then there are 900 matrices with a score greater then you.
- //giving you a signifigance of 0.900
- int index = findIndex(sumDelta[t], t);
- //the signifigance is the number of trees with the users score or higher
- sumDeltaSig.push_back((iters-index)/(float)iters);
+ if(userform == "discrete"){
+ form = new DLibshuff(matrix, iters, step, cutOff);
+ }
+ else{
+ form = new SLibshuff(matrix, iters, cutOff);
+ }
+
+ savedDXYValues = form->evaluateAll();
+ savedMinValues = form->getSavedMins();
+
+ if (m->control_pressed) { delete form; m->clearGroups(); delete matrix; delete groupMap; return 0; }
+
+ pValueCounts.resize(numGroups);
+ for(int i=0;i<numGroups;i++){
+ pValueCounts[i].assign(numGroups, 0);
+ }
+
+ if (m->control_pressed) { outputTypes.clear(); delete form; m->clearGroups(); delete matrix; delete groupMap; return 0; }
+
+ Progress* reading = new Progress();
+
+ for(int i=0;i<numGroups-1;i++) {
+ for(int j=i+1;j<numGroups;j++) {
+
+ if (m->control_pressed) { outputTypes.clear(); delete form; m->clearGroups(); delete matrix; delete groupMap; delete reading; return 0; }
+ reading->newLine(groupNames[i]+'-'+groupNames[j], iters);
+ int spoti = groupMap->groupIndex[groupNames[i]]; //neccessary in case user selects groups so you know where they are in the matrix
+ int spotj = groupMap->groupIndex[groupNames[j]];
+
+ for(int p=0;p<iters;p++) {
+
+ if (m->control_pressed) { outputTypes.clear(); delete form; m->clearGroups(); delete matrix; delete groupMap; delete reading; return 0; }
+
+ form->randomizeGroups(spoti,spotj);
+ if(form->evaluatePair(spoti,spotj) >= savedDXYValues[spoti][spotj]) { pValueCounts[i][j]++; }
+ if(form->evaluatePair(spotj,spoti) >= savedDXYValues[spotj][spoti]) { pValueCounts[j][i]++; }
+
+ if (m->control_pressed) { outputTypes.clear(); delete form; m->clearGroups(); delete matrix; delete groupMap; delete reading; return 0; }
+
+ reading->update(p);
+ }
+ form->resetGroup(spoti);
+ form->resetGroup(spotj);
+ }
}
+ if (m->control_pressed) { outputTypes.clear(); delete form; m->clearGroups(); delete matrix; delete groupMap; delete reading; return 0; }
+
+ reading->finish();
+ delete reading;
+
+ m->mothurOutEndLine();
printSummaryFile();
-
+ printCoverageFile();
+
//clear out users groups
- globaldata->Groups.clear();
+ m->clearGroups();
+ delete form;
+
+ delete matrix; delete groupMap;
+
+ if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
+
+ m->mothurOutEndLine();
+ m->mothurOut("Output File Names: "); m->mothurOutEndLine();
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
+ m->mothurOutEndLine();
return 0;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the LibShuffCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "LibShuffCommand", "execute");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the LibShuffCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
}
+
//**********************************************************************************************************************
-void LibShuffCommand::printCoverageFile() {
+
+int LibShuffCommand::printCoverageFile() {
try {
- //format output
- out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
-
- //loop through each distance
- for (int p = 0; p < cValues.size(); p++) {
- out << setprecision(6) << dist[p] << '\t';
- //print out coverage values
- for (int i = 0; i < numGroups; i++) {
- for (int j = 0; j < numGroups; j++) {
- out << cValues[p][i][j] << '\t';
+
+ ofstream outCov;
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(phylipfile));
+ summaryFile = getOutputFileName("coverage", variables);
+ m->openOutputFile(summaryFile, outCov);
+ outputNames.push_back(summaryFile); outputTypes["coverage"].push_back(summaryFile);
+ outCov.setf(ios::fixed, ios::floatfield); outCov.setf(ios::showpoint);
+ //cout.setf(ios::fixed, ios::floatfield); cout.setf(ios::showpoint);
+
+ map<double,vector<int> > allDistances;
+ map<double,vector<int> >::iterator it;
+
+ vector<vector<int> > indices(numGroups);
+ int numIndices = numGroups * numGroups;
+
+ int index = 0;
+ for(int i=0;i<numGroups;i++){
+ indices[i].assign(numGroups,0);
+ for(int j=0;j<numGroups;j++){
+ indices[i][j] = index++;
+
+ int spoti = groupMap->groupIndex[groupNames[i]]; //neccessary in case user selects groups so you know where they are in the matrix
+ int spotj = groupMap->groupIndex[groupNames[j]];
+
+ for(int k=0;k<savedMinValues[spoti][spotj].size();k++){
+
+ if(m->control_pressed) { outCov.close(); return 0; }
+
+ if(allDistances[savedMinValues[spoti][spotj][k]].size() != 0){
+ allDistances[savedMinValues[spoti][spotj][k]][indices[i][j]]++;
+ }
+ else{
+ allDistances[savedMinValues[spoti][spotj][k]].assign(numIndices, 0);
+ allDistances[savedMinValues[spoti][spotj][k]][indices[i][j]] = 1;
+ }
}
}
-
- for (int h = 0; h < deltaValues[p].size(); h++) {
- out << deltaValues[p][h] << '\t';
+ }
+ it=allDistances.begin();
+
+ //cout << setprecision(8);
+
+ vector<int> prevRow = it->second;
+ it++;
+
+ for(;it!=allDistances.end();it++){
+ for(int i=0;i<it->second.size();i++){
+ it->second[i] += prevRow[i];
+ }
+ prevRow = it->second;
+ }
+
+ vector<int> lastRow = allDistances.rbegin()->second;
+ outCov << setprecision(8);
+
+ outCov << "dist";
+ for (int i = 0; i < numGroups; i++){
+ outCov << '\t' << groupNames[i];
+ }
+ for (int i=0;i<numGroups;i++){
+ for(int j=i+1;j<numGroups;j++){
+ if(m->control_pressed) { outCov.close(); return 0; }
+ outCov << '\t' << groupNames[i] << '-' << groupNames[j] << '\t';
+ outCov << groupNames[j] << '-' << groupNames[i];
}
-
- out << endl;
}
+ outCov << endl;
+ for(it=allDistances.begin();it!=allDistances.end();it++){
+ outCov << it->first << '\t';
+ for(int i=0;i<numGroups;i++){
+ outCov << it->second[indices[i][i]]/(float)lastRow[indices[i][i]] << '\t';
+ }
+ for(int i=0;i<numGroups;i++){
+ for(int j=i+1;j<numGroups;j++){
+ if(m->control_pressed) { outCov.close(); return 0; }
+
+ outCov << it->second[indices[i][j]]/(float)lastRow[indices[i][j]] << '\t';
+ outCov << it->second[indices[j][i]]/(float)lastRow[indices[j][i]] << '\t';
+ }
+ }
+ outCov << endl;
+ }
+ outCov.close();
+
+ return 0;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the LibShuffCommand class Function printCoverageFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "LibShuffCommand", "printCoverageFile");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the LibShuffCommand class function printCoverageFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
}
+
//**********************************************************************************************************************
-void LibShuffCommand::printSummaryFile() {
+
+int LibShuffCommand::printSummaryFile() {
try {
- //format output
+
+ ofstream outSum;
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(phylipfile));
+ summaryFile = getOutputFileName("libshuffsummary",variables);
+ m->openOutputFile(summaryFile, outSum);
+ outputNames.push_back(summaryFile); outputTypes["libshuffsummary"].push_back(summaryFile);
+
outSum.setf(ios::fixed, ios::floatfield); outSum.setf(ios::showpoint);
+ cout.setf(ios::fixed, ios::floatfield); cout.setf(ios::showpoint);
- for (int i = 0; i < numGroups; i++) {
- for (int j = 0; j < numGroups; j++) {
- //don't output AA to AA
- if (i != j) {
- outSum << "Delta " + globaldata->Groups[i] + "-" + globaldata->Groups[j] << '\t'<< "DeltaSig " + globaldata->Groups[i] + "-" + globaldata->Groups[j] << '\t';
- cout << "Delta " + globaldata->Groups[i] + "-" + globaldata->Groups[j] << '\t'<< "DeltaSig " + globaldata->Groups[i] + "-" + globaldata->Groups[j] << '\t';
+ cout << setw(20) << left << "Comparison" << '\t' << setprecision(8) << "dCXYScore" << '\t' << "Significance" << endl;
+ m->mothurOutJustToLog("Comparison\tdCXYScore\tSignificance"); m->mothurOutEndLine();
+ outSum << setw(20) << left << "Comparison" << '\t' << setprecision(8) << "dCXYScore" << '\t' << "Significance" << endl;
+
+ int precision = (int)log10(iters);
+ for(int i=0;i<numGroups;i++){
+ for(int j=i+1;j<numGroups;j++){
+ if(m->control_pressed) { outSum.close(); return 0; }
+
+ int spoti = groupMap->groupIndex[groupNames[i]]; //neccessary in case user selects groups so you know where they are in the matrix
+ int spotj = groupMap->groupIndex[groupNames[j]];
+
+ if(pValueCounts[i][j]){
+ cout << setw(20) << left << groupNames[i]+'-'+groupNames[j] << '\t' << setprecision(8) << savedDXYValues[spoti][spotj] << '\t' << setprecision(precision) << pValueCounts[i][j]/(float)iters << endl;
+ m->mothurOutJustToLog(groupNames[i]+"-"+groupNames[j] + "\t" + toString(savedDXYValues[spoti][spotj]) + "\t" + toString((pValueCounts[i][j]/(float)iters))); m->mothurOutEndLine();
+ outSum << setw(20) << left << groupNames[i]+'-'+groupNames[j] << '\t' << setprecision(8) << savedDXYValues[spoti][spotj] << '\t' << setprecision(precision) << pValueCounts[i][j]/(float)iters << endl;
+ }
+ else{
+ cout << setw(20) << left << groupNames[i]+'-'+groupNames[j] << '\t' << setprecision(8) << savedDXYValues[spoti][spotj] << '\t' << '<' <<setprecision(precision) << 1/(float)iters << endl;
+ m->mothurOutJustToLog(groupNames[i]+"-"+groupNames[j] + "\t" + toString(savedDXYValues[spoti][spotj]) + "\t" + toString((1/(float)iters))); m->mothurOutEndLine();
+ outSum << setw(20) << left << groupNames[i]+'-'+groupNames[j] << '\t' << setprecision(8) << savedDXYValues[spoti][spotj] << '\t' << '<' <<setprecision(precision) << 1/(float)iters << endl;
+ }
+ if(pValueCounts[j][i]){
+ cout << setw(20) << left << groupNames[j]+'-'+groupNames[i] << '\t' << setprecision(8) << savedDXYValues[spotj][spoti] << '\t' << setprecision (precision) << pValueCounts[j][i]/(float)iters << endl;
+ m->mothurOutJustToLog(groupNames[j]+"-"+groupNames[i] + "\t" + toString(savedDXYValues[spotj][spoti]) + "\t" + toString((pValueCounts[j][i]/(float)iters))); m->mothurOutEndLine();
+ outSum << setw(20) << left << groupNames[j]+'-'+groupNames[i] << '\t' << setprecision(8) << savedDXYValues[spotj][spoti] << '\t' << setprecision (precision) << pValueCounts[j][i]/(float)iters << endl;
+ }
+ else{
+ cout << setw(20) << left << groupNames[j]+'-'+groupNames[i] << '\t' << setprecision(8) << savedDXYValues[spotj][spoti] << '\t' << '<' <<setprecision (precision) << 1/(float)iters << endl;
+ m->mothurOutJustToLog(groupNames[j]+"-"+groupNames[i] + "\t" + toString(savedDXYValues[spotj][spoti]) + "\t" + toString((1/(float)iters))); m->mothurOutEndLine();
+ outSum << setw(20) << left << groupNames[j]+'-'+groupNames[i] << '\t' << setprecision(8) << savedDXYValues[spotj][spoti] << '\t' << '<' <<setprecision (precision) << 1/(float)iters << endl;
}
- }
- }
- outSum << endl;
- cout << endl;
-
- //print out delta values
- for (int i = 0; i < sumDelta.size(); i++) {
- if (sumDeltaSig[i] > (1/(float)iters)) {
- outSum << setprecision(6) << sumDelta[i] << '\t' << setprecision(globaldata->getIters().length()) << sumDeltaSig[i] << '\t';
- cout << setprecision(6) << sumDelta[i] << '\t' << setprecision(globaldata->getIters().length()) << sumDeltaSig[i] << '\t';
- }else {
- outSum << setprecision(6) << sumDelta[i] << '\t' << setprecision(globaldata->getIters().length()) << "<" << (1/float(iters)) << '\t';
- cout << setprecision(6) << sumDelta[i] << '\t' << setprecision(globaldata->getIters().length()) << "<" << (1/float(iters)) << '\t';
}
}
- outSum << endl;
- cout << endl;
-
+ outSum.close();
+ return 0;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the LibShuffCommand class Function printSummaryFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "LibShuffCommand", "printSummaryFile");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the LibShuffCommand class function printSummaryFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
}
//**********************************************************************************************************************
+
void LibShuffCommand::setGroups() {
try {
+ vector<string> myGroups = m->getGroups();
//if the user has not entered specific groups to analyze then do them all
- if (globaldata->Groups.size() == 0) {
- numGroups = globaldata->gGroupmap->getNumGroups();
+ if (m->getNumGroups() == 0) {
+ numGroups = groupMap->getNumGroups();
for (int i=0; i < numGroups; i++) {
- globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
+ myGroups.push_back((groupMap->getNamesOfGroups())[i]);
}
- }else {
- if (globaldata->getGroups() != "all") {
+ } else {
+ if (savegroups != "all") {
//check that groups are valid
- for (int i = 0; i < globaldata->Groups.size(); i++) {
- if (globaldata->gGroupmap->isValidGroup(globaldata->Groups[i]) != true) {
- cout << globaldata->Groups[i] << " is not a valid group, and will be disregarded." << endl;
+ for (int i = 0; i < myGroups.size(); i++) {
+ if (groupMap->isValidGroup(myGroups[i]) != true) {
+ m->mothurOut(myGroups[i] + " is not a valid group, and will be disregarded."); m->mothurOutEndLine();
// erase the invalid group from globaldata->Groups
- globaldata->Groups.erase (globaldata->Groups.begin()+i);
+ myGroups.erase(myGroups.begin()+i);
}
}
//if the user only entered invalid groups
- if ((globaldata->Groups.size() == 0) || (globaldata->Groups.size() == 1)) {
- numGroups = globaldata->gGroupmap->getNumGroups();
+ if ((myGroups.size() == 0) || (myGroups.size() == 1)) {
+ numGroups = groupMap->getNumGroups();
for (int i=0; i < numGroups; i++) {
- globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
+ myGroups.push_back((groupMap->getNamesOfGroups())[i]);
}
- cout << "When using the groups parameter you must have at least 2 valid groups. I will run the command using all the groups in your groupfile." << endl;
- }else { numGroups = globaldata->Groups.size(); }
- }else { //users wants all groups
- numGroups = globaldata->gGroupmap->getNumGroups();
- globaldata->Groups.clear();
+ m->mothurOut("When using the groups parameter you must have at least 2 valid groups. I will run the command using all the groups in your groupfile."); m->mothurOutEndLine();
+ } else { numGroups = myGroups.size(); }
+ } else { //users wants all groups
+ numGroups = groupMap->getNumGroups();
+ myGroups.clear();
for (int i=0; i < numGroups; i++) {
- globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
+ myGroups.push_back((groupMap->getNamesOfGroups())[i]);
}
}
}
-
+
//sort so labels match
- sort(globaldata->Groups.begin(), globaldata->Groups.end());
+ sort(myGroups.begin(), myGroups.end());
- // number of comparisons i.e. with groups A,B,C = AA, AB, AC, BA, BB, BC...;
- for (int i=0; i<numGroups; i++) {
- for (int l = 0; l < numGroups; l++) {
- //set group comparison labels
- groupComb.push_back(globaldata->Groups[i] + "-" + globaldata->Groups[l]);
- }
- }
- }
- catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the LibShuffCommand class Function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the LibShuffCommand class function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
-}
-/***********************************************************/
-int LibShuffCommand::findIndex(float score, int index) {
- try{
- for (int i = 0; i < rsumDelta[index].size(); i++) {
- if (rsumDelta[index][i] >= score) { return i; }
- }
- return rsumDelta[index].size();
+ //sort
+ //sort(groupMap->namesOfGroups.begin(), groupMap->namesOfGroups.end());
+
+ for (int i = 0; i < (groupMap->getNamesOfGroups()).size(); i++) { groupMap->groupIndex[(groupMap->getNamesOfGroups())[i]] = i; }
+
+ groupNames = myGroups;
+ m->setGroups(myGroups);
+
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the LibShuffCommand class Function findIndex. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the LibShuffCommand class function findIndex. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "LibShuffCommand", "setGroups");
exit(1);
}
}
/***********************************************************/
-
projects / mothur.git / blobdiff