+++ /dev/null
-/*
- * libshuffcommand.cpp
- * Mothur
- *
- * Created by Sarah Westcott on 3/9/09.
- * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
- *
- */
-
-/* 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"
-
-
-
-//**********************************************************************************************************************
-vector<string> LibShuffCommand::setParameters(){
- try {
- CommandParameter pphylip("phylip", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pphylip);
- CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none",false,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) {
- m->errorOut(e, "LibShuffCommand", "setParameters");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-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(){
- 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);
- }
-}
-
-//**********************************************************************************************************************
-LibShuffCommand::LibShuffCommand(string option) {
- try {
- abort = false; calledHelp = false;
-
- //allow user to run help
- if(option == "help") { help(); abort = true; calledHelp = true; }
- else if(option == "citation") { citation(); abort = true; calledHelp = true;}
-
- else {
- 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; }
- }
-
- //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; }
- }
- }
-
- //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); }
-
- //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; }
-
- ifstream in;
- m->openInputFile(phylipfile, in);
- matrix = new FullMatrix(in, groupMap, sim); //reads the matrix file
- in.close();
-
- 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); }
-
- 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;
- }
- outGroups.close();
-
- 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; }
- }
-
-
- 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; }
-
- 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);
-
-
- 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
- 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) {
- m->errorOut(e, "LibShuffCommand", "execute");
- exit(1);
- }
-}
-
-//**********************************************************************************************************************
-
-int LibShuffCommand::printCoverageFile() {
- try {
-
- ofstream outCov;
- summaryFile = outputDir + m->getRootName(m->getSimpleName(phylipfile)) + "libshuff.coverage";
- 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;
- }
- }
- }
- }
- 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];
- }
- }
- 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) {
- m->errorOut(e, "LibShuffCommand", "printCoverageFile");
- exit(1);
- }
-}
-
-//**********************************************************************************************************************
-
-int LibShuffCommand::printSummaryFile() {
- try {
-
- ofstream outSum;
- summaryFile = outputDir + m->getRootName(m->getSimpleName(phylipfile)) + "libshuff.summary";
- 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);
-
- 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.close();
- return 0;
- }
- catch(exception& e) {
- m->errorOut(e, "LibShuffCommand", "printSummaryFile");
- 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 (m->getNumGroups() == 0) {
- numGroups = groupMap->getNumGroups();
- for (int i=0; i < numGroups; i++) {
- myGroups.push_back((groupMap->getNamesOfGroups())[i]);
- }
- } else {
- if (savegroups != "all") {
- //check that groups are valid
- 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
- myGroups.erase(myGroups.begin()+i);
- }
- }
-
- //if the user only entered invalid groups
- if ((myGroups.size() == 0) || (myGroups.size() == 1)) {
- numGroups = groupMap->getNumGroups();
- for (int i=0; i < numGroups; i++) {
- myGroups.push_back((groupMap->getNamesOfGroups())[i]);
- }
- 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++) {
- myGroups.push_back((groupMap->getNamesOfGroups())[i]);
- }
- }
- }
-
- //sort so labels match
- sort(myGroups.begin(), myGroups.end());
-
- //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) {
- m->errorOut(e, "LibShuffCommand", "setGroups");
- exit(1);
- }
-}
-
-/***********************************************************/
projects / mothur.git / blobdiff