+++ /dev/null
-/*
- * clusterdoturcommand.cpp
- * Mothur
- *
- * Created by westcott on 10/27/10.
- * Copyright 2010 Schloss Lab. All rights reserved.
- *
- */
-
-#include "clusterdoturcommand.h"
-#include "clusterclassic.h"
-
-//**********************************************************************************************************************
-vector<string> ClusterDoturCommand::setParameters(){
- try {
- CommandParameter pphylip("phylip", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pphylip);
- CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
- CommandParameter pcutoff("cutoff", "Number", "", "10", "", "", "",false,false); parameters.push_back(pcutoff);
- CommandParameter pprecision("precision", "Number", "", "100", "", "", "",false,false); parameters.push_back(pprecision);
- CommandParameter pmethod("method", "Multiple", "furthest-nearest-average-weighted", "average", "", "", "",false,false); parameters.push_back(pmethod);
- CommandParameter phard("hard", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(phard);
- 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, "ClusterDoturCommand", "setParameters");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-string ClusterDoturCommand::getHelpString(){
- try {
- string helpString = "";
- helpString += "The cluster.classic command clusters using the algorithm from dotur. \n";
- helpString += "The cluster.classic command parameter options are phylip, name, method, cuttoff, hard, sim, precision. Phylip is required, unless you have a valid current file.\n";
- helpString += "The cluster.classic command should be in the following format: \n";
- helpString += "cluster.classic(phylip=yourDistanceMatrix, method=yourMethod, cutoff=yourCutoff, precision=yourPrecision) \n";
- helpString += "The acceptable cluster methods are furthest, nearest, weighted and average. If no method is provided then average is assumed.\n";
- return helpString;
- }
- catch(exception& e) {
- m->errorOut(e, "ClusterDoturCommand", "getHelpString");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-ClusterDoturCommand::ClusterDoturCommand(){
- try {
- abort = true; calledHelp = true;
- setParameters();
- vector<string> tempOutNames;
- outputTypes["list"] = tempOutNames;
- outputTypes["rabund"] = tempOutNames;
- outputTypes["sabund"] = tempOutNames;
- }
- catch(exception& e) {
- m->errorOut(e, "ClusterDoturCommand", "ClusterCommand");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-//This function checks to make sure the cluster command has no errors and then clusters based on the method chosen.
-ClusterDoturCommand::ClusterDoturCommand(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();
-
- ValidParameters validParameter;
-
- //check to make sure all parameters are valid for command
- map<string,string>::iterator it;
- for (it = parameters.begin(); it != parameters.end(); it++) {
- if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {
- abort = true;
- }
- }
-
- //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("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("name");
- //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["name"] = inputDir + it->second; }
- }
-
- }
-
- //initialize outputTypes
- vector<string> tempOutNames;
- outputTypes["list"] = tempOutNames;
- outputTypes["rabund"] = tempOutNames;
- outputTypes["sabund"] = tempOutNames;
-
- //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 = ""; }
-
- //check for required parameters
- phylipfile = validParameter.validFile(parameters, "phylip", true);
- if (phylipfile == "not open") { 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 need to provide a phylip file with the cluster.classic command."); m->mothurOutEndLine();
- abort = true;
- }
- }else { m->setPhylipFile(phylipfile); }
-
-
- //check for optional parameter and set defaults
- namefile = validParameter.validFile(parameters, "name", true);
- if (namefile == "not open") { abort = true; }
- else if (namefile == "not found") { namefile = ""; }
- else { m->setNameFile(namefile); }
-
- string temp;
- temp = validParameter.validFile(parameters, "precision", false);
- if (temp == "not found") { temp = "100"; }
- //saves precision legnth for formatting below
- length = temp.length();
- m->mothurConvert(temp, precision);
-
- temp = validParameter.validFile(parameters, "cutoff", false);
- if (temp == "not found") { temp = "10"; }
- m->mothurConvert(temp, cutoff);
- cutoff += (5 / (precision * 10.0));
-
- temp = validParameter.validFile(parameters, "hard", false); if (temp == "not found") { temp = "T"; }
- hard = m->isTrue(temp);
-
- temp = validParameter.validFile(parameters, "sim", false); if (temp == "not found") { temp = "F"; }
- sim = m->isTrue(temp);
-
- method = validParameter.validFile(parameters, "method", false);
- if (method == "not found") { method = "average"; }
-
- if ((method == "furthest") || (method == "nearest") || (method == "average") || (method == "weighted")) {
- if (method == "furthest") { tag = "fn"; }
- else if (method == "nearest") { tag = "nn"; }
- else if (method == "average") { tag = "an"; }
- else if (method == "weighted") { tag = "wn"; }
- }else { m->mothurOut("Not a valid clustering method. Valid clustering algorithms are furthest, nearest, average, weighted."); m->mothurOutEndLine(); abort = true; }
- }
- }
- catch(exception& e) {
- m->errorOut(e, "ClusterDoturCommand", "ClusterCommand");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-
-int ClusterDoturCommand::execute(){
- try {
-
- if (abort == true) { if (calledHelp) { return 0; } return 2; }
-
- if(namefile != ""){
- nameMap = new NameAssignment(namefile);
- nameMap->readMap();
- }else{
- nameMap = NULL;
- }
-
- //reads phylip file storing data in 2D vector, also fills list and rabund
- ClusterClassic* cluster = new ClusterClassic(cutoff, method, sim);
- cluster->readPhylipFile(phylipfile, nameMap);
-
- if (m->control_pressed) { delete cluster; delete list; delete rabund; return 0; }
-
- list = cluster->getListVector();
- rabund = cluster->getRAbundVector();
-
- if (outputDir == "") { outputDir += m->hasPath(phylipfile); }
- fileroot = outputDir + m->getRootName(m->getSimpleName(phylipfile));
-
- m->openOutputFile(fileroot+ tag + ".sabund", sabundFile);
- m->openOutputFile(fileroot+ tag + ".rabund", rabundFile);
- m->openOutputFile(fileroot+ tag + ".list", listFile);
-
- outputNames.push_back(fileroot+ tag + ".sabund"); outputTypes["sabund"].push_back(fileroot+ tag + ".sabund");
- outputNames.push_back(fileroot+ tag + ".rabund"); outputTypes["rabund"].push_back(fileroot+ tag + ".rabund");
- outputNames.push_back(fileroot+ tag + ".list"); outputTypes["list"].push_back(fileroot+ tag + ".list");
-
- float previousDist = 0.00000;
- float rndPreviousDist = 0.00000;
- oldRAbund = *rabund;
- oldList = *list;
-
- //double saveCutoff = cutoff;
-
- int estart = time(NULL);
-
- while ((cluster->getSmallDist() < cutoff) && (cluster->getNSeqs() > 1)){
- if (m->control_pressed) { delete cluster; delete list; delete rabund; sabundFile.close();rabundFile.close();listFile.close(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear(); return 0; }
-
- cluster->update(cutoff);
-
- float dist = cluster->getSmallDist();
- float rndDist;
- if (hard) {
- rndDist = m->ceilDist(dist, precision);
- }else{
- rndDist = m->roundDist(dist, precision);
- }
-
- if(previousDist <= 0.0000 && dist != previousDist){
- printData("unique");
- }
- else if(rndDist != rndPreviousDist){
- printData(toString(rndPreviousDist, length-1));
- }
-
- previousDist = dist;
- rndPreviousDist = rndDist;
- oldRAbund = *rabund;
- oldList = *list;
- }
-
- if(previousDist <= 0.0000){
- printData("unique");
- }
- else if(rndPreviousDist<cutoff){
- printData(toString(rndPreviousDist, length-1));
- }
-
- sabundFile.close();
- rabundFile.close();
- listFile.close();
-
- delete cluster; delete nameMap; delete list; delete rabund;
-
- //if (saveCutoff != cutoff) {
- // if (hard) { saveCutoff = m->ceilDist(saveCutoff, precision); }
- // else { saveCutoff = m->roundDist(saveCutoff, precision); }
- // m->mothurOut("changed cutoff to " + toString(cutoff)); m->mothurOutEndLine();
- //}
-
- //set list file as new current listfile
- string current = "";
- itTypes = outputTypes.find("list");
- if (itTypes != outputTypes.end()) {
- if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setListFile(current); }
- }
-
- //set rabund file as new current rabundfile
- itTypes = outputTypes.find("rabund");
- if (itTypes != outputTypes.end()) {
- if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setRabundFile(current); }
- }
-
- //set sabund file as new current sabundfile
- itTypes = outputTypes.find("sabund");
- if (itTypes != outputTypes.end()) {
- if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setSabundFile(current); }
- }
-
- 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();
-
- m->mothurOut("It took " + toString(time(NULL) - estart) + " seconds to cluster"); m->mothurOutEndLine();
-
- return 0;
- }
- catch(exception& e) {
- m->errorOut(e, "ClusterDoturCommand", "execute");
- exit(1);
- }
-}
-
-//**********************************************************************************************************************
-
-void ClusterDoturCommand::printData(string label){
- try {
-
- oldRAbund.setLabel(label);
- oldRAbund.print(rabundFile);
- oldRAbund.getSAbundVector().print(sabundFile);
-
- oldRAbund.getSAbundVector().print(cout);
-
- oldList.setLabel(label);
- oldList.print(listFile);
- }
- catch(exception& e) {
- m->errorOut(e, "ClusterDoturCommand", "printData");
- exit(1);
- }
-}
-//**********************************************************************************************************************
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