--- /dev/null
+/*
+ * metastatscommand.cpp
+ * Mothur
+ *
+ * Created by westcott on 9/16/10.
+ * Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "metastatscommand.h"
+#include "metastats.h"
+
+//**********************************************************************************************************************
+
+MetaStatsCommand::MetaStatsCommand(string option) {
+ try {
+ globaldata = GlobalData::getInstance();
+ abort = false;
+ allLines = 1;
+ labels.clear();
+
+ //allow user to run help
+ if(option == "help") { help(); abort = true; }
+
+ else {
+ //valid paramters for this command
+ string AlignArray[] = {"groups","label","outputdir","iters","threshold","g","design","inputdir"};
+ vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
+
+ 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 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
+ }
+
+ //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("design");
+ //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["design"] = inputDir + it->second; }
+ }
+ }
+
+ //check for required parameters
+ designfile = validParameter.validFile(parameters, "design", true);
+ if (designfile == "not open") { abort = true; }
+ else if (designfile == "not found") { designfile = ""; m->mothurOut("You must provide an design file."); m->mothurOutEndLine(); abort = true; }
+
+ //make sure the user has already run the read.otu command
+ if ((globaldata->getSharedFile() == "")) {
+ m->mothurOut("You must read a list and a group, or a shared file before you can use the normalize.shared command."); m->mothurOutEndLine(); abort = true;
+ }
+
+ //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") { m->splitAtDash(label, labels); allLines = 0; }
+ else { allLines = 1; }
+ }
+
+ //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 = ""; pickedGroups = false; }
+ else {
+ pickedGroups = true;
+ m->splitAtDash(groups, Groups);
+ globaldata->Groups = Groups;
+ }
+
+ string temp = validParameter.validFile(parameters, "iters", false); if (temp == "not found") { temp = "1000"; }
+ convert(temp, iters);
+
+ temp = validParameter.validFile(parameters, "threshold", false); if (temp == "not found") { temp = "0.05"; }
+ convert(temp, threshold);
+
+ //temp = validParameter.validFile(parameters, "g", false); if (temp == "not found") { temp = "0"; }
+ //convert(temp, g);
+ }
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "MetaStatsCommand", "MetaStatsCommand");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
+
+void MetaStatsCommand::help(){
+ try {
+ m->mothurOut("Paper reference goes here....\n");
+ m->mothurOut("The metastats command can only be executed after a successful read.otu command of a list and group or shared file.\n");
+ m->mothurOut("The metastats command outputs a .... file. \n");
+ m->mothurOut("The metastats command parameters are iters, threshold, groups, design and label. No parameters are required.\n");
+ m->mothurOut("The design parameter allows you to assign your groups to sets when you are running metastat. mothur will run all pairwise comparisons of the sets. It is required. \n");
+ m->mothurOut("The design file looks like the group file. It is a 2 column tab delimited file, where the first column is the group name and the second column is the set the group belongs to.\n");
+ m->mothurOut("The iters parameter ...\n");
+ m->mothurOut("The threshold parameter ...\n");
+ m->mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like included. The group names are separated by dashes.\n");
+ m->mothurOut("The label parameter allows you to select what distance levels you would like, and are also separated by dashes.\n");
+ m->mothurOut("The metastats command should be in the following format: metastats(groups=yourGroups, label=yourLabels).\n");
+ m->mothurOut("Example metastats(groups=A-B-C).\n");
+ m->mothurOut("The default value for groups is all the groups in your groupfile, and all labels in your inputfile will be used.\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, "MetaStatsCommand", "help");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
+
+MetaStatsCommand::~MetaStatsCommand(){}
+
+//**********************************************************************************************************************
+
+int MetaStatsCommand::execute(){
+ try {
+
+ if (abort == true) { return 0; }
+
+ designMap = new GroupMap(designfile);
+ designMap->readDesignMap();
+
+ read = new ReadOTUFile(globaldata->inputFileName);
+ read->read(&*globaldata);
+ input = globaldata->ginput;
+ lookup = input->getSharedRAbundVectors();
+ string lastLabel = lookup[0]->getLabel();
+
+ //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;
+
+ //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) { for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } globaldata->Groups.clear(); delete read; for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+
+ if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
+
+ m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
+ process(lookup);
+
+ processedLabels.insert(lookup[0]->getLabel());
+ userLabels.erase(lookup[0]->getLabel());
+ }
+
+ 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);
+ m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
+
+ process(lookup);
+
+ 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[i] = NULL; }
+
+ if (m->control_pressed) { globaldata->Groups.clear(); delete read; for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+
+ //get next line to process
+ lookup = input->getSharedRAbundVectors();
+ }
+
+ if (m->control_pressed) { globaldata->Groups.clear(); delete read; for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } 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++) {
+ m->mothurOut("Your file does not include the label " + *it);
+ if (processedLabels.count(lastLabel) != 1) {
+ m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
+ needToRun = true;
+ }else {
+ m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
+ }
+ }
+
+ //run last label if you need to
+ if (needToRun == true) {
+ for (int i = 0; i < lookup.size(); i++) { if (lookup[i] != NULL) { delete lookup[i]; } }
+ lookup = input->getSharedRAbundVectors(lastLabel);
+
+ m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
+
+ process(lookup);
+
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+ }
+
+ //reset groups parameter
+ globaldata->Groups.clear();
+ delete input; globaldata->ginput = NULL;
+ delete read;
+
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } 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, "MetaStatsCommand", "execute");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+int MetaStatsCommand::process(vector<SharedRAbundVector*>& thisLookUp){
+ try {
+ if (pickedGroups) { eliminateZeroOTUS(thisLookUp); }
+
+ string outputFileName = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + thisLookUp[0]->getLabel() + ".metastats";
+ outputNames.push_back(outputFileName);
+ int nameLength = outputFileName.length();
+ char * output = new char[nameLength];
+ strcpy(output, outputFileName.c_str());
+
+ //build matrix from shared rabunds
+ double** data;
+ data = new double*[thisLookUp[0]->getNumBins()];
+
+ for (int j = 0; j < thisLookUp[0]->getNumBins(); j++) {
+ data[j] = new double[thisLookUp.size()];
+ for (int i = 0; i < thisLookUp.size(); i++) {
+ data[j][i] = (thisLookUp[i]->getAbundance(j));
+ }
+ }
+
+ if (g == 0) { g = thisLookUp.size() / 2; }
+
+ metastat_main(output, thisLookUp[0]->getNumBins(), thisLookUp.size(), threshold, iters, data, g);
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "MetaStatsCommand", "normalize");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int MetaStatsCommand::eliminateZeroOTUS(vector<SharedRAbundVector*>& thislookup) {
+ try {
+
+ vector<SharedRAbundVector*> newLookup;
+ for (int i = 0; i < thislookup.size(); i++) {
+ SharedRAbundVector* temp = new SharedRAbundVector();
+ temp->setLabel(thislookup[i]->getLabel());
+ temp->setGroup(thislookup[i]->getGroup());
+ newLookup.push_back(temp);
+ }
+
+ //for each bin
+ for (int i = 0; i < thislookup[0]->getNumBins(); i++) {
+ if (m->control_pressed) { for (int j = 0; j < newLookup.size(); j++) { delete newLookup[j]; } return 0; }
+
+ //look at each sharedRabund and make sure they are not all zero
+ bool allZero = true;
+ for (int j = 0; j < thislookup.size(); j++) {
+ if (thislookup[j]->getAbundance(i) != 0) { allZero = false; break; }
+ }
+
+ //if they are not all zero add this bin
+ if (!allZero) {
+ for (int j = 0; j < thislookup.size(); j++) {
+ newLookup[j]->push_back(thislookup[j]->getAbundance(i), thislookup[j]->getGroup());
+ }
+ }
+ }
+
+ for (int j = 0; j < thislookup.size(); j++) { delete thislookup[j]; }
+
+ thislookup = newLookup;
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "MetaStatsCommand", "eliminateZeroOTUS");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
projects / mothur.git / commitdiff