--- /dev/null
+//
+// GetCoreMicroBiomeCommand.cpp
+// Mothur
+//
+// Created by John Westcott on 5/8/12.
+// Copyright (c) 2012 Schloss Lab. All rights reserved.
+//
+
+#include "GetCoreMicroBiomeCommand.h"
+
+
+//**********************************************************************************************************************
+vector<string> GetCoreMicroBiomeCommand::setParameters(){
+ try {
+ CommandParameter pshared("shared", "InputTypes", "", "", "SharedRel", "SharedRel", "none",false,false); parameters.push_back(pshared);
+ CommandParameter prelabund("relabund", "InputTypes", "", "", "SharedRel", "SharedRel", "none",false,false); parameters.push_back(prelabund);
+ CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
+ CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
+ CommandParameter poutput("output", "Multiple", "fraction-count", "fraction", "", "", "",false,false); parameters.push_back(poutput);
+ CommandParameter pabund("abundance", "Number", "", "-1", "", "", "",false,false); parameters.push_back(pabund);
+ CommandParameter psamples("samples", "Number", "", "-1", "", "", "",false,false); parameters.push_back(psamples);
+ 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, "GetCoreMicroBiomeCommand", "setParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string GetCoreMicroBiomeCommand::getHelpString(){
+ try {
+ string helpString = "";
+ helpString += "The get.coremicrobiome determines the fraction of OTUs that are found in varying numbers of samples for different minimum relative abundances.\n";
+ helpString += "The get.coremicrobiome parameters are: shared, relabund, groups, label, output, abundance and samples. Shared or relabund is required.\n";
+ helpString += "The label parameter is used to analyze specific labels in your input.\n";
+ helpString += "The groups parameter allows you to specify which of the groups you would like analyzed.\n";
+ helpString += "The output parameter is used to specify whether you would like the fraction of OTU's or OTU count outputted. Options are fraction or count. Default=fraction.\n";
+ helpString += "The abundance parameter allows you to specify an abundance you would like the OTU names outputted for. Must be an integer between 0 and 100, indicating the relative abundance. \n";
+ helpString += "The samples parameter allows you to specify the minimum number of samples you would like the OTU names outputted for. Must be an interger between 1 and number of samples in your file.\n";
+ helpString += "The new command should be in the following format: get.coremicrobiome(shared=yourSharedFile)\n";
+ helpString += "get.coremicrobiom(shared=final.an.shared, abund=30)\n";
+ return helpString;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetCoreMicroBiomeCommand", "getHelpString");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+GetCoreMicroBiomeCommand::GetCoreMicroBiomeCommand(){
+ try {
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["coremicrobiom"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetCoreMicroBiomeCommand", "GetCoreMicroBiomeCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+GetCoreMicroBiomeCommand::GetCoreMicroBiomeCommand(string option) {
+ try {
+ abort = false; calledHelp = false; allLines = 1;
+
+ //allow user to run help
+ if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
+
+ else {
+ //valid paramters for this command
+ vector<string> myArray = setParameters();
+
+ OptionParser parser(option);
+ map<string,string> parameters = parser.getParameters();
+
+ ValidParameters validParameter;
+ map<string,string>::iterator it;
+ //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; }
+ }
+
+
+ //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("relabund");
+ //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["relabund"] = inputDir + it->second; }
+ }
+
+ 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; }
+ }
+ }
+
+
+ //check for parameters
+ sharedfile = validParameter.validFile(parameters, "shared", true);
+ if (sharedfile == "not open") { abort = true; }
+ else if (sharedfile == "not found") { sharedfile = ""; }
+ else { inputFileName = sharedfile; format = "sharedfile"; m->setSharedFile(sharedfile); }
+
+ relabundfile = validParameter.validFile(parameters, "relabund", true);
+ if (relabundfile == "not open") { abort = true; }
+ else if (relabundfile == "not found") { relabundfile = ""; }
+ else { inputFileName = relabundfile; format = "relabund"; m->setRelAbundFile(relabundfile); }
+
+ if ((relabundfile == "") && (sharedfile == "")) {
+ //is there are current file available for either of these?
+ //give priority to shared, then relabund
+ sharedfile = m->getSharedFile();
+ if (sharedfile != "") { inputFileName = sharedfile; format="sharedfile"; m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
+ else {
+ relabundfile = m->getRelAbundFile();
+ if (relabundfile != "") { inputFileName = relabundfile; format="relabund"; m->mothurOut("Using " + relabundfile + " as input file for the relabund parameter."); m->mothurOutEndLine(); }
+ else {
+ m->mothurOut("No valid current files. You must provide a shared or relabund."); m->mothurOutEndLine();
+ 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 = m->hasPath(inputFileName); //if user entered a file with a path then preserve it
+ }
+
+ string groups = validParameter.validFile(parameters, "groups", false);
+ if (groups == "not found") { groups = ""; }
+ else { m->splitAtDash(groups, Groups); }
+ m->setGroups(Groups);
+
+ string label = validParameter.validFile(parameters, "label", false);
+ if (label == "not found") { label = ""; }
+ else {
+ if(label != "all") { m->splitAtDash(label, labels); allLines = 0; }
+ else { allLines = 1; }
+ }
+
+ output = validParameter.validFile(parameters, "output", false); if(output == "not found"){ output = "fraction"; }
+
+ if ((output != "fraction") && (output != "count")) { m->mothurOut(output + " is not a valid output form. Options are fraction and count. I will use fraction."); m->mothurOutEndLine(); output = "fraction"; }
+
+ string temp = validParameter.validFile(parameters, "abundance", false); if (temp == "not found"){ temp = "-1"; }
+ m->mothurConvert(temp, abund);
+
+ if (abund != -1) {
+ if ((abund < 0) || (abund > 100)) { m->mothurOut(toString(abund) + " is not a valid number for abund. Must be an integer between 0 and 100.\n"); }
+ }
+
+ temp = validParameter.validFile(parameters, "samples", false); if (temp == "not found"){ temp = "-1"; }
+ m->mothurConvert(temp, samples);
+
+ }
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetCoreMicroBiomeCommand", "GetCoreMicroBiomeCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+int GetCoreMicroBiomeCommand::execute(){
+ try {
+
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
+
+ InputData input(inputFileName, format);
+ vector<SharedRAbundFloatVector*> lookup = input.getSharedRAbundFloatVectors();
+ string lastLabel = lookup[0]->getLabel();
+
+ if (samples != -1) {
+ if ((samples < 1) || (samples > lookup.size())) { m->mothurOut(toString(samples) + " is not a valid number for samples. Must be an integer between 1 and the number of samples in your file. Your file contains " + toString(lookup.size()) + " samples, so I will use that.\n"); samples = lookup.size(); }
+ }
+
+
+ //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]; } for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
+
+ if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
+
+ m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
+
+ createTable(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.getSharedRAbundFloatVectors(lastLabel);
+ m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
+
+ createTable(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) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
+
+ //get next line to process
+ lookup = input.getSharedRAbundFloatVectors();
+ }
+
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } 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.getSharedRAbundFloatVectors(lastLabel);
+
+ m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
+
+ createTable(lookup);
+
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+ }
+
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
+
+ //output files created by command
+ 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, "GetCoreMicroBiomeCommand", "execute");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+int GetCoreMicroBiomeCommand::createTable(vector<SharedRAbundFloatVector*>& lookup){
+ try {
+
+ string outputFileName = outputDir + m->getRootName(m->getSimpleName(inputFileName)) + lookup[0]->getLabel() + ".core.microbiom";
+ outputNames.push_back(outputFileName); outputTypes["coremicrobiom"].push_back(outputFileName);
+ ofstream out;
+ m->openOutputFile(outputFileName, out);
+
+ int numSamples = lookup.size();
+ int numOtus = lookup[0]->getNumBins();
+
+ //table is 100 by numsamples
+ //question we are answering is: what fraction of OTUs in a study have a relative abundance at or above %X
+ //in at least %Y samples. x goes from 0 to 100, y from 1 to numSamples
+ vector< vector<double> > table; table.resize(101);
+ for (int i = 0; i < table.size(); i++) { table[i].resize(numSamples, 0.0); }
+
+ map<int, vector<string> > otuNames;
+ if ((abund != -1) && (samples == -1)) { //fill with all samples
+ for (int i = 0; i < numSamples; i++) {
+ vector<string> temp;
+ otuNames[i+1] = temp;
+ }
+ }else if ((abund == -1) && (samples != -1)) { //fill with all relabund
+ for (int i = 0; i < 101; i++) {
+ vector<string> temp;
+ otuNames[i] = temp;
+ }
+ }else if ((abund != -1) && (samples != -1)) { //only one line is wanted
+ vector<string> temp;
+ otuNames[abund] = temp;
+ }
+
+ for (int i = 0; i < numOtus; i++) {
+
+ if (m->control_pressed) { break; }
+
+ //count number of samples in this otu with a relabund >= spot in count
+ vector<int> counts; counts.resize(101, 0);
+
+ for (int j = 0; j < lookup.size(); j++) {
+ double relabund = lookup[j]->getAbundance(i);
+ int wholeRelabund = (int) (floor(relabund*100));
+ for (int k = 0; k < wholeRelabund+1; k++) { counts[k]++; }
+ }
+
+ //add this otus info to table
+ for (int j = 0; j < table.size(); j++) {
+ for (int k = 0; k < counts[j]; k++) { table[j][k]++; }
+
+ if ((abund == -1) && (samples != -1)) { //we want all OTUs with this number of samples
+ if (counts[j] >= samples) { otuNames[j].push_back(m->currentBinLabels[i]); }
+ }else if ((abund != -1) && (samples == -1)) { //we want all OTUs with this relabund
+ if (j == abund) {
+ for (int k = 0; k < counts[j]; k++) { otuNames[k+1].push_back(m->currentBinLabels[i]); }
+ }
+ }else if ((abund != -1) && (samples != -1)) { //we want only OTUs with this relabund for this number of samples
+ if ((j == abund) && (counts[j] >= samples)) {
+ otuNames[j].push_back(m->currentBinLabels[i]);
+ }
+ }
+ }
+ }
+
+ //format output
+ if (output == "fraction") { out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint); }
+ out << "NumSamples\t";
+
+ //convert table counts to percents
+ for (int i = 0; i < table.size(); i++) {
+ out << "Relabund-" << i << "%\t";
+ if (m->control_pressed) { break; }
+ for (int j = 0; j < table[i].size(); j++) { if (output == "fraction") { table[i][j] /= (double) numOtus; } }
+ }
+ out << endl;
+
+ for (int i = 0; i < numSamples; i++) {
+ if (m->control_pressed) { break; }
+ out << i+1 << '\t';
+ for (int j = 0; j < table.size(); j++) { out << table[j][i] << '\t'; }
+ out << endl;
+ }
+
+ out.close();
+
+ if (m->control_pressed) { return 0; }
+
+ if ((samples != -1) || (abund != -1)) {
+ string outputFileName2 = outputDir + m->getRootName(m->getSimpleName(inputFileName)) + lookup[0]->getLabel() + ".core.microbiomlist";
+ outputNames.push_back(outputFileName2); outputTypes["coremicrobiom"].push_back(outputFileName2);
+ ofstream out2;
+ m->openOutputFile(outputFileName2, out2);
+
+ if ((abund == -1) && (samples != -1)) { //we want all OTUs with this number of samples
+ out2 << "Relabund%\tOTUList_for_samples=" << samples << "\n";
+ }else if ((abund != -1) && (samples == -1)) { //we want all OTUs with this relabund
+ out2 << "Samples\tOTUList_for_abund=" << abund << "\n";
+ }else if ((abund != -1) && (samples != -1)) { //we want only OTUs with this relabund for this number of samples
+ out2 << "Relabund%\tOTUList_for_samples=" << samples << "\n";
+ }
+
+ for (map<int, vector<string> >::iterator it = otuNames.begin(); it != otuNames.end(); it++) {
+ if (m->control_pressed) { break; }
+
+ vector<string> temp = it->second;
+ string list = m->makeList(temp);
+
+ out2 << it->first << '\t' << list << endl;
+ }
+
+ out2.close();
+ }
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetCoreMicroBiomeCommand", "createTable");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
+
+
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