+++ /dev/null
-/*
- * otuhierarchycommand.cpp
- * Mothur
- *
- * Created by westcott on 1/19/10.
- * Copyright 2010 Schloss Lab. All rights reserved.
- *
- */
-
-#include "otuhierarchycommand.h"
-
-//**********************************************************************************************************************
-vector<string> OtuHierarchyCommand::setParameters(){
- try {
- CommandParameter poutput("output", "Multiple", "name-number", "name", "", "", "",false,false); parameters.push_back(poutput);
- CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(plist);
- CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
- 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, "OtuHierarchyCommand", "setParameters");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-string OtuHierarchyCommand::getHelpString(){
- try {
- string helpString = "";
- helpString += "The otu.hierarchy command is used to see how otus relate at two distances. \n";
- helpString += "The otu.hierarchy command parameters are list, label and output. list and label parameters are required. \n";
- helpString += "The output parameter allows you to output the names of the sequence in the OTUs or the OTU numbers. Options are name and number, default is name. \n";
- helpString += "The otu.hierarchy command should be in the following format: \n";
- helpString += "otu.hierarchy(list=yourListFile, label=yourLabels).\n";
- helpString += "Example otu.hierarchy(list=amazon.fn.list, label=0.01-0.03).\n";
- helpString += "The otu.hierarchy command outputs a .otu.hierarchy file which is described on the wiki.\n";
- helpString += "Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListFile).\n";
- return helpString;
- }
- catch(exception& e) {
- m->errorOut(e, "OtuHierarchyCommand", "getHelpString");
- exit(1);
- }
-}
-
-//**********************************************************************************************************************
-OtuHierarchyCommand::OtuHierarchyCommand(){
- try {
- abort = true; calledHelp = true;
- setParameters();
- vector<string> tempOutNames;
- outputTypes["otuheirarchy"] = tempOutNames;
- }
- catch(exception& e) {
- m->errorOut(e, "OtuHierarchyCommand", "OtuHierarchyCommand");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-OtuHierarchyCommand::OtuHierarchyCommand(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;
- 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; }
- }
-
- //initialize outputTypes
- vector<string> tempOutNames;
- outputTypes["otuheirarchy"] = tempOutNames;
-
- //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("list");
- //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["list"] = inputDir + it->second; }
- }
- }
-
- listFile = validParameter.validFile(parameters, "list", true);
- if (listFile == "not found") {
- listFile = m->getListFile();
- if (listFile != "") { m->mothurOut("Using " + listFile + " as input file for the list parameter."); m->mothurOutEndLine(); }
- else {
- m->mothurOut("No valid current list file. You must provide a list file."); m->mothurOutEndLine();
- abort = true;
- }
- }else if (listFile == "not open") { abort = true; }
- else { m->setListFile(listFile); }
-
- //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(listFile); //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...
- label = validParameter.validFile(parameters, "label", false);
- if (label == "not found") { m->mothurOut("label is a required parameter for the otu.hierarchy command."); m->mothurOutEndLine(); abort = true; }
- else {
- m->splitAtDash(label, labels);
- if (labels.size() != 2) { m->mothurOut("You must provide 2 labels."); m->mothurOutEndLine(); abort = true; }
- }
-
- output = validParameter.validFile(parameters, "output", false); if (output == "not found") { output = "name"; }
-
- if ((output != "name") && (output != "number")) { m->mothurOut("output options are name and number. I will use name."); m->mothurOutEndLine(); output = "name"; }
- }
-
- }
- catch(exception& e) {
- m->errorOut(e, "OtuHierarchyCommand", "OtuHierarchyCommand");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-
-int OtuHierarchyCommand::execute(){
- try {
-
- if (abort == true) { if (calledHelp) { return 0; } return 2; }
-
- //get listvectors that correspond to labels requested, (or use smart distancing to get closest listvector)
- vector<ListVector> lists = getListVectors();
-
- if (m->control_pressed) { outputTypes.clear(); return 0; }
-
- //determine which is little and which is big, putting little first
- if (lists.size() == 2) {
- //if big is first swap them
- if (lists[0].getNumBins() < lists[1].getNumBins()) {
- reverse(lists.begin(), lists.end());
- }
- }else{
- m->mothurOut("error getting listvectors, unable to read 2 different vectors, check your label inputs."); m->mothurOutEndLine(); return 0;
- }
-
- //map sequences to bin number in the "little" otu
- map<string, int> littleBins;
- for (int i = 0; i < lists[0].getNumBins(); i++) {
-
- if (m->control_pressed) { return 0; }
-
- string names = lists[0].get(i);
-
- //parse bin
- while (names.find_first_of(',') != -1) {
- string name = names.substr(0,names.find_first_of(','));
- names = names.substr(names.find_first_of(',')+1, names.length());
- littleBins[name] = i;
- }
-
- //get last name
- littleBins[names] = i;
- }
-
- ofstream out;
- string outputFileName = outputDir + m->getRootName(m->getSimpleName(listFile)) + lists[0].getLabel() + "-" + lists[1].getLabel() + ".otu.hierarchy";
- m->openOutputFile(outputFileName, out);
-
- //go through each bin in "big" otu and output the bins in "little" otu which created it
- for (int i = 0; i < lists[1].getNumBins(); i++) {
-
- if (m->control_pressed) { outputTypes.clear(); out.close(); m->mothurRemove(outputFileName); return 0; }
-
- string names = lists[1].get(i);
-
- //output column 1
- if (output == "name") { out << names << '\t'; }
- else { out << i << '\t'; }
-
- map<int, int> bins; //bin numbers in little that are in this bin in big
- map<int, int>::iterator it;
-
- //parse bin
- while (names.find_first_of(',') != -1) {
- string name = names.substr(0,names.find_first_of(','));
- names = names.substr(names.find_first_of(',')+1, names.length());
- bins[littleBins[name]] = littleBins[name];
- }
-
- //get last name
- bins[littleBins[names]] = littleBins[names];
-
- string col2 = "";
- for (it = bins.begin(); it != bins.end(); it++) {
- if (output == "name") { col2 += lists[0].get(it->first) + "\t"; }
- else { col2 += toString(it->first) + "\t"; }
- }
-
- //output column 2
- out << col2 << endl;
- }
-
- out.close();
-
- if (m->control_pressed) { outputTypes.clear(); m->mothurRemove(outputFileName); return 0; }
-
- m->mothurOutEndLine();
- m->mothurOut("Output File Name: "); m->mothurOutEndLine();
- m->mothurOut(outputFileName); m->mothurOutEndLine(); outputNames.push_back(outputFileName); outputTypes["otuheirarchy"].push_back(outputFileName);
- m->mothurOutEndLine();
-
- return 0;
- }
- catch(exception& e) {
- m->errorOut(e, "OtuHierarchyCommand", "execute");
- exit(1);
- }
-}
-
-//**********************************************************************************************************************
-//returns a vector of listVectors where "little" vector is first
-vector<ListVector> OtuHierarchyCommand::getListVectors() {
- try {
-
- int pos; //to use in smart distancing, position of last read in file
- int lastPos;
- vector<ListVector> lists;
-
- //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;
-
- //open file
- ifstream in;
- m->openInputFile(listFile, in);
-
- //get first list vector in file
- ListVector* list = NULL;
- string lastLabel = "";
- if (!in.eof()) {
- pos = in.tellg();
- lastPos = pos;
- list = new ListVector(in);
- m->gobble(in);
- lastLabel = list->getLabel();
- }
-
- while ((list != NULL) && (userLabels.size() != 0)) {
-
- if (m->control_pressed) { in.close(); delete list; return lists; }
-
- //is this a listvector that we want?
- if(labels.count(list->getLabel()) == 1){
-
- //make copy of listvector
- ListVector temp(*list);
- lists.push_back(temp);
-
- processedLabels.insert(list->getLabel());
- userLabels.erase(list->getLabel());
- }
-
- //you have a label the user want that is smaller than this label and the last label has not already been processed
- if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
- string saveLabel = list->getLabel();
- int savePos = in.tellg();
-
- //get smart distance line
- delete list;
- in.seekg(lastPos);
- if (!in.eof()) {
- list = new ListVector(in);
- }else { list = NULL; }
-
- //make copy of listvector
- ListVector temp(*list);
- lists.push_back(temp);
-
- processedLabels.insert(list->getLabel());
- userLabels.erase(list->getLabel());
-
- //restore real lastlabel to save below
- list->setLabel(saveLabel);
- in.seekg(savePos);
- }
-
- lastLabel = list->getLabel();
- lastPos = pos;
-
- //get next line
- delete list;
- if (!in.eof()) {
- pos = in.tellg();
- list = new ListVector(in);
- m->gobble(in);
- }else { list = NULL; }
- }
-
- if (m->control_pressed) { in.close(); return lists; }
-
- //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();
- }
- }
-
- if (m->control_pressed) { in.close(); return lists; }
-
- //run last label if you need to
- if (needToRun == true) {
- if (list != NULL) { delete list; }
-
- in.seekg(lastPos);
- if (!in.eof()) {
- list = new ListVector(in);
-
- //make copy of listvector
- ListVector temp(*list);
- lists.push_back(temp);
-
- delete list;
- }
- }
-
- in.close();
- return lists;
- }
- catch(exception& e) {
- m->errorOut(e, "OtuHierarchyCommand", "getListVectors");
- exit(1);
- }
-}
-
-//**********************************************************************************************************************
-
-
-
-
-
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