--- /dev/null
+/*
+ * removeotuscommand.cpp
+ * Mothur
+ *
+ * Created by westcott on 11/12/10.
+ * Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "removeotuscommand.h"
+#include "inputdata.h"
+#include "sharedutilities.h"
+
+
+//**********************************************************************************************************************
+vector<string> RemoveOtusCommand::getValidParameters(){
+ try {
+ string Array[] = { "group", "accnos","label", "groups","list","outputdir","inputdir" };
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "RemoveOtusCommand", "getValidParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+RemoveOtusCommand::RemoveOtusCommand(){
+ try {
+ abort = true;
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["group"] = tempOutNames;
+ outputTypes["list"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "RemoveOtusCommand", "RemoveOtusCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> RemoveOtusCommand::getRequiredParameters(){
+ try {
+ string Array[] = {"group","label", "list"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "RemoveOtusCommand", "getRequiredParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> RemoveOtusCommand::getRequiredFiles(){
+ try {
+ vector<string> myArray;
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "RemoveOtusCommand", "getRequiredFiles");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+RemoveOtusCommand::RemoveOtusCommand(string option) {
+ try {
+ abort = false;
+
+ //allow user to run help
+ if(option == "help") { help(); abort = true; }
+
+ else {
+ //valid paramters for this command
+ string Array[] = { "group", "accnos","label", "groups", "list","outputdir","inputdir" };
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+
+ 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["group"] = tempOutNames;
+ outputTypes["list"] = 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 = ""; }
+
+ //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("accnos");
+ //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["accnos"] = inputDir + it->second; }
+ }
+
+ 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; }
+ }
+
+ 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
+ accnosfile = validParameter.validFile(parameters, "accnos", true);
+ if (accnosfile == "not open") { abort = true; }
+ else if (accnosfile == "not found") { accnosfile = ""; }
+
+ groupfile = validParameter.validFile(parameters, "group", true);
+ if (groupfile == "not open") { abort = true; }
+ else if (groupfile == "not found") { groupfile = ""; m->mothurOut("You must provide a group file."); m->mothurOutEndLine(); abort = true; }
+
+ listfile = validParameter.validFile(parameters, "list", true);
+ if (listfile == "not open") { abort = true; }
+ else if (listfile == "not found") { listfile = ""; m->mothurOut("You must provide a list file."); m->mothurOutEndLine(); abort = true; }
+
+ groups = validParameter.validFile(parameters, "groups", false);
+ if (groups == "not found") { groups = ""; }
+ else {
+ m->splitAtDash(groups, Groups);
+ }
+
+ label = validParameter.validFile(parameters, "label", false);
+ if (label == "not found") { label = ""; m->mothurOut("You must provide a label to process."); m->mothurOutEndLine(); abort = true; }
+
+ if ((accnosfile == "") && (Groups.size() == 0)) { m->mothurOut("You must provide an accnos file or specify groups using the groups parameter."); m->mothurOutEndLine(); abort = true; }
+ }
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "RemoveOtusCommand", "RemoveOtusCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+void RemoveOtusCommand::help(){
+ try {
+ m->mothurOut("The remove.otus command removes otus containing sequences from a specfic group or set of groups.\n");
+ m->mothurOut("It outputs a new list file containing the otus containing sequences NOT from in the those specified groups.\n");
+ m->mothurOut("The remove.otus command parameters are accnos, group, list, label and groups. The group, list and label parameters are required.\n");
+ m->mothurOut("You must also provide an accnos containing the list of groups to get or set the groups parameter to the groups you wish to select.\n");
+ m->mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like. You can separate group names with dashes.\n");
+ m->mothurOut("The label parameter allows you to specify which distance you want to process.\n");
+ m->mothurOut("The remove.otus command should be in the following format: remove.otus(accnos=yourAccnos, list=yourListFile, group=yourGroupFile, label=yourLabel).\n");
+ m->mothurOut("Example remove.otus(accnos=amazon.accnos, list=amazon.fn.list, group=amazon.groups, label=0.03).\n");
+ m->mothurOut("or remove.otus(groups=pasture, list=amazon.fn.list, amazon.groups, label=0.03).\n");
+ m->mothurOut("Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListFile).\n\n");
+ }
+ catch(exception& e) {
+ m->errorOut(e, "RemoveOtusCommand", "help");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
+
+int RemoveOtusCommand::execute(){
+ try {
+
+ if (abort == true) { return 0; }
+
+ groupMap = new GroupMap(groupfile);
+ groupMap->readMap();
+
+ //get groups you want to remove
+ if (accnosfile != "") { readAccnos(); }
+
+ //make sure groups are valid
+ //takes care of user setting groupNames that are invalid or setting groups=all
+ SharedUtil* util = new SharedUtil();
+ util->setGroups(Groups, groupMap->namesOfGroups);
+ delete util;
+
+ if (m->control_pressed) { delete groupMap; return 0; }
+
+ //read through the list file keeping any otus that contain any sequence from the groups selected
+ readListGroup();
+
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+
+ if (outputNames.size() != 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, "RemoveOtusCommand", "execute");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int RemoveOtusCommand::readListGroup(){
+ try {
+ string thisOutputDir = outputDir;
+ if (outputDir == "") { thisOutputDir += m->hasPath(listfile); }
+ string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + "pick." + label + m->getExtension(listfile);
+
+ ofstream out;
+ m->openOutputFile(outputFileName, out);
+
+ string GroupOutputDir = outputDir;
+ if (outputDir == "") { GroupOutputDir += m->hasPath(groupfile); }
+ string outputGroupFileName = GroupOutputDir + m->getRootName(m->getSimpleName(groupfile)) + "pick." + label + m->getExtension(groupfile);
+
+ ofstream outGroup;
+ m->openOutputFile(outputGroupFileName, outGroup);
+
+ InputData* input = new InputData(listfile, "list");
+ ListVector* list = input->getListVector();
+ string lastLabel = list->getLabel();
+
+ //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
+ set<string> labels; labels.insert(label);
+ set<string> processedLabels;
+ set<string> userLabels = labels;
+
+ bool wroteSomething = false;
+
+ //as long as you are not at the end of the file or done wih the lines you want
+ while((list != NULL) && (userLabels.size() != 0)) {
+
+ if (m->control_pressed) { delete list; delete input; out.close(); outGroup.close(); remove(outputFileName.c_str()); remove(outputGroupFileName.c_str());return 0; }
+
+ if(labels.count(list->getLabel()) == 1){
+ processList(list, groupMap, out, outGroup, wroteSomething);
+
+ processedLabels.insert(list->getLabel());
+ userLabels.erase(list->getLabel());
+ }
+
+ if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ string saveLabel = list->getLabel();
+
+ delete list;
+
+ list = input->getListVector(lastLabel);
+
+ processList(list, groupMap, out, outGroup, wroteSomething);
+
+ processedLabels.insert(list->getLabel());
+ userLabels.erase(list->getLabel());
+
+ //restore real lastlabel to save below
+ list->setLabel(saveLabel);
+ }
+
+ lastLabel = list->getLabel();
+
+ delete list; list = NULL;
+
+ //get next line to process
+ list = input->getListVector();
+ }
+
+
+ if (m->control_pressed) { if (list != NULL) { delete list; } delete input; out.close(); outGroup.close(); remove(outputFileName.c_str()); remove(outputGroupFileName.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) {
+ if (list != NULL) { delete list; }
+
+ list = input->getListVector(lastLabel);
+
+ processList(list, groupMap, out, outGroup, wroteSomething);
+
+ delete list; list = NULL;
+ }
+
+ out.close();
+ outGroup.close();
+
+ if (wroteSomething == false) { m->mothurOut("At distance " + label + " your file ONLY contains otus containing sequences from the groups you wish to remove."); m->mothurOutEndLine(); }
+ outputTypes["list"].push_back(outputFileName); outputNames.push_back(outputFileName);
+ outputTypes["group"].push_back(outputGroupFileName); outputNames.push_back(outputGroupFileName);
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "RemoveOtusCommand", "readList");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int RemoveOtusCommand::processList(ListVector*& list, GroupMap*& groupMap, ofstream& out, ofstream& outGroup, bool& wroteSomething){
+ try {
+
+ //make a new list vector
+ ListVector newList;
+ newList.setLabel(list->getLabel());
+
+ int numOtus = 0;
+ //for each bin
+ for (int i = 0; i < list->getNumBins(); i++) {
+ if (m->control_pressed) { return 0; }
+
+ //parse out names that are in accnos file
+ string binnames = list->get(i);
+
+ bool removeBin = false;
+ string groupFileOutput = "";
+
+ //parse names
+ string individual = "";
+ int length = binnames.length();
+ for(int j=0;j<length;j++){
+ if(binnames[j] == ','){
+ string group = groupMap->getGroup(individual);
+ if (group == "not found") { m->mothurOut("[ERROR]: " + individual + " is not in your groupfile. please correct."); m->mothurOutEndLine(); group = "NOTFOUND"; }
+
+ if (m->inUsersGroups(group, Groups)) { removeBin = true; break; }
+ groupFileOutput += individual + "\t" + group + "\n";
+ individual = "";
+
+ }
+ else{ individual += binnames[j]; }
+ }
+
+ if (!removeBin) {
+ //get last name
+ string group = groupMap->getGroup(individual);
+ if (group == "not found") { m->mothurOut("[ERROR]: " + individual + " is not in your groupfile. please correct."); m->mothurOutEndLine(); group = "NOTFOUND"; }
+
+ if (m->inUsersGroups(group, Groups)) { removeBin = true; }
+ groupFileOutput += individual + "\t" + group + "\n";
+
+ //if there are no sequences from the groups we want to remove in this bin add to new list, output to groupfile
+ newList.push_back(binnames);
+ outGroup << groupFileOutput;
+ numOtus++;
+ }
+ }
+
+ //print new listvector
+ if (newList.getNumBins() != 0) {
+ wroteSomething = true;
+ newList.print(out);
+ }
+
+ m->mothurOut(newList.getLabel() + " - removed " + toString(numOtus) + " of the " + toString(list->getNumBins()) + " OTUs."); m->mothurOutEndLine();
+
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "RemoveOtusCommand", "processList");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+void RemoveOtusCommand::readAccnos(){
+ try {
+ Groups.clear();
+
+ ifstream in;
+ m->openInputFile(accnosfile, in);
+ string name;
+
+ while(!in.eof()){
+ in >> name;
+
+ Groups.push_back(name);
+
+ m->gobble(in);
+ }
+ in.close();
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "RemoveOtusCommand", "readAccnos");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+
+
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