+++ /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::setParameters(){
- try {
- CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pgroup);
- CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(plist);
- CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(paccnos);
- CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
- 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, "RemoveOtusCommand", "setParameters");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-string RemoveOtusCommand::getHelpString(){
- try {
- string helpString = "";
- helpString += "The remove.otus command removes otus containing sequences from a specfic group or set of groups.\n";
- helpString += "It outputs a new list file containing the otus containing sequences NOT from in the those specified groups.\n";
- helpString += "The remove.otus command parameters are accnos, group, list, label and groups. The group and list parameters are required, unless you have valid current files.\n";
- helpString += "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";
- helpString += "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";
- helpString += "The label parameter allows you to specify which distance you want to process.\n";
- helpString += "The remove.otus command should be in the following format: remove.otus(accnos=yourAccnos, list=yourListFile, group=yourGroupFile, label=yourLabel).\n";
- helpString += "Example remove.otus(accnos=amazon.accnos, list=amazon.fn.list, group=amazon.groups, label=0.03).\n";
- helpString += "or remove.otus(groups=pasture, list=amazon.fn.list, amazon.groups, label=0.03).\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, "RemoveOtusCommand", "getHelpString");
- exit(1);
- }
-}
-
-///**********************************************************************************************************************
-RemoveOtusCommand::RemoveOtusCommand(){
- try {
- abort = true; calledHelp = true;
- setParameters();
- vector<string> tempOutNames;
- outputTypes["group"] = tempOutNames;
- outputTypes["list"] = tempOutNames;
- }
- catch(exception& e) {
- m->errorOut(e, "RemoveOtusCommand", "RemoveOtusCommand");
- exit(1);
- }
-}
-
-//**********************************************************************************************************************
-RemoveOtusCommand::RemoveOtusCommand(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["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 = ""; }
- else { m->setAccnosFile(accnosfile); }
-
- groupfile = validParameter.validFile(parameters, "group", true);
- if (groupfile == "not open") { abort = true; }
- else if (groupfile == "not found") {
- groupfile = m->getGroupFile();
- if (groupfile != "") { m->mothurOut("Using " + groupfile + " as input file for the group parameter."); m->mothurOutEndLine(); }
- else { m->mothurOut("You have no current group file and the group parameter is required."); m->mothurOutEndLine(); abort = true; }
- }else { m->setGroupFile(groupfile); }
-
- listfile = validParameter.validFile(parameters, "list", true);
- if (listfile == "not open") { abort = true; }
- else 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("You have no current list file and the list parameter is required."); m->mothurOutEndLine(); abort = true; }
- }else { m->setListFile(listfile); }
-
- 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 did not provide a label, I will use the first label in your inputfile."); m->mothurOutEndLine(); label=""; }
-
- 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);
- }
-}
-//**********************************************************************************************************************
-
-int RemoveOtusCommand::execute(){
- try {
-
- if (abort == true) { if (calledHelp) { return 0; } return 2; }
-
- 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();
- vector<string> allGroups = groupMap->getNamesOfGroups();
- util->setGroups(Groups, allGroups);
- 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++) { m->mothurRemove(outputNames[i]); } 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();
-
- //set fasta file as new current fastafile
- string current = "";
- itTypes = outputTypes.find("group");
- if (itTypes != outputTypes.end()) {
- if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setGroupFile(current); }
- }
-
- itTypes = outputTypes.find("list");
- if (itTypes != outputTypes.end()) {
- if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setListFile(current); }
- }
- }
-
- 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();
-
- //using first label seen if none is provided
- if (label == "") { label = lastLabel; }
-
- //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(); m->mothurRemove(outputFileName); m->mothurRemove(outputGroupFileName);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(); m->mothurRemove(outputFileName); m->mothurRemove(outputGroupFileName); 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 (!removeBin) {
- //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;
- }else {
- numOtus++;
- }
- }else {
- 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();
-
- return 0;
-
- }
- 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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