+++ /dev/null
-/*
- * removerarecommand.cpp
- * mothur
- *
- * Created by westcott on 1/21/11.
- * Copyright 2011 Schloss Lab. All rights reserved.
- *
- */
-
-#include "removerarecommand.h"
-#include "sequence.hpp"
-#include "groupmap.h"
-#include "sharedutilities.h"
-#include "inputdata.h"
-
-//**********************************************************************************************************************
-vector<string> RemoveRareCommand::setParameters(){
- try {
- CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(plist);
- CommandParameter prabund("rabund", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(prabund);
- CommandParameter psabund("sabund", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(psabund);
- CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pshared);
- CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pgroup);
- CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
- CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
- CommandParameter pnseqs("nseqs", "Number", "", "0", "", "", "",false,true); parameters.push_back(pnseqs);
- CommandParameter pbygroup("bygroup", "Boolean", "", "f", "", "", "",false,true); parameters.push_back(pbygroup);
- 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, "RemoveRareCommand", "setParameters");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-string RemoveRareCommand::getHelpString(){
- try {
- string helpString = "";
- helpString += "The remove.rare command parameters are list, rabund, sabund, shared, group, label, groups, bygroup and nseqs.\n";
- helpString += "The remove.rare command reads one of the following file types: list, rabund, sabund or shared file. It outputs a new file after removing the rare otus.\n";
- helpString += "The groups parameter allows you to specify which of the groups you would like analyzed. Default=all. You may separate group names with dashes.\n";
- helpString += "The label parameter is used to analyze specific labels in your input. default=all. You may separate label names with dashes.\n";
- helpString += "The bygroup parameter is only valid with the shared file. default=f, meaning remove any OTU that has nseqs or fewer sequences across all groups.\n";
- helpString += "bygroups=T means remove any OTU that has nseqs or fewer sequences in each group (if groupA has 1 sequence and group B has 100 sequences in OTUZ and nseqs=1, then set the groupA count for OTUZ to 0 and keep groupB's count at 100.) \n";
- helpString += "The nseqs parameter allows you to set the cutoff for an otu to be deemed rare. It is required.\n";
- helpString += "The remove.rare command should be in the following format: remove.rare(shared=yourSharedFile, nseqs=yourRareCutoff).\n";
- helpString += "Example remove.rare(shared=amazon.fn.shared, nseqs=2).\n";
- helpString += "Note: No spaces between parameter labels (i.e. shared), '=' and parameters (i.e.yourSharedFile).\n";
- return helpString;
- }
- catch(exception& e) {
- m->errorOut(e, "RemoveRareCommand", "getHelpString");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-RemoveRareCommand::RemoveRareCommand(){
- try {
- abort = true; calledHelp = true;
- setParameters();
- vector<string> tempOutNames;
- outputTypes["rabund"] = tempOutNames;
- outputTypes["sabund"] = tempOutNames;
- outputTypes["list"] = tempOutNames;
- outputTypes["group"] = tempOutNames;
- outputTypes["shared"] = tempOutNames;
- }
- catch(exception& e) {
- m->errorOut(e, "RemoveRareCommand", "RemoveRareCommand");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-RemoveRareCommand::RemoveRareCommand(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 {
- 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["rabund"] = tempOutNames;
- outputTypes["sabund"] = tempOutNames;
- outputTypes["list"] = tempOutNames;
- outputTypes["group"] = tempOutNames;
- outputTypes["shared"] = 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("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; }
- }
-
- it = parameters.find("sabund");
- //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["sabund"] = inputDir + it->second; }
- }
-
- it = parameters.find("rabund");
- //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["rabund"] = 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 file parameters
- listfile = validParameter.validFile(parameters, "list", true);
- if (listfile == "not open") { abort = true; }
- else if (listfile == "not found") { listfile = ""; }
- else { m->setListFile(listfile); }
-
- sabundfile = validParameter.validFile(parameters, "sabund", true);
- if (sabundfile == "not open") { abort = true; }
- else if (sabundfile == "not found") { sabundfile = ""; }
- else { m->setSabundFile(sabundfile); }
-
- rabundfile = validParameter.validFile(parameters, "rabund", true);
- if (rabundfile == "not open") { abort = true; }
- else if (rabundfile == "not found") { rabundfile = ""; }
- else { m->setRabundFile(rabundfile); }
-
- groupfile = validParameter.validFile(parameters, "group", true);
- if (groupfile == "not open") { groupfile = ""; abort = true; }
- else if (groupfile == "not found") { groupfile = ""; }
- else { m->setGroupFile(groupfile); }
-
- sharedfile = validParameter.validFile(parameters, "shared", true);
- if (sharedfile == "not open") { sharedfile = ""; abort = true; }
- else if (sharedfile == "not found") { sharedfile = ""; }
- else { m->setSharedFile(sharedfile); }
-
- if ((sharedfile == "") && (listfile == "") && (rabundfile == "") && (sabundfile == "")) {
- //is there are current file available for any of these?
- //give priority to shared, then list, then rabund, then sabund
- //if there is a current shared file, use it
- sharedfile = m->getSharedFile();
- if (sharedfile != "") { m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
- else {
- listfile = m->getListFile();
- if (listfile != "") { m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); }
- else {
- rabundfile = m->getRabundFile();
- if (rabundfile != "") { m->mothurOut("Using " + rabundfile + " as input file for the rabund parameter."); m->mothurOutEndLine(); }
- else {
- sabundfile = m->getSabundFile();
- if (sabundfile != "") { m->mothurOut("Using " + sabundfile + " as input file for the sabund parameter."); m->mothurOutEndLine(); }
- else {
- m->mothurOut("No valid current files. You must provide a list, sabund, rabund or shared file."); m->mothurOutEndLine();
- abort = true;
- }
- }
- }
- }
- }
-
- groups = validParameter.validFile(parameters, "groups", false);
- if (groups == "not found") { groups = "all"; }
- m->splitAtDash(groups, Groups);
-
- label = validParameter.validFile(parameters, "label", false);
- if (label == "not found") { label = ""; }
- else {
- if(label != "all") { m->splitAtDash(label, labels); allLines = 0; }
- else { allLines = 1; }
- }
-
- string temp = validParameter.validFile(parameters, "nseqs", false);
- if (temp == "not found") { m->mothurOut("nseqs is a required parameter."); m->mothurOutEndLine(); abort = true; }
- else { m->mothurConvert(temp, nseqs); }
-
- temp = validParameter.validFile(parameters, "bygroup", false); if (temp == "not found") { temp = "f"; }
- byGroup = m->isTrue(temp);
-
- if (byGroup && (sharedfile == "")) { m->mothurOut("The byGroup parameter is only valid with a shared file."); m->mothurOutEndLine(); }
-
- if ((groupfile != "") && (listfile == "")) { m->mothurOut("A groupfile is only valid with a list file."); m->mothurOutEndLine(); groupfile = ""; }
- }
-
- }
- catch(exception& e) {
- m->errorOut(e, "RemoveRareCommand", "RemoveRareCommand");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-
-int RemoveRareCommand::execute(){
- try {
-
- if (abort == true) { if (calledHelp) { return 0; } return 2; }
-
- if (m->control_pressed) { return 0; }
-
- //read through the correct file and output lines you want to keep
- if (sabundfile != "") { processSabund(); }
- if (rabundfile != "") { processRabund(); }
- if (listfile != "") { processList(); }
- if (sharedfile != "") { processShared(); }
-
- 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 rabund file as new current rabundfile
- string current = "";
- itTypes = outputTypes.find("rabund");
- if (itTypes != outputTypes.end()) {
- if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setRabundFile(current); }
- }
-
- itTypes = outputTypes.find("sabund");
- if (itTypes != outputTypes.end()) {
- if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setSabundFile(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); }
- }
-
- itTypes = outputTypes.find("shared");
- if (itTypes != outputTypes.end()) {
- if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setSharedFile(current); }
- }
- }
-
- return 0;
- }
-
- catch(exception& e) {
- m->errorOut(e, "RemoveRareCommand", "execute");
- exit(1);
- }
-}
-
-//**********************************************************************************************************************
-int RemoveRareCommand::processList(){
- try {
- string thisOutputDir = outputDir;
- if (outputDir == "") { thisOutputDir += m->hasPath(listfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + "pick" + m->getExtension(listfile);
- string outputGroupFileName = thisOutputDir + m->getRootName(m->getSimpleName(groupfile)) + "pick" + m->getExtension(groupfile);
-
- ofstream out, outGroup;
- m->openOutputFile(outputFileName, out);
-
- bool wroteSomething = false;
-
- //you must provide a label because the names in the listfile need to be consistent
- string thisLabel = "";
- if (allLines) { m->mothurOut("For the listfile you must select one label, using first label in your listfile."); m->mothurOutEndLine(); }
- else if (labels.size() > 1) { m->mothurOut("For the listfile you must select one label, using " + (*labels.begin()) + "."); m->mothurOutEndLine(); thisLabel = *labels.begin(); }
- else { thisLabel = *labels.begin(); }
-
- InputData input(listfile, "list");
- ListVector* list = input.getListVector();
-
- //get first one or the one we want
- if (thisLabel != "") {
- //use smart distancing
- set<string> userLabels; userLabels.insert(thisLabel);
- set<string> processedLabels;
- string lastLabel = list->getLabel();
- while((list != NULL) && (userLabels.size() != 0)) {
- if(userLabels.count(list->getLabel()) == 1){
- processedLabels.insert(list->getLabel());
- userLabels.erase(list->getLabel());
- break;
- }
-
- if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
- processedLabels.insert(list->getLabel());
- userLabels.erase(list->getLabel());
- delete list;
- list = input.getListVector(lastLabel);
- break;
- }
- lastLabel = list->getLabel();
- delete list;
- list = input.getListVector();
- }
- if (userLabels.size() != 0) {
- m->mothurOut("Your file does not include the label " + thisLabel + ". I will use " + lastLabel + "."); m->mothurOutEndLine();
- list = input.getListVector(lastLabel);
- }
- }
-
- //if groupfile is given then use it
- GroupMap* groupMap;
- if (groupfile != "") {
- groupMap = new GroupMap(groupfile); groupMap->readMap();
- SharedUtil util;
- vector<string> namesGroups = groupMap->getNamesOfGroups();
- util.setGroups(Groups, namesGroups);
- m->openOutputFile(outputGroupFileName, outGroup);
- }
-
-
- if (list != NULL) {
- //make a new list vector
- ListVector newList;
- newList.setLabel(list->getLabel());
-
- //for each bin
- for (int i = 0; i < list->getNumBins(); i++) {
- if (m->control_pressed) { if (groupfile != "") { delete groupMap; outGroup.close(); m->mothurRemove(outputGroupFileName); } out.close(); m->mothurRemove(outputFileName); return 0; }
-
- //parse out names that are in accnos file
- string binnames = list->get(i);
- vector<string> names;
- string saveBinNames = binnames;
- m->splitAtComma(binnames, names);
-
- vector<string> newGroupFile;
- if (groupfile != "") {
- vector<string> newNames;
- saveBinNames = "";
- for(int k = 0; k < names.size(); k++) {
- string group = groupMap->getGroup(names[k]);
-
- if (m->inUsersGroups(group, Groups)) {
- newGroupFile.push_back(names[k] + "\t" + group);
-
- newNames.push_back(names[k]);
- saveBinNames += names[k] + ",";
- }
- }
- names = newNames;
- saveBinNames = saveBinNames.substr(0, saveBinNames.length()-1);
- }
-
- if (names.size() > nseqs) { //keep bin
- newList.push_back(saveBinNames);
- for(int k = 0; k < newGroupFile.size(); k++) { outGroup << newGroupFile[k] << endl; }
- }
- }
-
- //print new listvector
- if (newList.getNumBins() != 0) {
- wroteSomething = true;
- newList.print(out);
- }
- }
-
- out.close();
- if (groupfile != "") { outGroup.close(); outputTypes["group"].push_back(outputGroupFileName); outputNames.push_back(outputGroupFileName); }
-
- if (wroteSomething == false) { m->mothurOut("Your file contains only rare sequences."); m->mothurOutEndLine(); }
- outputTypes["list"].push_back(outputFileName); outputNames.push_back(outputFileName);
-
- return 0;
- }
- catch(exception& e) {
- m->errorOut(e, "RemoveRareCommand", "processList");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-int RemoveRareCommand::processSabund(){
- try {
- string thisOutputDir = outputDir;
- if (outputDir == "") { thisOutputDir += m->hasPath(sabundfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(sabundfile)) + "pick" + m->getExtension(sabundfile);
- outputTypes["sabund"].push_back(outputFileName); outputNames.push_back(outputFileName);
-
- ofstream out;
- m->openOutputFile(outputFileName, out);
-
- //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
- InputData input(sabundfile, "sabund");
- SAbundVector* sabund = input.getSAbundVector();
- string lastLabel = sabund->getLabel();
- set<string> processedLabels;
- set<string> userLabels = labels;
-
- while((sabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
-
- if (m->control_pressed) { delete sabund; out.close(); return 0; }
-
- if(allLines == 1 || labels.count(sabund->getLabel()) == 1){
-
- m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
- processedLabels.insert(sabund->getLabel());
- userLabels.erase(sabund->getLabel());
-
- if (sabund->getMaxRank() > nseqs) {
- for(int i = 1; i <=nseqs; i++) { sabund->set(i, 0); }
- }else { sabund->clear(); }
-
- if (sabund->getNumBins() > 0) { sabund->print(out); }
- }
-
- if ((m->anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
- string saveLabel = sabund->getLabel();
-
- delete sabund;
- sabund = input.getSAbundVector(lastLabel);
-
- m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
- processedLabels.insert(sabund->getLabel());
- userLabels.erase(sabund->getLabel());
-
- if (sabund->getMaxRank() > nseqs) {
- for(int i = 1; i <=nseqs; i++) { sabund->set(i, 0); }
- }else { sabund->clear(); }
-
- if (sabund->getNumBins() > 0) { sabund->print(out); }
-
- //restore real lastlabel to save below
- sabund->setLabel(saveLabel);
- }
-
- lastLabel = sabund->getLabel();
-
- delete sabund;
- sabund = input.getSAbundVector();
- }
-
- if (m->control_pressed) { out.close(); 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 (sabund != NULL) { delete sabund; }
- sabund = input.getSAbundVector(lastLabel);
-
- m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
-
- if (sabund->getMaxRank() > nseqs) {
- for(int i = 1; i <=nseqs; i++) { sabund->set(i, 0); }
- }else { sabund->clear(); }
-
- if (sabund->getNumBins() > 0) { sabund->print(out); }
-
- delete sabund;
- }
-
- return 0;
- }
- catch(exception& e) {
- m->errorOut(e, "RemoveRareCommand", "processSabund");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-int RemoveRareCommand::processRabund(){
- try {
- string thisOutputDir = outputDir;
- if (outputDir == "") { thisOutputDir += m->hasPath(rabundfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(rabundfile)) + "pick" + m->getExtension(rabundfile);
- outputTypes["rabund"].push_back(outputFileName); outputNames.push_back(outputFileName);
-
- ofstream out;
- m->openOutputFile(outputFileName, out);
-
- //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
- InputData input(rabundfile, "rabund");
- RAbundVector* rabund = input.getRAbundVector();
- string lastLabel = rabund->getLabel();
- set<string> processedLabels;
- set<string> userLabels = labels;
-
- while((rabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
-
- if (m->control_pressed) { delete rabund; out.close(); return 0; }
-
- if(allLines == 1 || labels.count(rabund->getLabel()) == 1){
-
- m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
- processedLabels.insert(rabund->getLabel());
- userLabels.erase(rabund->getLabel());
-
- RAbundVector newRabund; newRabund.setLabel(rabund->getLabel());
- for (int i = 0; i < rabund->getNumBins(); i++) {
- if (rabund->get(i) > nseqs) {
- newRabund.push_back(rabund->get(i));
- }
- }
- if (newRabund.getNumBins() > 0) { newRabund.print(out); }
- }
-
- if ((m->anyLabelsToProcess(rabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
- string saveLabel = rabund->getLabel();
-
- delete rabund;
- rabund = input.getRAbundVector(lastLabel);
-
- m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
- processedLabels.insert(rabund->getLabel());
- userLabels.erase(rabund->getLabel());
-
- RAbundVector newRabund; newRabund.setLabel(rabund->getLabel());
- for (int i = 0; i < rabund->getNumBins(); i++) {
- if (rabund->get(i) > nseqs) {
- newRabund.push_back(rabund->get(i));
- }
- }
- if (newRabund.getNumBins() > 0) { newRabund.print(out); }
-
- //restore real lastlabel to save below
- rabund->setLabel(saveLabel);
- }
-
- lastLabel = rabund->getLabel();
-
- delete rabund;
- rabund = input.getRAbundVector();
- }
-
- if (m->control_pressed) { out.close(); 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 (rabund != NULL) { delete rabund; }
- rabund = input.getRAbundVector(lastLabel);
-
- m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
-
- RAbundVector newRabund; newRabund.setLabel(rabund->getLabel());
- for (int i = 0; i < rabund->getNumBins(); i++) {
- if (rabund->get(i) > nseqs) {
- newRabund.push_back(rabund->get(i));
- }
- }
- if (newRabund.getNumBins() > 0) { newRabund.print(out); }
-
- delete rabund;
- }
-
- return 0;
- }
- catch(exception& e) {
- m->errorOut(e, "RemoveRareCommand", "processRabund");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-int RemoveRareCommand::processShared(){
- try {
- m->setGroups(Groups);
-
- string thisOutputDir = outputDir;
- if (outputDir == "") { thisOutputDir += m->hasPath(sharedfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(sharedfile)) + "pick" + m->getExtension(sharedfile);
- outputTypes["shared"].push_back(outputFileName); outputNames.push_back(outputFileName);
-
- ofstream out;
- m->openOutputFile(outputFileName, out);
-
- //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
- InputData input(sharedfile, "sharedfile");
- vector<SharedRAbundVector*> lookup = input.getSharedRAbundVectors();
- string lastLabel = lookup[0]->getLabel();
- set<string> processedLabels;
- set<string> userLabels = labels;
-
- while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
-
- if (m->control_pressed) { for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } out.close(); return 0; }
-
- if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
-
- m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
- processedLabels.insert(lookup[0]->getLabel());
- userLabels.erase(lookup[0]->getLabel());
-
- if (!m->printedHeaders) { lookup[0]->printHeaders(out); }
- processLookup(lookup, out);
- }
-
- 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();
- processedLabels.insert(lookup[0]->getLabel());
- userLabels.erase(lookup[0]->getLabel());
-
- if (!m->printedHeaders) { lookup[0]->printHeaders(out); }
- processLookup(lookup, out);
-
- //restore real lastlabel to save below
- lookup[0]->setLabel(saveLabel);
- }
-
- lastLabel = lookup[0]->getLabel();
-
- for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
- lookup = input.getSharedRAbundVectors();
- }
-
- if (m->control_pressed) { out.close(); 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();
-
- if (!m->printedHeaders) { lookup[0]->printHeaders(out); }
- processLookup(lookup, out);
-
- for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
- }
-
- return 0;
- }
- catch(exception& e) {
- m->errorOut(e, "RemoveRareCommand", "processSabund");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-int RemoveRareCommand::processLookup(vector<SharedRAbundVector*>& lookup, ofstream& out){
- try {
-
- vector<SharedRAbundVector> newRabunds; newRabunds.resize(lookup.size());
- for (int i = 0; i < lookup.size(); i++) {
- newRabunds[i].setGroup(lookup[i]->getGroup());
- newRabunds[i].setLabel(lookup[i]->getLabel());
- }
-
- if (byGroup) {
-
- //for each otu
- for (int i = 0; i < lookup[0]->getNumBins(); i++) {
- bool allZero = true;
-
- if (m->control_pressed) { return 0; }
-
- //for each group
- for (int j = 0; j < lookup.size(); j++) {
-
- //are you rare?
- if (lookup[j]->getAbundance(i) > nseqs) {
- newRabunds[j].push_back(lookup[j]->getAbundance(i), newRabunds[j].getGroup());
- allZero = false;
- }else {
- newRabunds[j].push_back(0, newRabunds[j].getGroup());
- }
- }
-
- //eliminates zero otus
- if (allZero) { for (int j = 0; j < newRabunds.size(); j++) { newRabunds[j].pop_back(); } }
- }
- }else {
- //for each otu
- for (int i = 0; i < lookup[0]->getNumBins(); i++) {
-
- if (m->control_pressed) { return 0; }
-
- int totalAbund = 0;
- //get total otu abundance
- for (int j = 0; j < lookup.size(); j++) {
- newRabunds[j].push_back(lookup[j]->getAbundance(i), newRabunds[j].getGroup());
- totalAbund += lookup[j]->getAbundance(i);
- }
-
- //eliminates otus below rare cutoff
- if (totalAbund <= nseqs) { for (int j = 0; j < newRabunds.size(); j++) { newRabunds[j].pop_back(); } }
- }
- }
-
- //do we have any otus above the rare cutoff
- if (newRabunds[0].getNumBins() != 0) {
- for (int j = 0; j < newRabunds.size(); j++) {
- out << newRabunds[j].getLabel() << '\t' << newRabunds[j].getGroup() << '\t';
- newRabunds[j].print(out);
- }
- }
-
- return 0;
- }
- catch(exception& e) {
- m->errorOut(e, "RemoveRareCommand", "processLookup");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-
-
-
-
projects / mothur.git / blobdiff