--- /dev/null
+/*
+ * parselistcommand.cpp
+ * Mothur
+ *
+ * Created by westcott on 2/24/10.
+ * Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "parselistscommand.h"
+
+//**********************************************************************************************************************
+vector<string> ParseListCommand::setParameters(){
+ try {
+ CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(plist);
+ CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pgroup);
+ 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, "ParseListCommand", "setParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string ParseListCommand::getHelpString(){
+ try {
+ string helpString = "";
+ helpString += "The parse.list command reads a list and group file and generates a list file for each group in the groupfile. \n";
+ helpString += "The parse.list command parameters are list, group and label.\n";
+ helpString += "The list and group parameters are required.\n";
+ helpString += "The label parameter is used to read specific labels in your input you want to use.\n";
+ helpString += "The parse.list command should be used in the following format: parse.list(list=yourListFile, group=yourGroupFile, label=yourLabels).\n";
+ helpString += "Example: parse.list(list=abrecovery.fn.list, group=abrecovery.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, "ParseListCommand", "getHelpString");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+ParseListCommand::ParseListCommand(){
+ try {
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["list"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ParseListCommand", "ParseListCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+ParseListCommand::ParseListCommand(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["list"] = 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; }
+ }
+
+ 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; }
+ }
+ }
+
+
+ //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 = ""; }
+
+ //check for required parameters
+ 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("No valid current list file. You must provide a list file."); m->mothurOutEndLine();
+ abort = true;
+
+ }
+ }else { m->setListFile(listfile); }
+
+ groupfile = validParameter.validFile(parameters, "group", true);
+ if (groupfile == "not open") { abort = true; }
+ else if (groupfile == "not found") {
+ groupfile = m->getListFile();
+ if (groupfile != "") {
+ m->mothurOut("Using " + groupfile + " as input file for the group parameter."); m->mothurOutEndLine();
+ groupMap = new GroupMap(groupfile);
+
+ int error = groupMap->readMap();
+ if (error == 1) { abort = true; }
+ }else { m->mothurOut("No valid current group file. You must provide a group file."); m->mothurOutEndLine(); abort = true; }
+ }else {
+ m->setGroupFile(groupfile);
+ groupMap = new GroupMap(groupfile);
+
+ int error = groupMap->readMap();
+ if (error == 1) { abort = true; }
+ }
+
+ //do you have all files needed
+ if ((listfile == "") || (groupfile == "")) { m->mothurOut("You must enter both a listfile and groupfile for the parse.list command. "); m->mothurOutEndLine(); abort = true; }
+
+ //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") { label = ""; allLines = 1; }
+ else {
+ if(label != "all") { m->splitAtDash(label, labels); allLines = 0; }
+ else { allLines = 1; }
+ }
+ }
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ParseListCommand", "ParseListCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int ParseListCommand::execute(){
+ try {
+
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
+
+ //set fileroot
+ string fileroot = outputDir + m->getRootName(m->getSimpleName(listfile));
+
+ //fill filehandles with neccessary ofstreams
+ int i;
+ ofstream* temp;
+ vector<string> gGroups = groupMap->getNamesOfGroups();
+ for (i=0; i<gGroups.size(); i++) {
+ temp = new ofstream;
+ filehandles[gGroups[i]] = temp;
+
+ string filename = fileroot + gGroups[i] + ".list";
+ outputNames.push_back(filename); outputTypes["list"].push_back(filename);
+ m->openOutputFile(filename, *temp);
+ }
+
+ //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;
+
+ input = new InputData(listfile, "list");
+ list = input->getListVector();
+ string lastLabel = list->getLabel();
+
+ if (m->control_pressed) {
+ delete input; delete list; delete groupMap;
+ vector<string> gGroups = groupMap->getNamesOfGroups();
+ for (i=0; i<gGroups.size(); i++) { (*(filehandles[gGroups[i]])).close(); delete filehandles[gGroups[i]]; }
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear();
+ return 0;
+ }
+
+ while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
+
+ if (m->control_pressed) {
+ delete input; delete list; delete groupMap;
+ for (i=0; i<gGroups.size(); i++) { (*(filehandles[gGroups[i]])).close(); delete filehandles[gGroups[i]]; }
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear();
+ return 0;
+ }
+
+ if(allLines == 1 || labels.count(list->getLabel()) == 1){
+
+ m->mothurOut(list->getLabel()); m->mothurOutEndLine();
+ parse(list);
+
+ 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); //get new list vector to process
+
+ m->mothurOut(list->getLabel()); m->mothurOutEndLine();
+ parse(list);
+
+ processedLabels.insert(list->getLabel());
+ userLabels.erase(list->getLabel());
+
+ //restore real lastlabel to save below
+ list->setLabel(saveLabel);
+ }
+
+
+ lastLabel = list->getLabel();
+
+ delete list;
+ list = input->getListVector(); //get new list vector to process
+ }
+
+ if (m->control_pressed) {
+ delete input; delete groupMap;
+ for (i=0; i<gGroups.size(); i++) { (*(filehandles[gGroups[i]])).close(); delete filehandles[gGroups[i]]; }
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear();
+ 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();
+ }
+
+ }
+
+ if (m->control_pressed) {
+ delete input; delete groupMap;
+ for (i=0; i<gGroups.size(); i++) { (*(filehandles[gGroups[i]])).close(); delete filehandles[gGroups[i]]; }
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear();
+ return 0;
+ }
+
+ //run last label if you need to
+ if (needToRun == true) {
+ if (list != NULL) { delete list; }
+ list = input->getListVector(lastLabel); //get new list vector to process
+
+ m->mothurOut(list->getLabel()); m->mothurOutEndLine();
+ parse(list);
+
+ delete list;
+ }
+
+ for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
+ (*(filehandles[it3->first])).close();
+ delete it3->second;
+ }
+
+
+ delete groupMap;
+ delete input;
+
+ if (m->control_pressed) {
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear();
+ return 0;
+ }
+
+ //set fasta file as new current fastafile
+ string current = "";
+ itTypes = outputTypes.find("list");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setListFile(current); }
+ }
+
+ 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, "ParseListCommand", "execute");
+ exit(1);
+ }
+}
+/**********************************************************************************************************************/
+int ParseListCommand::parse(ListVector* thisList) {
+ try {
+
+ map<string, string> groupVector;
+ map<string, string>::iterator itGroup;
+ map<string, int> groupNumBins;
+
+ //print label
+ for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
+ groupNumBins[it3->first] = 0;
+ groupVector[it3->first] = "";
+ }
+
+
+ for (int i = 0; i < thisList->getNumBins(); i++) {
+ if (m->control_pressed) { return 0; }
+
+ map<string, string> groupBins;
+ string bin = list->get(i);
+
+ vector<string> names;
+ m->splitAtComma(bin, names); //parses bin into individual sequence names
+
+ //parse bin into list of sequences in each group
+ for (int j = 0; j < names.size(); j++) {
+ string group = groupMap->getGroup(names[j]);
+
+ if (group == "not found") { m->mothurOut(names[j] + " is not in your groupfile. please correct."); m->mothurOutEndLine(); exit(1); }
+
+ itGroup = groupBins.find(group);
+ if(itGroup == groupBins.end()) {
+ groupBins[group] = names[j]; //add first name
+ groupNumBins[group]++;
+ }else{ //add another name
+ groupBins[group] = groupBins[group] + "," + names[j];
+ }
+ }
+
+ //print parsed bin info to files
+ for (itGroup = groupBins.begin(); itGroup != groupBins.end(); itGroup++) {
+ groupVector[itGroup->first] += itGroup->second + '\t';
+ }
+
+ }
+
+ //end list vector
+ for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
+ (*(filehandles[it3->first])) << thisList->getLabel() << '\t' << groupNumBins[it3->first] << '\t' << groupVector[it3->first] << endl; // label numBins listvector for that group
+ }
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ParseListCommand", "parse");
+ exit(1);
+ }
+}
+
+/**********************************************************************************************************************/
+
+
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