--- /dev/null
+/*
+ * getlistcountcommand.cpp
+ * Mothur
+ *
+ * Created by westcott on 10/12/09.
+ * Copyright 2009 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "getlistcountcommand.h"
+
+//**********************************************************************************************************************
+vector<string> GetListCountCommand::setParameters(){
+ try {
+ CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(plist);
+ CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
+ CommandParameter parasort("sort", "Multiple", "name-otu", "otu", "", "", "",false,false); parameters.push_back(parasort);
+ 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, "GetListCountCommand", "setParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string GetListCountCommand::getHelpString(){
+ try {
+ string helpString = "";
+ helpString += "The get.otulist command parameters are list, sort and label. list is required, unless you have a valid current list file.\n";
+ helpString += "The label parameter allows you to select what distance levels you would like a output files created for, and are separated by dashes.\n";
+ helpString += "The sort parameter allows you to select how you want the output displayed. Options are otu and name.\n";
+ helpString += "If otu is selected the output will be otu number followed by the list of names in that otu.\n";
+ helpString += "If name is selected the output will be a sequence name followed by its otu number.\n";
+ helpString += "The get.otulist command should be in the following format: get.otulist(list=yourlistFile, label=yourLabels).\n";
+ helpString += "Example get.otulist(list=amazon.fn.list, label=0.10).\n";
+ helpString += "The default value for label is all lines in your inputfile.\n";
+ helpString += "The get.otulist command outputs a .otu file for each distance you specify listing the bin number and the names of the sequences in that bin.\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, "GetListCountCommand", "getHelpString");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+GetListCountCommand::GetListCountCommand(){
+ try {
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["otu"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetListCountCommand", "GetListCountCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+GetListCountCommand::GetListCountCommand(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["otu"] = 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; }
+ }
+ }
+
+ //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 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 if (listfile == "not open") { abort = true; }
+ else { m->setListFile(listfile); }
+
+
+ //check for optional parameter and set defaults
+ // ...at some point should added some additional type checking...
+ sort = validParameter.validFile(parameters, "sort", false); if (sort == "not found") { sort = "otu"; }
+ if ((sort != "otu") && (sort != "name")) { m->mothurOut( sort + " is not a valid sort option. Options are otu and name. I will use otu."); m->mothurOutEndLine(); sort = "otu"; }
+
+ label = validParameter.validFile(parameters, "label", false);
+ if (label == "not found") { label = ""; }
+ else {
+ if(label != "all") { m->splitAtDash(label, labels); allLines = 0; }
+ else { allLines = 1; }
+ }
+ }
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetListCountCommand", "GetListCountCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+int GetListCountCommand::execute(){
+ try {
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
+
+ input = new InputData(listfile, "list");
+ 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> processedLabels;
+ set<string> userLabels = labels;
+
+ if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
+
+ while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
+
+ if(allLines == 1 || labels.count(list->getLabel()) == 1){
+
+ process(list);
+
+ if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
+
+ 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);
+
+ process(list);
+
+ if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
+
+
+ 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();
+ }
+
+
+ //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);
+
+ process(list);
+
+ if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
+
+ delete list;
+ }
+
+ delete input;
+
+ 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, "GetListCountCommand", "execute");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
+//return 1 if error, 0 otherwise
+void GetListCountCommand::process(ListVector* list) {
+ try {
+ string binnames;
+ if (outputDir == "") { outputDir += m->hasPath(listfile); }
+ string outputFileName = outputDir + m->getRootName(m->getSimpleName(listfile)) + list->getLabel() + ".otu";
+ m->openOutputFile(outputFileName, out);
+ outputNames.push_back(outputFileName); outputTypes["otu"].push_back(outputFileName);
+
+ m->mothurOut(list->getLabel()); m->mothurOutEndLine();
+
+ //for each bin in the list vector
+ for (int i = 0; i < list->getNumBins(); i++) {
+ if (m->control_pressed) { break; }
+
+ binnames = list->get(i);
+
+ if (sort == "otu") {
+ out << i+1 << '\t' << binnames << endl;
+ }else{ //sort = name
+ vector<string> names;
+ m->splitAtComma(binnames, names);
+
+ for (int j = 0; j < names.size(); j++) {
+ out << names[j] << '\t' << i+1 << endl;
+ }
+ }
+ }
+
+ out.close();
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetListCountCommand", "process");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+
projects / mothur.git / blobdiff