+++ /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