+++ /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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