--- /dev/null
+/*
+ * countgroupscommand.cpp
+ * Mothur
+ *
+ * Created by westcott on 8/9/11.
+ * Copyright 2011 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "countgroupscommand.h"
+#include "sharedutilities.h"
+#include "inputdata.h"
+
+//**********************************************************************************************************************
+vector<string> CountGroupsCommand::setParameters(){
+ try {
+ CommandParameter pshared("shared", "InputTypes", "", "", "sharedGroup", "sharedGroup", "none",false,false); parameters.push_back(pshared);
+ CommandParameter pgroup("group", "InputTypes", "", "", "sharedGroup", "sharedGroup", "none",false,false); parameters.push_back(pgroup);
+ CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(paccnos);
+ CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
+ 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, "CountGroupsCommand", "setParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string CountGroupsCommand::getHelpString(){
+ try {
+ string helpString = "";
+ helpString += "The count.groups command counts sequences from a specfic group or set of groups from the following file types: group or shared file.\n";
+ helpString += "The count.groups command parameters are accnos, group, shared and groups. You must provide a group or shared file.\n";
+ helpString += "The accnos parameter allows you to provide a file containing the list of groups.\n";
+ helpString += "The groups parameter allows you to specify which of the groups in your groupfile you would like. You can separate group names with dashes.\n";
+ helpString += "The count.groups command should be in the following format: count.groups(accnos=yourAccnos, group=yourGroupFile).\n";
+ helpString += "Example count.groups(accnos=amazon.accnos, group=amazon.groups).\n";
+ helpString += "or count.groups(groups=pasture, group=amazon.groups).\n";
+ helpString += "Note: No spaces between parameter labels (i.e. group), '=' and parameters (i.e.yourGroupFile).\n";
+ return helpString;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CountGroupsCommand", "getHelpString");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+CountGroupsCommand::CountGroupsCommand(){
+ try {
+ abort = true; calledHelp = true;
+ setParameters();
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CountGroupsCommand", "CountGroupsCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+CountGroupsCommand::CountGroupsCommand(string option) {
+ try {
+ abort = false; calledHelp = false;
+
+ //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; }
+ }
+
+ //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("accnos");
+ //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["accnos"] = 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("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 required parameters
+ accnosfile = validParameter.validFile(parameters, "accnos", true);
+ if (accnosfile == "not open") { abort = true; }
+ else if (accnosfile == "not found") { accnosfile = ""; }
+ else { m->setAccnosFile(accnosfile); }
+
+ groups = validParameter.validFile(parameters, "groups", false);
+ if (groups == "not found") { groups = ""; }
+ else {
+ m->splitAtDash(groups, Groups);
+ m->Groups = Groups;
+ }
+
+ sharedfile = validParameter.validFile(parameters, "shared", true);
+ if (sharedfile == "not open") { sharedfile = ""; abort = true; }
+ else if (sharedfile == "not found") { sharedfile = ""; }
+ else { m->setSharedFile(sharedfile); }
+
+ groupfile = validParameter.validFile(parameters, "group", true);
+ if (groupfile == "not open") { groupfile = ""; abort = true; }
+ else if (groupfile == "not found") { groupfile = ""; }
+ else { m->setGroupFile(groupfile); }
+
+ if ((sharedfile == "") && (groupfile == "")) {
+ //give priority to shared, then group
+ sharedfile = m->getSharedFile();
+ if (sharedfile != "") { m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
+ else {
+ groupfile = m->getGroupFile();
+ if (groupfile != "") { m->mothurOut("Using " + groupfile + " as input file for the group parameter."); m->mothurOutEndLine(); }
+ else {
+ m->mothurOut("You have no current groupfile or sharedfile and one is required."); m->mothurOutEndLine(); abort = true;
+ }
+ }
+ }
+
+ if ((accnosfile == "") && (Groups.size() == 0)) { Groups.push_back("all"); m->Groups = Groups; }
+ }
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CountGroupsCommand", "CountGroupsCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+int CountGroupsCommand::execute(){
+ try {
+
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
+
+ //get groups you want to remove
+ if (accnosfile != "") { readAccnos(); }
+
+ if (groupfile != "") {
+ GroupMap groupMap(groupfile);
+ groupMap.readMap();
+
+ //make sure groups are valid
+ //takes care of user setting groupNames that are invalid or setting groups=all
+ SharedUtil util;
+ util.setGroups(Groups, groupMap.namesOfGroups);
+
+ for (int i = 0; i < Groups.size(); i++) {
+ m->mothurOut(Groups[i] + " contains " + toString(groupMap.getNumSeqs(Groups[i])) + "."); m->mothurOutEndLine();
+ }
+ }
+
+ if (m->control_pressed) { return 0; }
+
+ if (sharedfile != "") {
+ InputData input(sharedfile, "sharedfile");
+ vector<SharedRAbundVector*> lookup = input.getSharedRAbundVectors();
+
+ for (int i = 0; i < lookup.size(); i++) {
+ m->mothurOut(lookup[i]->getGroup() + " contains " + toString(lookup[i]->getNumSeqs()) + "."); m->mothurOutEndLine();
+ delete lookup[i];
+ }
+ }
+
+ return 0;
+ }
+
+ catch(exception& e) {
+ m->errorOut(e, "CountGroupsCommand", "execute");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+void CountGroupsCommand::readAccnos(){
+ try {
+ Groups.clear();
+
+ ifstream in;
+ m->openInputFile(accnosfile, in);
+ string name;
+
+ while(!in.eof()){
+ in >> name;
+
+ Groups.push_back(name);
+
+ m->gobble(in);
+ }
+ in.close();
+
+ m->Groups = Groups;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CountGroupsCommand", "readAccnos");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+
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