+++ /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 specific 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->setGroups(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->setGroups(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;
- vector<string> nameGroups = groupMap.getNamesOfGroups();
- util.setGroups(Groups, nameGroups);
-
- 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->setGroups(Groups);
-
- }
- catch(exception& e) {
- m->errorOut(e, "CountGroupsCommand", "readAccnos");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-
-
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