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/*
* 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","summary",false,false,true); parameters.push_back(pshared);
CommandParameter pgroup("group", "InputTypes", "", "", "sharedGroup", "sharedGroup", "none","summary",false,false,true); parameters.push_back(pgroup);
CommandParameter pcount("count", "InputTypes", "", "", "sharedGroup", "sharedGroup", "none","summary",false,false,true); parameters.push_back(pcount);
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::getOutputPattern(string type) {
try {
string pattern = "";
if (type == "summary") { pattern = "[filename],count.summary"; }
else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
return pattern;
}
catch(exception& e) {
m->errorOut(e, "PrimerDesignCommand", "getOutputPattern");
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, count 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();
vector<string> tempOutNames;
outputTypes["summary"] = tempOutNames;
}
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; }
}
it = parameters.find("count");
//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["count"] = inputDir + it->second; }
}
}
vector<string> tempOutNames;
outputTypes["summary"] = tempOutNames;
//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); }
countfile = validParameter.validFile(parameters, "count", true);
if (countfile == "not open") { countfile = ""; abort = true; }
else if (countfile == "not found") { countfile = ""; }
else {
m->setCountTableFile(countfile);
CountTable ct;
if (!ct.testGroups(countfile)) { m->mothurOut("[ERROR]: Your count file does not have any group information, aborting."); m->mothurOutEndLine(); abort=true; }
}
if ((groupfile != "") && (countfile != "")) {
m->mothurOut("[ERROR]: you may only use one of the following: group or count."); m->mothurOutEndLine(); abort=true;
}
if ((sharedfile == "") && (groupfile == "") && (countfile == "")) {
//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 {
countfile = m->getCountTableFile();
if (countfile != "") { m->mothurOut("Using " + countfile + " as input file for the count parameter."); m->mothurOutEndLine(); }
else {
m->mothurOut("You have no current groupfile, countfile 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 != "") { m->readAccnos(accnosfile, Groups); m->setGroups(Groups); }
if (groupfile != "") {
map<string, string> variables;
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(groupfile); }
variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(groupfile));
string outputFileName = getOutputFileName("summary", variables);
outputNames.push_back(outputFileName); outputTypes["summary"].push_back(outputFileName);
ofstream out;
m->openOutputFile(outputFileName, out);
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);
int total = 0;
for (int i = 0; i < Groups.size(); i++) {
int num = groupMap.getNumSeqs(Groups[i]);
total += num;
m->mothurOut(Groups[i] + " contains " + toString(num) + "."); m->mothurOutEndLine();
out << Groups[i] << '\t' << num << endl;
}
out.close();
m->mothurOut("\nTotal seqs: " + toString(total) + "."); m->mothurOutEndLine();
}
if (m->control_pressed) { return 0; }
if (countfile != "") {
map<string, string> variables;
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(countfile); }
variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(countfile));
string outputFileName = getOutputFileName("summary", variables);
outputNames.push_back(outputFileName); outputTypes["summary"].push_back(outputFileName);
ofstream out;
m->openOutputFile(outputFileName, out);
CountTable ct;
ct.readTable(countfile, true, false);
//make sure groups are valid
//takes care of user setting groupNames that are invalid or setting groups=all
SharedUtil util;
vector<string> nameGroups = ct.getNamesOfGroups();
util.setGroups(Groups, nameGroups);
int total = 0;
for (int i = 0; i < Groups.size(); i++) {
int num = ct.getGroupCount(Groups[i]);
total += num;
m->mothurOut(Groups[i] + " contains " + toString(num) + "."); m->mothurOutEndLine();
out << Groups[i] << '\t' << num << endl;
}
out.close();
m->mothurOut("\nTotal seqs: " + toString(total) + "."); m->mothurOutEndLine();
}
if (m->control_pressed) { return 0; }
if (sharedfile != "") {
InputData input(sharedfile, "sharedfile");
vector<SharedRAbundVector*> lookup = input.getSharedRAbundVectors();
map<string, string> variables;
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(countfile); }
variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(countfile));
string outputFileName = getOutputFileName("summary", variables);
outputNames.push_back(outputFileName); outputTypes["summary"].push_back(outputFileName);
ofstream out;
m->openOutputFile(outputFileName, out);
int total = 0;
for (int i = 0; i < lookup.size(); i++) {
int num = lookup[i]->getNumSeqs();
total += num;
m->mothurOut(lookup[i]->getGroup() + " contains " + toString(num) + "."); m->mothurOutEndLine();
delete lookup[i];
out << lookup[i]->getGroup() << '\t' << num << endl;
}
out.close();
m->mothurOut("\nTotal seqs: " + toString(total) + "."); m->mothurOutEndLine();
}
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, "CountGroupsCommand", "execute");
exit(1);
}
}
//**********************************************************************************************************************
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