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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 "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 pseed("seed", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pseed);
CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
abort = false; calledHelp = false;
vector<string> tempOutNames;
outputTypes["summary"] = tempOutNames;
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->setControl_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";
return helpString;
}
catch(exception& e) {
m->errorOut(e, "CountGroupsCommand", "getHelpString");
exit(1);
}
}
//**********************************************************************************************************************
CountGroupsCommand::CountGroupsCommand(string option) : Command() {
try {
//allow user to run help
if(option == "help") { help(); abort = true; calledHelp = true; }
else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else if(option == "category") { abort = true; calledHelp = true; }
else {
OptionParser parser(option, setParameters());
map<string,string> parameters = parser.getParameters();
ValidParameters validParameter;
//check for required parameters
accnosfile = validParameter.validFile(parameters, "accnos");
if (accnosfile == "not open") { abort = true; }
else if (accnosfile == "not found") { accnosfile = ""; }
else { current->setAccnosFile(accnosfile); }
groups = validParameter.valid(parameters, "groups");
if (groups == "not found") { groups = ""; }
else {
util.splitAtDash(groups, Groups);
if (Groups.size() != 0) { if (Groups[0]== "all") { Groups.clear(); } }
}
sharedfile = validParameter.validFile(parameters, "shared");
if (sharedfile == "not open") { sharedfile = ""; abort = true; }
else if (sharedfile == "not found") { sharedfile = ""; }
else { current->setSharedFile(sharedfile); }
groupfile = validParameter.validFile(parameters, "group");
if (groupfile == "not open") { groupfile = ""; abort = true; }
else if (groupfile == "not found") { groupfile = ""; }
else { current->setGroupFile(groupfile); }
countfile = validParameter.validFile(parameters, "count");
if (countfile == "not open") { countfile = ""; abort = true; }
else if (countfile == "not found") { countfile = ""; }
else {
current->setCountFile(countfile);
CountTable ct;
if (!ct.testGroups(countfile)) { m->mothurOut("[ERROR]: Your count file does not have any group information, aborting.\n"); abort=true; }
}
if ((groupfile != "") && (countfile != "")) {
m->mothurOut("[ERROR]: you may only use one of the following: group or count.\n"); abort=true;
}
if ((sharedfile == "") && (groupfile == "") && (countfile == "")) {
//give priority to shared, then group
sharedfile = current->getSharedFile();
if (sharedfile != "") { m->mothurOut("Using " + sharedfile + " as input file for the shared parameter.\n"); }
else {
groupfile = current->getGroupFile();
if (groupfile != "") { m->mothurOut("Using " + groupfile + " as input file for the group parameter.\n"); }
else {
countfile = current->getCountFile();
if (countfile != "") { m->mothurOut("Using " + countfile + " as input file for the count parameter.\n"); }
else {
m->mothurOut("You have no current groupfile, countfile or sharedfile and one is required.\n"); abort = true;
}
}
}
}
}
}
catch(exception& e) {
m->errorOut(e, "CountGroupsCommand", "CountGroupsCommand");
exit(1);
}
}
//**********************************************************************************************************************
int CountGroupsCommand::execute(){
try {
if (abort) { if (calledHelp) { return 0; } return 2; }
//get groups you want to remove
if (accnosfile != "") { util.readAccnos(accnosfile, Groups); }
if (groupfile != "") {
map<string, string> variables;
string thisOutputDir = outputdir;
if (outputdir == "") { thisOutputDir += util.hasPath(groupfile); }
variables["[filename]"] = thisOutputDir + util.getRootName(util.getSimpleName(groupfile));
string outputFileName = getOutputFileName("summary", variables);
outputNames.push_back(outputFileName); outputTypes["summary"].push_back(outputFileName);
ofstream out;
util.openOutputFile(outputFileName, out);
GroupMap groupMap(groupfile);
groupMap.readMap();
vector<string> nameGroups = groupMap.getNamesOfGroups();
if (Groups.size() == 0) { 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) + ".\n");
out << Groups[i] << '\t' << num << endl;
}
out.close();
m->mothurOut("\nSize of smallest group: " + toString(groupMap.getNumSeqsSmallestGroup()) + ".\n");
m->mothurOut("\nTotal seqs: " + toString(total) + ".\n");
}
if (m->getControl_pressed()) { return 0; }
if (countfile != "") {
map<string, string> variables;
string thisOutputDir = outputdir;
if (outputdir == "") { thisOutputDir += util.hasPath(countfile); }
variables["[filename]"] = thisOutputDir + util.getRootName(util.getSimpleName(countfile));
string outputFileName = getOutputFileName("summary", variables);
outputNames.push_back(outputFileName); outputTypes["summary"].push_back(outputFileName);
ofstream out;
util.openOutputFile(outputFileName, out);
CountTable ct;
ct.readTable(countfile, true, false);
vector<string> nameGroups = ct.getNamesOfGroups();
if (Groups.size() == 0) { 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) + ".\n");
out << Groups[i] << '\t' << num << endl;
}
out.close();
m->mothurOut("\nSize of smallest group: " + toString(ct.getNumSeqsSmallestGroup()) + ".\n");
m->mothurOut("\nTotal seqs: " + toString(total) + ".\n");
}
if (m->getControl_pressed()) { return 0; }
if (sharedfile != "") {
InputData input(sharedfile, "sharedfile", Groups);
SharedRAbundVectors* lookup = input.getSharedRAbundVectors();
Groups = lookup->getNamesGroups();
map<string, string> variables;
string thisOutputDir = outputdir;
if (outputdir == "") { thisOutputDir += util.hasPath(sharedfile); }
variables["[filename]"] = thisOutputDir + util.getRootName(util.getSimpleName(sharedfile));
string outputFileName = getOutputFileName("summary", variables);
outputNames.push_back(outputFileName); outputTypes["summary"].push_back(outputFileName);
ofstream out;
util.openOutputFile(outputFileName, out);
int total = 0;
vector<string> groups = lookup->getNamesGroups();
for (int i = 0; i < groups.size(); i++) {
int num = lookup->getNumSeqs(groups[i]);
total += num;
m->mothurOut(groups[i] + " contains " + toString(num) + ".\n");
out << groups[i] << '\t' << num << endl;
}
out.close();
m->mothurOut("\nSize of smallest group: " + toString(lookup->getNumSeqsSmallestGroup()) + ".\n");
delete lookup;
m->mothurOut("\nTotal seqs: " + toString(total) + ".\n");
}
m->mothurOut("\nOutput File Names: \n");
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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