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/*
* summarytaxcommand.cpp
* Mothur
*
* Created by westcott on 9/23/11.
* Copyright 2011 Schloss Lab. All rights reserved.
*
*/
#include "summarytaxcommand.h"
#include "phylosummary.h"
//**********************************************************************************************************************
vector<string> SummaryTaxCommand::setParameters(){
try {
CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "none", "none","summary",false,true,true); parameters.push_back(ptaxonomy);
CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none","",false,false,true); parameters.push_back(pname);
CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none","",false,false,true); parameters.push_back(pcount);
CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none","",false,false,true); parameters.push_back(pgroup);
CommandParameter preftaxonomy("reftaxonomy", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(preftaxonomy);
CommandParameter prelabund("relabund", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(prelabund);
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, "SummaryTaxCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
string SummaryTaxCommand::getHelpString(){
try {
string helpString = "";
helpString += "The summary.tax command reads a taxonomy file and an optional name file, and summarizes the taxonomy information.\n";
helpString += "The summary.tax command parameters are taxonomy, count, group, name and relabund. taxonomy is required, unless you have a valid current taxonomy file.\n";
helpString += "The name parameter allows you to enter a name file associated with your taxonomy file. \n";
helpString += "The group parameter allows you add a group file so you can have the summary totals broken up by group.\n";
helpString += "The count parameter allows you add a count file so you can have the summary totals broken up by group.\n";
helpString += "The reftaxonomy parameter allows you give the name of the reference taxonomy file used when you classified your sequences. It is not required, but providing it will keep the rankIDs in the summary file static.\n";
helpString += "The relabund parameter allows you to indicate you want the summary file values to be relative abundances rather than raw abundances. Default=F. \n";
helpString += "The summary.tax command should be in the following format: \n";
helpString += "summary.tax(taxonomy=yourTaxonomyFile) \n";
helpString += "Note: No spaces between parameter labels (i.e. taxonomy), '=' and parameters (i.e.yourTaxonomyFile).\n";
return helpString;
}
catch(exception& e) {
m->errorOut(e, "SummaryTaxCommand", "getHelpString");
exit(1);
}
}
//**********************************************************************************************************************
string SummaryTaxCommand::getOutputPattern(string type) {
try {
string pattern = "";
if (type == "summary") { pattern = "[filename],tax.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, "SummaryTaxCommand", "getOutputPattern");
exit(1);
}
}
//**********************************************************************************************************************
SummaryTaxCommand::SummaryTaxCommand(){
try {
abort = true; calledHelp = true;
setParameters();
vector<string> tempOutNames;
outputTypes["summary"] = tempOutNames;
}
catch(exception& e) {
m->errorOut(e, "SummaryTaxCommand", "SummaryTaxCommand");
exit(1);
}
}
//***************************************************************************************************************
SummaryTaxCommand::SummaryTaxCommand(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 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("taxonomy");
//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["taxonomy"] = inputDir + it->second; }
}
it = parameters.find("name");
//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["name"] = 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("reftaxonomy");
//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["reftaxonomy"] = 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; }
}
}
//initialize outputTypes
vector<string> tempOutNames;
outputTypes["summary"] = tempOutNames;
//check for required parameters
taxfile = validParameter.validFile(parameters, "taxonomy", true);
if (taxfile == "not open") { abort = true; }
else if (taxfile == "not found") {
taxfile = m->getTaxonomyFile();
if (taxfile != "") { m->mothurOut("Using " + taxfile + " as input file for the taxonomy parameter."); m->mothurOutEndLine(); }
else { m->mothurOut("You have no current taxonomy file and the taxonomy parameter is required."); m->mothurOutEndLine(); abort = true; }
}else { m->setTaxonomyFile(taxfile); }
namefile = validParameter.validFile(parameters, "name", true);
if (namefile == "not open") { namefile = ""; abort = true; }
else if (namefile == "not found") { namefile = ""; }
else { m->setNameFile(namefile); }
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); }
if ((namefile != "") && (countfile != "")) {
m->mothurOut("[ERROR]: you may only use one of the following: name or count."); 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;
}
refTaxonomy = validParameter.validFile(parameters, "reftaxonomy", true);
if (refTaxonomy == "not found") { refTaxonomy = ""; m->mothurOut("reftaxonomy is not required, but if given will keep the rankIDs in the summary file static."); m->mothurOutEndLine(); }
else if (refTaxonomy == "not open") { refTaxonomy = ""; 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 = "";
outputDir += m->hasPath(taxfile); //if user entered a file with a path then preserve it
}
string temp = validParameter.validFile(parameters, "relabund", false); if (temp == "not found"){ temp = "false"; }
relabund = m->isTrue(temp);
if (countfile == "") {
if (namefile == "") {
vector<string> files; files.push_back(taxfile);
parser.getNameFile(files);
}
}
}
}
catch(exception& e) {
m->errorOut(e, "SummaryTaxCommand", "SummaryTaxCommand");
exit(1);
}
}
//***************************************************************************************************************
int SummaryTaxCommand::execute(){
try{
if (abort == true) { if (calledHelp) { return 0; } return 2; }
int start = time(NULL);
GroupMap* groupMap = NULL;
CountTable* ct = NULL;
if (groupfile != "") {
groupMap = new GroupMap(groupfile);
groupMap->readMap();
}else if (countfile != "") {
ct = new CountTable();
ct->readTable(countfile, true, false);
}
PhyloSummary* taxaSum;
if (countfile != "") {
if (refTaxonomy != "") { taxaSum = new PhyloSummary(refTaxonomy, ct, relabund); }
else { taxaSum = new PhyloSummary(ct, relabund); }
}else {
if (refTaxonomy != "") { taxaSum = new PhyloSummary(refTaxonomy, groupMap, relabund); }
else { taxaSum = new PhyloSummary(groupMap, relabund); }
}
if (m->control_pressed) { if (groupMap != NULL) { delete groupMap; } if (ct != NULL) { delete ct; } delete taxaSum; return 0; }
int numSeqs = 0;
if ((namefile == "") || (countfile != "")) { numSeqs = taxaSum->summarize(taxfile); }
else if (namefile != "") {
map<string, vector<string> > nameMap;
map<string, vector<string> >::iterator itNames;
m->readNames(namefile, nameMap);
if (m->control_pressed) { if (groupMap != NULL) { delete groupMap; } if (ct != NULL) { delete ct; } delete taxaSum; return 0; }
ifstream in;
m->openInputFile(taxfile, in);
//read in users taxonomy file and add sequences to tree
string name, taxon;
while(!in.eof()){
if (m->control_pressed) { break; }
in >> name >> taxon; m->gobble(in);
itNames = nameMap.find(name);
if (itNames == nameMap.end()) {
m->mothurOut("[ERROR]: " + name + " is not in your name file please correct."); m->mothurOutEndLine(); exit(1);
}else{
for (int i = 0; i < itNames->second.size(); i++) {
numSeqs++;
taxaSum->addSeqToTree(itNames->second[i], taxon); //add it as many times as there are identical seqs
}
itNames->second.clear();
nameMap.erase(itNames->first);
}
}
in.close();
}else { numSeqs = taxaSum->summarize(taxfile); }
if (m->control_pressed) { if (groupMap != NULL) { delete groupMap; } if (ct != NULL) { delete ct; } delete taxaSum; return 0; }
//print summary file
ofstream outTaxTree;
map<string, string> variables;
variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(taxfile));
string summaryFile = getOutputFileName("summary",variables);
m->openOutputFile(summaryFile, outTaxTree);
taxaSum->print(outTaxTree);
outTaxTree.close();
delete taxaSum;
if (groupMap != NULL) { delete groupMap; } if (ct != NULL) { delete ct; }
if (m->control_pressed) { m->mothurRemove(summaryFile); return 0; }
m->mothurOutEndLine();
m->mothurOut("It took " + toString(time(NULL) - start) + " secs to create the summary file for " + toString(numSeqs) + " sequences."); m->mothurOutEndLine(); m->mothurOutEndLine();
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
m->mothurOut(summaryFile); m->mothurOutEndLine(); outputNames.push_back(summaryFile); outputTypes["summary"].push_back(summaryFile);
m->mothurOutEndLine();
return 0;
}
catch(exception& e) {
m->errorOut(e, "SummaryTaxCommand", "execute");
exit(1);
}
}
/**************************************************************************************/
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