//**********************************************************************************************************************
vector<string> SummaryTaxCommand::setParameters(){
try {
- CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(ptaxonomy);
- CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
- CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pgroup);
- CommandParameter preftaxonomy("reftaxonomy", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(preftaxonomy);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ 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); }
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, group and name. taxonomy is required, unless you have a valid current taxonomy file.\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";
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 {
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
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; }
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) {
if (abort == true) { if (calledHelp) { return 0; } return 2; }
int start = time(NULL);
- PhyloSummary* taxaSum;
- if (refTaxonomy != "") {
- taxaSum = new PhyloSummary(refTaxonomy, groupfile);
- }else {
- taxaSum = new PhyloSummary(groupfile);
- }
+ 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);
+ }
- if (m->control_pressed) { delete taxaSum; return 0; }
+ 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 == "") { numSeqs = taxaSum->summarize(taxfile); }
- else {
+ 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) { delete taxaSum; return 0; }
+ if (m->control_pressed) { if (groupMap != NULL) { delete groupMap; } if (ct != NULL) { delete ct; } delete taxaSum; return 0; }
ifstream in;
m->openInputFile(taxfile, in);
string name, taxon;
while(!in.eof()){
+
+ if (m->control_pressed) { break; }
+
in >> name >> taxon; m->gobble(in);
itNames = nameMap.find(name);
}
}
in.close();
- }
+ }else { numSeqs = taxaSum->summarize(taxfile); }
- if (m->control_pressed) { delete taxaSum; return 0; }
+ if (m->control_pressed) { if (groupMap != NULL) { delete groupMap; } if (ct != NULL) { delete ct; } delete taxaSum; return 0; }
//print summary file
ofstream outTaxTree;
- string summaryFile = outputDir + m->getRootName(m->getSimpleName(taxfile)) + "tax.summary";
+ 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 Name: "); 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();
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