exit(1);
}
}
+//**********************************************************************************************************************
+string GetSharedOTUCommand::getOutputFileNameTag(string type, string inputName=""){
+ try {
+ string outputFileName = "";
+ map<string, vector<string> >::iterator it;
+
+ //is this a type this command creates
+ it = outputTypes.find(type);
+ if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
+ else {
+ if (type == "fasta") { outputFileName = "shared.fasta"; }
+ else if (type == "accnos") { outputFileName = "accnos"; }
+ else if (type == "sharedseqs") { outputFileName = "shared.seqs"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
+ }
+ return outputFileName;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetSharedOTUCommand", "getOutputFileNameTag");
+ exit(1);
+ }
+}
+
//**********************************************************************************************************************
GetSharedOTUCommand::GetSharedOTUCommand(){
try {
if (outputDir == "") { outputDir += m->hasPath(listfile); }
if (output != "accnos") {
- outputFileNames = outputDir + m->getRootName(m->getSimpleName(listfile)) + shared->getLabel() + userGroups + ".shared.seqs";
+ outputFileNames = outputDir + m->getRootName(m->getSimpleName(listfile)) + shared->getLabel() + userGroups + "." + getOutputFileNameTag("sharedseqs");
}else {
- outputFileNames = outputDir + m->getRootName(m->getSimpleName(listfile)) + shared->getLabel() + userGroups + ".accnos";
+ outputFileNames = outputDir + m->getRootName(m->getSimpleName(listfile)) + shared->getLabel() + userGroups + "." + getOutputFileNameTag("accnos");
}
m->openOutputFile(outputFileNames, outNames);
vector<string> namesOfSeqsInThisBin;
- string names = shared->get(i);
- while ((names.find_first_of(',') != -1)) {
- string name = names.substr(0,names.find_first_of(','));
- names = names.substr(names.find_first_of(',')+1, names.length());
+ string names = shared->get(i);
+ vector<string> binNames;
+ m->splitAtComma(names, binNames);
+ for(int j = 0; j < binNames.size(); j++) {
+ string name = binNames[j];
//find group
string seqGroup = groupMap->getGroup(name);
else { atLeastOne[seqGroup]++; }
}
- //get last name
- string seqGroup = groupMap->getGroup(names);
- if (output != "accnos") {
- namesOfSeqsInThisBin.push_back((names + "|" + seqGroup + "|" + toString(i+1)));
- }else { namesOfSeqsInThisBin.push_back(names); }
-
- if (seqGroup == "not found") { m->mothurOut(names + " is not in your groupfile. Please correct."); m->mothurOutEndLine(); exit(1); }
-
- //is this seq in one of hte groups we care about
- it = groupFinder.find(seqGroup);
- if (it == groupFinder.end()) { uniqueOTU = false; } //you have a sequence from a group you don't want
- else { atLeastOne[seqGroup]++; }
-
-
//make sure you have at least one seq from each group you want
bool sharedByAll = true;
map<string, int>::iterator it2;
//if fasta file provided output new fasta file
if ((fastafile != "") && wroteSomething) {
if (outputDir == "") { outputDir += m->hasPath(fastafile); }
- string outputFileFasta = outputDir + m->getRootName(m->getSimpleName(fastafile)) + shared->getLabel() + userGroups + ".shared.fasta";
+ string outputFileFasta = outputDir + m->getRootName(m->getSimpleName(fastafile)) + shared->getLabel() + userGroups + "." + getOutputFileNameTag("fasta");
ofstream outFasta;
m->openOutputFile(outputFileFasta, outFasta);
outputNames.push_back(outputFileFasta); outputTypes["fasta"].push_back(outputFileFasta);