//**********************************************************************************************************************
vector<string> GetSharedOTUCommand::setParameters(){
try {
- CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pfasta);
- CommandParameter pgroup("group", "InputTypes", "", "", "none", "FNGLT", "none",false,true); parameters.push_back(pgroup);
- CommandParameter plist("list", "InputTypes", "", "", "none", "FNGLT", "none",false,true); parameters.push_back(plist);
- CommandParameter poutput("output", "Multiple", "accnos-default", "default", "", "", "",false,false); parameters.push_back(poutput);
- CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
- CommandParameter punique("unique", "String", "", "", "", "", "",false,false); parameters.push_back(punique);
- CommandParameter pshared("shared", "String", "", "", "", "", "",false,false); parameters.push_back(pshared);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "FNGLT", "none","fasta",false,false); parameters.push_back(pfasta);
+ CommandParameter pgroup("group", "InputTypes", "", "", "none", "FNGLT", "none","sharedseq",false,true,true); parameters.push_back(pgroup);
+ CommandParameter plist("list", "InputTypes", "", "", "none", "FNGLT", "none","sharedseq",false,true,true); parameters.push_back(plist);
+ CommandParameter poutput("output", "Multiple", "accnos-default", "default", "", "", "","",false,false); parameters.push_back(poutput);
+ CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+ CommandParameter punique("unique", "String", "", "", "", "", "","",false,false,true); parameters.push_back(punique);
+ CommandParameter pshared("shared", "String", "", "", "", "", "","",false,false,true); parameters.push_back(pshared);
+ 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); }
}
}
//**********************************************************************************************************************
-string GetSharedOTUCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string GetSharedOTUCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
+
+ if (type == "fasta") { pattern = "[filename],[distance],[group],shared.fasta"; }
+ else if (type == "accnos") { pattern = "[filename],[distance],[group],accnos"; }
+ else if (type == "sharedseqs") { pattern = "[filename],[distance],[group],shared.seqs"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
- //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);
- }
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetSharedOTUCommand", "getOutputPattern");
+ exit(1);
+ }
}
-
//**********************************************************************************************************************
GetSharedOTUCommand::GetSharedOTUCommand(){
try {
string outputFileNames;
if (outputDir == "") { outputDir += m->hasPath(listfile); }
- if (output != "accnos") {
- outputFileNames = outputDir + m->getRootName(m->getSimpleName(listfile)) + shared->getLabel() + userGroups + "." + getOutputFileNameTag("sharedseqs");
- }else {
- outputFileNames = outputDir + m->getRootName(m->getSimpleName(listfile)) + shared->getLabel() + userGroups + "." + getOutputFileNameTag("accnos");
- }
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(listfile));
+ variables["[distance]"] = shared->getLabel();
+ variables["[group]"] = userGroups;
+ if (output != "accnos") { outputFileNames = getOutputFileName("sharedseqs", variables); }
+ else { outputFileNames = getOutputFileName("accnos", variables); }
+
m->openOutputFile(outputFileNames, outNames);
bool wroteSomething = false;
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 + "." + getOutputFileNameTag("fasta");
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastafile));
+ string outputFileFasta = getOutputFileName("fasta", variables);
ofstream outFasta;
m->openOutputFile(outputFileFasta, outFasta);
outputNames.push_back(outputFileFasta); outputTypes["fasta"].push_back(outputFileFasta);