else if (type == "name") { pattern = "[filename],pick,[extension]"; }
else if (type == "group") { pattern = "[filename],pick,[extension]"; }
else if (type == "count") { pattern = "[filename],pick,[extension]"; }
- else if (type == "list") { pattern = "[filename],pick,[extension]"; }
+ else if (type == "list") { pattern = "[filename],[distance],pick,[extension]"; }
else if (type == "qfile") { pattern = "[filename],pick,[extension]"; }
else if (type == "accnosreport") { pattern = "[filename],pick.accnos.report"; }
else if (type == "alignreport") { pattern = "[filename],pick.align.report"; }
map<string, string> variables;
variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(listfile));
variables["[extension]"] = m->getExtension(listfile);
- string outputFileName = getOutputFileName("list", variables);
- ofstream out;
- m->openOutputFile(outputFileName, out);
ifstream in;
m->openInputFile(listfile, in);
while(!in.eof()){
selectedCount = 0;
-
- if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; }
//read in list vector
ListVector list(in);
//make a new list vector
ListVector newList;
newList.setLabel(list.getLabel());
+
+ variables["[distance]"] = list.getLabel();
+ string outputFileName = getOutputFileName("list", variables);
+
+ ofstream out;
+ m->openOutputFile(outputFileName, out);
+ outputTypes["list"].push_back(outputFileName); outputNames.push_back(outputFileName);
+
+ vector<string> binLabels = list.getLabels();
+ vector<string> newBinLabels;
+
+ if (m->control_pressed) { in.close(); out.close(); return 0; }
//for each bin
for (int i = 0; i < list.getNumBins(); i++) {
m->splitAtComma(binnames, bnames);
string newNames = "";
- for (int i = 0; i < bnames.size(); i++) {
- string name = bnames[i];
+ for (int j = 0; j < bnames.size(); j++) {
+ string name = bnames[j];
//if that name is in the .accnos file, add it
if (names.count(name) != 0) { newNames += name + ","; selectedCount++; if (m->debug) { sanity["list"].insert(name); } }
}
//if there are names in this bin add to new list
if (newNames != "") {
newNames = newNames.substr(0, newNames.length()-1); //rip off extra comma
- newList.push_back(newNames);
+ newList.push_back(newNames);
+ newBinLabels.push_back(binLabels[i]);
}
}
//print new listvector
if (newList.getNumBins() != 0) {
wroteSomething = true;
+ newList.setLabels(newBinLabels);
+ newList.printHeaders(out);
newList.print(out);
}
m->gobble(in);
+ out.close();
}
in.close();
- out.close();
+
if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine(); }
- outputNames.push_back(outputFileName); outputTypes["list"].push_back(outputFileName);
m->mothurOut("Selected " + toString(selectedCount) + " sequences from your list file."); m->mothurOutEndLine();