+//uchime can't handle some of the things allowed in mothurs fasta files. This functions "cleans up" the file.
+int ChimeraUchimeCommand::prepFile(string filename, string output) {
+ try {
+
+ ifstream in;
+ m->openInputFile(filename, in);
+
+ ofstream out;
+ m->openOutputFile(output, out);
+
+ while (!in.eof()) {
+ if (m->control_pressed) { break; }
+
+ Sequence seq(in); m->gobble(in);
+
+ if (seq.getName() != "") { seq.printSequence(out); }
+ }
+ in.close();
+ out.close();
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ChimeraUchimeCommand", "prepFile");
+ exit(1);
+ }
+}
+/**************************************************************************************************/