Insdels following the human mutation nomenclature are correctly identified, but are tagged as type "null" instead of "DELETETION_INSERTION". Behaviour can only be observed when using the exact backus naur grammar. Fuzzy grammar identifies the correct mutation type. Bug might be related to Bug#6.
To reproduce this bug:
import java.util.List;
import de.hu.berlin.wbi.objects.MutationMention;
import seth.SETH;
public class Test {
/**
* @param args
*/
public static void main(String[] args) {
String mutationString ="p.Glu746_Thr751delinsAla";
//Incorrect Type
SETH sethExact = new SETH("resources/mutations.txt", true, true);
List<MutationMention> ms = sethExact.findMutations(mutationString);
for(MutationMention m : ms){
System.out.println(m.getText() + " type=" +m.getType());
}
//Correct Type
SETH sethInexact = new SETH("resources/mutations.txt", false, true);
ms = sethInexact.findMutations(mutationString);
for(MutationMention m : ms){
System.out.println(m.getText() + " type=" +m.getType());
}
}
}
Insdels following the human mutation nomenclature are correctly identified, but are tagged as type "null" instead of "DELETETION_INSERTION". Behaviour can only be observed when using the exact backus naur grammar. Fuzzy grammar identifies the correct mutation type. Bug might be related to Bug#6.
To reproduce this bug:
test code: https://github.com/rockt/SETH/blob/master/src/test/java/de/hu/berlin/wbi/issues/Issue7Test.java