[Biojava-l] Parsing exception reading sequence from GenbankRichSequenceDB

[Scott Frees]

Hello –

I have developed an application that searches and compares
g-quadruplexes within mRNA.  The web application has been running
without any problems on several different web servers for over a year.
 Suddenly, just this week, it is unable to download sequence data
using GenbankRichSequenceDB – has anyone else has had this problem?

We are using BioJava 1.8.1

Below is the exception trace, and the code that follows is a small
test app that generates the exception.  This code worked without any
problems prior to Tuesday this week, and we haven't made any
modification to our application.
------------------------------------------------------
org.biojava.bio.BioException: Failed to read Genbank sequence
	at org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence(GenbankRichSequenceDB.java:163)
	at Tester.main(Tester.java:11)
Caused by: org.biojava.bio.BioException: Could not read sequence
	at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:113)
	at org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence(GenbankRichSequenceDB.java:159)
	... 1 more
Caused by: org.biojava.bio.seq.io.ParseException:

A Exception Has Occurred During Parsing.
Please submit the details that follow to biojava-l at biojava.org or post
a bug report to http://bugzilla.open-bio.org/

Format_object=org.biojavax.bio.seq.io.GenbankFormat
Accession=null
Id=null
Comments=Bad section
Parse_block=<?xml   version="1.0"?>
Stack trace follows ....

	at org.biojavax.bio.seq.io.GenbankFormat.readSection(GenbankFormat.java:620)
	at org.biojavax.bio.seq.io.GenbankFormat.readRichSequence(GenbankFormat.java:279)
	at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:110)
	... 2 more
Caused by: java.lang.StringIndexOutOfBoundsException: String index out
of range: -4
	at java.lang.String.substring(Unknown Source)
	at java.lang.String.substring(Unknown Source)
	at org.biojavax.bio.seq.io.GenbankFormat.readSection(GenbankFormat.java:610)
	... 4 more
-----------------------------


import org.biojava.bio.BioException;
import org.biojava.bio.seq.db.IllegalIDException;
import org.biojavax.bio.db.ncbi.GenbankRichSequenceDB;
import org.biojavax.bio.seq.RichSequence;

public class Tester {
	public static void main(String args[]) {
		String id = "NM_001110.2";  // Issue occurs with any ID
		GenbankRichSequenceDB  ncbi = new GenbankRichSequenceDB();
		try {
			RichSequence rs = ncbi.getRichSequence(id);
			System.out.println(rs.seqString());
		} catch (IllegalIDException e) {
			e.printStackTrace();
		} catch (BioException e) {
			e.printStackTrace();
		}
	}
}