[Biojava-l] Parsing exception reading sequence from GenbankRichSequenceDB

[George Waldon]

Hello Scott,

This appears to be an exception thrown by the parser. Is-there a way  
you can fetch the sequence(s) as a text file before the exception  
occurs? It would be interesting to see if you can reproduce the  
exception; you can send me the file if you want.

Regards,
George

Quoting Scott Frees <sfrees at ramapo.edu>:

> 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();
> 		}
> 	}
> }
>
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>



--------------------------------
George Waldon