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Re: [Biojava-l] Parsing exception reading sequence from GenbankRichSequenceDB George Waldon Thu Feb 16 18:00:46 2012

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 <[EMAIL PROTECTED]>:

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 [EMAIL PROTECTED] 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


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