[Biojava-l] [biojavax] EMBL parser error

[Richard Holland]

That was indeed a bug. I have made a change to the date parsing in
EMBLFormat and committed it to CVS. Could you test it for me please?

cheers,
Richard

On Fri, 2006-04-07 at 11:20 +0200, Morgane THOMAS-CHOLLIER wrote:
> Hello,
> 
> I am currently using biojavax that I checked out today from CVS to parse 
> an EMBL file, exported from EBI SRS server.
> 
> I ran into this error :
> 
> Exception in thread "main" org.biojava.bio.BioException: Could not read 
> sequence
>     at 
> org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:111)
>     at 
> org.embnet.be.biojavax.tryout.EMBLParseTest.main(EMBLParseTest.java:34)
> Caused by: org.biojava.bio.seq.io.ParseException: Bad date type found: 86
>     at 
> org.biojavax.bio.seq.io.EMBLFormat.readRichSequence(EMBLFormat.java:278)
>     at 
> org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:108)
>     ... 1 more
> 
> The EMBL file is :
> 
> ID   DQ158013   standard; genomic DNA; VRT; 118 BP.
> XX
> AC   DQ158013;
> XX
> SV   DQ158013.1
> XX
> DT   19-JAN-2006 (Rel. 86, Created)
> DT   19-JAN-2006 (Rel. 86, Last updated, Version 1)
> XX
> DE   Triturus helveticus clone Thel.b9 HOXB9 (Hoxb9) gene, partial cds.
> 
> Removing the two lines that comprise the date information resolves the 
> problem.
> 
> Thanks,
> 
> Morgane.
> 
-- 
Richard Holland
European Bioinformatics Institute
Wellcome Trust Genome Campus, Hinxton
Cambridge CB10 1SD, UK
Tel: +44-(0)1223-494416
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