[Biojava-l] Problem with EMBL and RichStreamReader

[Antje Wollherr]

Hallo Richard,

thank you for the fast response. Now I understand, what the error
message means. Sorry for asking stupid questions but sometimes  I don't
see the wood for the trees. ;)

Cheers,

Antje


On Thu, 2008-03-06 at 13:29 +0000, Richard Holland wrote:
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> The error message says it all:
> 
>  Comments=Unable to handle contig assemblies just yet
> 
> BioJava does not yet support EMBL contig files such as AL009126.
> 
> cheers,
> Richard
> 
> Antje Wollherr wrote:
> > Hello biojava people,
> > 
> > I am new to this list and also not very familiar with BioJava. I was
> > trying to parse an EMBL File and extract the dna sequence with
> > RichSequence.IOTools.readEMBLDNA(br, ns); . 
> > 
> > For most of the embl files this isn't a problem, but the file with
> > accssion number AL009126 (Bacillus subtilis 168) caused an BioExcpetion
> > saying the sequence could not be read.
> > 
> > Can somebody tell where the problem is or how it can be solved?
> > I'm using BioJava 1.5.
> > 
> > Thank you a lot
> > 
> > Antje
> > 
> > Here is the error message:
> > 
> >  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.EMBLFormat
> > Accession=AL009126
> > Id=not set
> > Comments=Unable to handle contig assemblies just yet
> > Parse_block=
> > Stack trace follows ....
> > 
> > 
> > 	at org.biojavax.bio.seq.io.EMBLFormat.readSection(EMBLFormat.java:730)
> > 	at
> > org.biojavax.bio.seq.io.EMBLFormat.readRichSequence(EMBLFormat.java:284)
> > 	at
> > org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:110)
> > 	... 2 more
> > 
> > 
> > _______________________________________________
> > Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biojava-l
> > 
> 
> - --
> Richard Holland (BioMart)
> EMBL EBI, Wellcome Trust Genome Campus,
> Hinxton, Cambridgeshire CB10 1SD, UK
> Tel. +44 (0)1223 494416
> 
> http://www.biomart.org/
> http://www.biojava.org/
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-- 
Antje Wollherr, Diplom-Bioinformatikerin
Göttinger Genomlabor
Institut für Mikrobiologie und Genetik
Grisebachstraße 8
37077 Göttingen

Email: awollhe at gwdg.de
Tel.: 0551 393843
Fax: 0551 394195