[Biojava-l] Problem with EMBL and RichStreamReader

[Richard Holland]

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

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/
-----BEGIN PGP SIGNATURE-----
Version: GnuPG v1.4.2.2 (GNU/Linux)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org

iD8DBQFHz/G64C5LeMEKA/QRAn5tAJ9i3ocloh8HoPXW2BP4sINhkV1+jgCff44m
DJIY1k+vicFOMoX4GCwdwGs=
=8JwO
-----END PGP SIGNATURE-----