[Biojava-l] reading sequences from xml files...

[Matthew Pocock]

 --- Jan Würthner <jan.wuerthner at uni-duesseldorf.de>
wrote: 
> 
> Hi,
> 
> does anyone know, if there is a biojava way to
> construct a Sequence object by 
> reading sequence data from an XML file?

Hi Jan,

Asking if we have parsers for XML is a bit like asking
if we have parsers for ASCII - there are loads of ways
to encode the same data with XML. We currently support
(to a greater or lesser extent) game, agave, das-xml
and XFF.

> 
> I store all the information in XML files (e.g.
> connecting via 
>
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=text&db=Nucleotide&dopt=XML&uid=1234).

OK - reading this now. It looks like a semi-sane XML
version of genbank/embl. You should fairly easily be
able to write a sax or stax handler for this that
calls methods on a SeqIOListener.

> I know that SeqIOTools offers methods for reading
> sequences from files 
> (fileToBioJava()), but unfortunately XML is not
> among the supported formats.

What do you do at the moment? Do you have your own
parsers, or do you use somebody elses?

> 
> kind regards
> Jan Würthner

Matthew

________________________________________________________________________
Want to chat instantly with your online friends?  Get the FREE Yahoo!
Messenger http://mail.messenger.yahoo.co.uk