Bioperl: extracting CDS from an EMBL formatted file

[Ewan Birney]

On Tue, 1 Jun 1999, Catherine Letondal wrote:

> 
> Hi,
> 
> Is there a simple way with a bioperl module to extract
> CDS features from an Embl formatted file containing several
> entries? 

I am writing this at the moment. The latest CVS version has code
in development which represents EMBL/GenBank entries (IO at the moment
from EMBL .dat files). It is not ready for use yet, but you could be
an early tester (in a couple of weeks perhaps). The reading of the CDS
stuff works ok for me at the moment, so there is no real problem in 
the parsing, I just need to tidy it up/add some more twiddles to the
parser.


> I have tried Boulder::Genbank which works perfectly
> as long as you have a Genbank formatted file (as far as I know
> there is no converter which keeps the CDS features - readseq
> and fmtseq don't).
> 
> Thanks a lot,
> 
> -- 
> Catherine Letondal -- letondal@pasteur.fr -- +33 (1) 40 61 31 91
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Ewan Birney
<birney@sanger.ac.uk>
http://www.sanger.ac.uk/Users/birney/

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