[Bioperl-l] Bio::SeqIO::swiss

[Ewan Birney]

On Fri, 28 Jul 2000, L.Pollak wrote:

> Hi to everyone!
> 
> while i was implementing save functions for this protein control panel 
> thingy i discovered that the write abilities of Bio::SeqIO::swiss are 
> rather unfinished... (it can't write features for instance)

Bad. :( 

> 
> so i'll do some work on this, ok?
> 

Indeed. You might want to make use of the FTHelper, but I think
swissprot's feature model is slightly different from EMBL/GenBank's.

> greetings,
> Lorenz
> 
> PS: the current progress of my program may be of interest:
> 
> done:
> + read one swissprot sequence from file
> + retrieve sequence from db/flat file indexes
>   (genpept is already working, others need
>    saved settings for paths and other stuff)
> + save sequence to swissprot file (same/other)
> + show seq stats
> + edit description
> + edit/add/del comments
> + edit/add/del dblinks
> + edit/add/del references
> 
> working on:
> * edit/add/del features (with subfeatures)
> * improvement of swissprot output
> 
> not started:
> - the whole blast / hmmer stuff
> - edit sequence so that features and other things that have 
>   start/end values remain consistent
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