[Bioperl-l] contributing? sure!

[Ewan Birney]

On Tue, 11 Jul 2000, Lorenz Pollak wrote:

> thanks for the immediate answer!
> 
> I would like to start by doing some easier coding, so that I can
> understand the whole bioperl step by step...
> 
> (I'm still having some difficulties with technical terms and
> abbreviations like EMBOSS or XS...)
> 
> So converting scripts or adding easier extension like those below would be
> a good thing, I think!
> 
> >  o There are a bunch of modules that need to be converted/written in
> > bioperl
> > 
> >     - Ian Korf's BPLite modules
> >     - RepeatMasker module
> >     - Genscan module (? could donate from Ensembl)
> 
> These are to be found in bioperl.org's script section, right?   
>  

Nope. ;)

   BPLite is at http://sapiens.wustl.edu/~ikorf/BPlite.pm

   RepeatMasker - you'll need some repeat masker output and write your own

   Genscan - should donate from Ensembl...

> >  o There are a bunch of easish extensions for bioperl
> > 
> >     - GenBank format flat file indexer (should be trivial)
> >     - swissprot format flat file indexer 
> > 
> 
> Where can I get information on GenBank/swissprot format or have example
> flat files ?
> 

Example flat file in bioperl-live/t/test.genbank
                                 /t/test.swissprot

Actually GenBank has already been written (Bio::Index::GenBank). But
swissprot has not - it should be about 15 minutes to write ;)
Bio::Index::Swissprot - look at Bio::Index::GenBank to get the idea.


(Most of the functionality is provided by Bio::Index::AbstractSeq)


Make sure you work against the current head of cvs
(http://cvs.bioperl.org) and off you go - submit the module to me first
and I'll check it in once I have sanity checked it.


> 
> >  o We have no decent beginners documentation.
> 
> beginner in which sense? (beginner in bioinformatics or in bioperl or in
> using bioperl ? :-) 
> 

Both.


> 
> regards,
> Lorenz
> 

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