Bioperl: SeqIO drivers

[Ewan Birney]

On Wed, 10 May 2000, Hilmar Lapp wrote:

> Ewan Birney wrote:
> > Can you write a very short example about how you would extend/override
> > a SeqIO system using your new code? Basicaly I am happy for it to go in
> > if it look s sane and works basically like the old stuff...
> > 
> 
> # install a driver for your own format, which you've put in mydriver.pm
> # and the files end in .fmt, you call the format myfmt
> %driver_spec = ('MODULE' => 'mydriver.pm', 'REGEXP' => "\\.fmt\$");
> Bio::SeqIO->registerDriver("myfmt", %driver_spec);
> # then from anywhere in the program
> $seqin = Bio::SeqIO->new('-file' => 'input.fmt'); # will return an object
>                                                   # of mydriver.pm


Hilmar - as far as I can see the only change you are making is that you
can change the hash of 

	file_extension => SeqIO/xxxxxx.pm


is that correct? Is there something I am missing here?

> 
> # to replace a driver for an existing format with your own:
> %driver_spec = Bio::SeqIO->getDriver("fasta");
> # retain the format recognition expression, just replace the module name
> $driver_spec{'MODULE'} = "myfasta.pm";
> # and re-install
> Bio::SeqIO->registerDriver("fasta", %driver_spec);
> # then from anyhwere in your program
> $seqin = Bio::SeqIO->new('-file' => 'seqs.fasta'); # will now return an object
>                                                    # of myfasta.pm
> 
> There is now code which initializes SeqIO such that the existing formats are
> already "registered". I'm not so familiar with perl guts, but I think there's
> something like a BEGIN section in a module that is executed upon 
> use a_module;
> anywhere. So, by this section one could even have modules registering
> themselves once you include them as a use statement.
> 
> I used a hash as driver property spec because this can be extended at any
> time, and you can set your own tags at runtime, which would then be accessible
> to your driver module (given that you know which special tags your driver
> understands).
> 
> 	Hilmar
> 
> -- 
> -----------------------------------------------------------------------
> Hilmar Lapp                                      email: hlapp@gmx.net
> NFI Vienna, IFD/Bioinformatics                   phone: +43 1 86634 631
> A-1235 Vienna                                      fax: +43 1 86634 727
> ROI: Bioinformatics (arrays, expression, seqs), Programming, Databases,
>      Mountain Biking (hard tail, hard fork: feel the trail)
> -----------------------------------------------------------------------
> =========== Bioperl Project Mailing List Message Footer =======
> Project URL: http://bio.perl.org/
> For info about how to (un)subscribe, where messages are archived, etc:
> http://www.techfak.uni-bielefeld.de/bcd/Perl/Bio/vsns-bcd-perl.html
> ====================================================================
> 

-----------------------------------------------------------------
Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
<birney@ebi.ac.uk>. 
-----------------------------------------------------------------

=========== Bioperl Project Mailing List Message Footer =======
Project URL: http://bio.perl.org/
For info about how to (un)subscribe, where messages are archived, etc:
http://www.techfak.uni-bielefeld.de/bcd/Perl/Bio/vsns-bcd-perl.html
====================================================================