[Bioperl-l] 0.7.2

[Ewan Birney]

On Fri, 6 Jul 2001, Jason Stajich wrote:

> On Fri, 6 Jul 2001, Vladimir Babenko wrote:
> 
> >    Thanks, but it didn't work. I wonder how could I make parser to use
> > Bio::SeqFeature::Transcript instead of Bio::SeqFeature::Generic? While using
> > Bio::Seq it always goes to Generic SeqFeature module.
> 
> yep, that's intentional.  You are asking the parser to interpret the
> feature tags, see that one is mRNA and make them into transcripts.  Some
> other people Dave Block among them, are grappling with the best way to do
> this.  It really means either adding a filter into the parser modules to
> know how to instantiate Transcripts, or build an object that will take a
> Sequence object, look at all the features contained within, and aggregate
> some of them into a Gene/transcript object.
> 
> Or you could write some code that would loop through all of the features
> that are in a seq after parsing a file, if the feature was mrna, build a
> transcript from it and add that new feature to the sequence object.  
> 
> I'm concerned about putting this type of magic directly in the parser
> objects - would rather it be a post-processing procedure, but I can be
> convinced otherwise.

Something has to do the magic and the magic should definitely be

   (a) separated from the "raw" parsing

   (b) configurable about whether it is used or not in the SeqIO system

but at the end of the day, I think the default out-of-the box SeqIO system
should come with "the magic switched on" by default. Very much the Perl
way to do this ;)



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Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
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