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Re: bioperl newbie's question: simple GFF3 peocessing

by BioLion (Curate)
on Jul 31, 2010 at 09:23 UTC ( #852232=note: print w/replies, xml ) Need Help??

in reply to bioperl newbie's question: simple GFF3 peocessing

Hi daverave, you can do all you want and more using BioDB::GFF and the related Bio::DB::GFF::Feature. These will let you load a GFF file into a database (which can be in memory if you want) and extract features of whatever type you like and also sub-group them by attributes.

There is example code for doing much of this on their respective CPAN pages, so have a go, see how far you get and come back to us if you are still struggling - remember to include code/input/error messages/output that you write/use/get/want.

Good luck - hope this helps.

Just a something something...

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Re^2: bioperl newbie's question: simple GFF3 peocessing
by daverave (Scribe) on Jul 31, 2010 at 09:41 UTC
    Thank you very much BioLion.

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[Your Mother]: Corion: I have lost the link to the pmdev guide(s). Do you have that handy?
[karlgoethebier]: Discipulus: see per lop please how to avoid the classic <c>perl 'rm -rfv *|'</>
[Eily]: karlgoethebier: more like grata non persona :P
Discipulus personae non gratae..
[Corion]: Your Mother: Hmm - I have the pmdev nodelet, which has some links, but I'm not sure what links/guides there are
[Corion]: pmdev wiki maybe?
[Discipulus]: uh neat karl!

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