> Hey Chris,
>
> I can adapt whatever you write to cover some form of GFF; every GFF
> format is different in how it deals with exons, AFAICT. (OK, a slight
> exaggeration ;)
>
> How about using this as an example:
>
> http://hgdownload.cse.ucsc.edu/goldenPath/galGal3/database/refGene.tx...
>
> and adapting the attached code? It's not my cleanest code ever (to say
> the least) but it should save you from having to muck around with the
> file formats.
I know this would be a tall order, but it would be awesome to have
some kind of automatic mapping between these feature types. I can't
speak for the earlier GFF versions, but GFF3 uses the Parent attribute
to associate genes->mRNA->exons etc. You would create the graph
representing the complete set (or some part) of Parent-child
relationships? In other words, have the children be accessible through
the parent automagically, e.g.,
myGene = annotDB['NM_027672']
mRNAs = myGene.mRNA
exons = mRNAs[0].exons
for exon in exons:
print exon.start, exon.stop
I'm thinking of mapping from the annotationDB (gff file) to itself.
Would you need to create a separate table defining these relationships
(like splices in
http://www.doe-mbi.ucla.edu/~leec/newpygrdocs/tutorials/worldbase.html#worldbase-schema-a-simple-framework-for-managing-database-schemas)?
It would be great to have all of this information available via pygr.
--Jake
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