retrofitting a db to add additional relationships about gffutils HOT 4 CLOSED

By the way, keep in mind #6 when adding infrastructure for this issue.

from gffutils.

From #20:

In ENSEMBL, exons have different ENSE ids if they are of different frames. Ideally, the same exon locus exon:chr1:100-200:+:. would be a parent to both CDS:chr1:100-200:+:2 and CDS:chr1:100-150:+:0. So somehow the parent exon locus would have to match up with the different ENSE ids of the CDSs

Assuming the existence of FeatureDB.add_relation, would this work? :

db = FeatureDB('filename.db')
exon = db["exon:chr1:100-200:+:."]

# Get CDSs that fall within this exon
for cds in db.region(exon, featuretype='CDS', completely_within=True):

    # Maybe some filtering here to confirm that these are the 
    # CDSs you're looking for...

    def child_func(parent, child):
        child.attributes['parent_exon'] = parent['ENSE']
        return child

    db.add_relation(
        parent=exon, child=cds, level=1,
        parent_func=lambda x: x, child_func=child_func)

from gffutils.

Yes I think this would work!

from gffutils.

As of 715a615 there's now an add_relation method. Can you give it a shot when you get a chance? Usage should be what I sketched out above.

from gffutils.