[Biopython-dev] [Bug 2762] GFF capability in SeqIO

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2762





------- Comment #1 from biopython-bugzilla at maubp.freeserve.co.uk  2009-02-18 08:54 EST -------
This looks like a nice idea, and possible with some simplifications to match
our existing object scheme.  For example, the current SeqRecord and SeqFeature
classes do not let us explicitly define parent (part-of) relationships between
SeqFeature objects (e.g. GFF3 examples where a CDS has a parent mRNA, or an
exon may have multiple parent mRNAs).  We do have the idea of sub-features, but
this only allows a single parent and thus won't work here.  This parent
information could be recorded as just another SeqFeature qualifier dictionary
entry.

P.S. It is nice to see there is an online GFF3 validator :)


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