[Bioperl-l] [Gmod-schema] Circular genomes in Chado/BioPerl
jimhu at tamu.edu
Tue Sep 9 12:05:59 EDT 2008
I was thinking this would be handled by making the end=parent feature
length x 2 + end coord. end/parent length = number of times crosses
On Sep 8, 2008, at 2:57 PM, Aaron Mackey wrote:
> How can you handle features that may cross the origin more than once?
> The modulus, though simple, seems to be only half the solution. It
> also makes it difficult to place features in the genome "by eye"
> (having to do the modulus subtraction in my head), or in
> sorting/filtering operations.
> I have an alternative that I wondered if you considered: allow the
> start/end to have an additional "circular revolution" prefix:
> a typical range tuple like: 100 200 -
> is thus shorthand for: 0:100 0:200 -
> (i.e. both the 100 and 200 are in the same "revolution" around the
> and is then distinguishable from an "around the genome + 100"
> feature of:
> 1:100 0:200 -
> Just an alternative to consider (if you haven't already). I'm not
> wedded to the syntax, but I wouldn't want to see new columns in GFF
> just for this. Essentially, what you want is some form of compound
> polar coordinates, it seems.
> On Mon, Sep 8, 2008 at 2:44 PM, Jim Hu <jimhu at tamu.edu> wrote:
>> In discussions with GMOD about Gbrowse, we've come up with a
>> proposal for
>> handling circular genomes and features that cross the origin in such
>> genomes. This applies to lots of prokaryotic and viral genomes,
>> and might
>> be valuable for some ways of representing terminally redundant linear
>> 1) Keep the requirement that start < end
>> 2) allow end > parent feature length
>> 3) parent feature gets an is_circular boolean
>> 4) use modular arithmetic to calculate the real position of end on
>> parent feature.
>> We'd like to do this in a way that will be consistent with Chado
>> and BioPerl
>> representation of features as much as possible (realizing that
>> there is the
>> usual interbase or not coordinate issue). What do people think?
>> Lincoln is
>> on board for modifying the GFF3 spec.
>> Jim Hu
>> Jim Hu
>> Associate Professor
>> Dept. of Biochemistry and Biophysics
>> 2128 TAMU
>> Texas A&M Univ.
>> College Station, TX 77843-2128
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Dept. of Biochemistry and Biophysics
Texas A&M Univ.
College Station, TX 77843-2128
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