[Bioperl-l] CDS across contigs

[Ewan Birney]

On Mon, 8 Jul 2002, Mike Muratet wrote:

> Greetings
>
> I recall this problem has surfaced before and maybe been answered, but I
> can't find where.
>
> One occasionally comes across CDS features defined as:
>
>      CDS
> join(AB005248.1:83409..83646,1..236,315..437,525..641, 718..771)
>
> (This one is from A. thaliana.) The location() method will return a
> SplitLocationI object, but you can't get the sequence by the subseq()
> method, of course. Is the solution to get the id from the sublocation
> and fetch the sequence somehow?


Yup - I am planning to fix this in a nicer way inside 1.2 series but it
will have to involve going out to a database at some point...


>
> Thanks
>
> Mike
>
>
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