[Bioperl-l] Sequences for joined features (in a Genbank file)

[Ewan Birney]

On Tue, 26 Feb 2002 jchuang@ucsf-104-53.ucsf.edu wrote:

> Hi,
>
> I'm trying to extract the DNA sequence from features of genbank files
> (e.g. the CDS). The seq function does this great whenever I have a
> contiguous sequence, but it doesn't appear to work properly when the
> feature is made up of joined sequences.  Instead of a patching together of
> all the joined subsequences, I get the sequence starting with the first
> start site and ending with the last end site.
>
> Is there a way to extract the patched together sequence instead? I
> couldn't tell from the docs if this feature had been implemented. The
> Location modules look relevant, but I didn't see a way to use them on
> sequence objects.

This is a common request and ... no... we don't do this. We should. I'll
talk to Jason today about the best way to handle this.


>
> Thanks for any help.
>
> Jeff
>
> --
> Jeffrey Chuang
> UC San Francisco - Dept. of Biochemistry and Biophysics
> 513 Parnassus Avenue
> Box 0448
> San Francisco, CA 94143-0001
> W: 415-514-2616
> jchuang@ucsf-104-53.ucsf.edu
>
>
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