[Bioperl-l] CDS complement statements from GenBank

[Galeb Abu-Ali]

I was using the wrong module, Bio::Location::Simple was what I needed.
thanks much!

galeb

On Sun, Mar 27, 2011 at 1:59 PM, Jason Stajich <jason at bioperl.org> wrote:

> they won't be split locations they will be Bio::Location::Simple locations
> then - I don't understand if that is causing you problems?
>
>
>
> Galeb Abu-Ali wrote:
>
>> Hi,
>>
>> I'm trying to parse CDS complement statements from GenBank files of
>> bacterial genomes. I know it works for 'join' statements with
>> Bio::Location::SplitLocationI, but there is no spliced genes in
>> bacterial annotations and therefore no 'join()' statements. When I
>> replace 'complement' with 'join' in the bacterial GenBank file,
>> Bio::Location::SplitLocationI gets the coordinates. I took a look at
>> SplitLocationI.pm and Split.pm to see if I could replace 'join' with
>> 'complement' to get it to work but no luck. At your convenience,
>> please advise.
>>
>> cheers,
>>
>> galeb
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>>
>
> --
> Jason Stajich
> jason at bioperl.org
> http://bioperl.org/wiki
>
>