[Bioperl-l] subsection of genbank file

[Liam Elbourne]

Hi Roy,

Thanks for that, works well, but there are no _gsf_tag_hash values?  
I'm particularly interested in the locus id, obviously the translation  
could be problematic if the whole gene is not included after  
truncation, but things like the note, product, protein_id would be  
good. I had a look at the code for the method and couldn't see any  
obvious why those values didn't make it across. Should I submit this  
as a bug, or is there something I'm missing?


Regards,
Liam.



On 18/09/2009, at 8:43 PM, Roy Chaudhuri wrote:

> Hi Liam,
>
> I just discovered your message, which has not yet been replied to.  
> What you require has been discussed in a recent thread:
> http://bioperl.org/pipermail/bioperl-l/2009-August/031071.html
>
> Try using trunc_with_features from Bio::SeqUtils:
>
> my $sub_seqobj=Bio::SeqUtils->trunc_with_features($seqobj, 300, 2000);
> Cheers.
> Roy.
>
> Liam Elbourne wrote:
>> Hi All,
>> Is there a method or methodology that will produce a fully fledged  
>> Seq  object with all the associated metadata given a start and end   
>> position? To clarify, I create a sequence object from a genbank file:
>> ****
>> my $io  = Bio::Seqio->new(as per usual);
>> my $seqobj = $io->next_seq();
>> ****
>> I now want:
>> my $sub_seqobj = $seqobj between 300 and 2000
>> where $sub_seqobj is a Seq object (which I appreciate is an   
>> 'aggregate' of objects) too. The "trunc" method only returns a   
>> PrimarySeq object which lacks all the annotation etc. I've  
>> previously  done this task by iterating through feature by feature  
>> and parsing out  what I needed, but thought there might be a more  
>> elegant approach...
>> Regards,
>> Liam Elbourne.
>
> -- 
> Dr. Roy Chaudhuri
> Department of Veterinary Medicine
> University of Cambridge, U.K.
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______________________________

Dr Liam Elbourne
Research Fellow (Bioinformatics)
Paulsen Laboratory
Macquarie University
Sydney
Australia.

http://www2.oxfam.org.au/trailwalker/Sydney/team/228