[Bioperl-l] subsection of genbank file

[Roy Chaudhuri]

Hi Liam,

Yes, that is a bug - I think it is to do with the Feature Annotation 
rollback from 1.6, it works fine with 1.5.2. Looks like the tests I 
wrote don't check for the presence of tags, just the coordinates of the 
feature, so this hasn't been picked up. Submit it to Bugzilla, and I'll 
take a look when I get a chance.

Cheers.
Roy.

Liam Elbourne wrote:
> 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
> 
> 
>