[Bioperl-l] subsection of genbank file

[Roy Chaudhuri]

Hi Liam,

My mistake, it looks like the bug had already been reported and fixed, 
which means I get to go home earlier. I've marked your bug as a 
duplicate of bug 2810.

You can get the patched version by installing bioperl-live (just 
downloading the bioperl-live SeqUtils.pm and putting it in the correct 
place on your system would probably also work).

Cheers.
Roy.

Roy Chaudhuri wrote:
> 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.
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>> ac.uk ([131.111.51.215]:49455)
>>> by ppsw-7.c
>> ______________________________
>>
>> Dr Liam Elbourne
>> Research Fellow (Bioinformatics)
>> Paulsen Laboratory
>> Macquarie University
>> Sydney
>> Australia.
>>
>> http://www2.oxfam.org.au/trailwalker/Sydney/team/228
>>
>>
>>
> 
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