[Bioperl-l] subsection of genbank file

[Chris Fields]

That should be out in the latest alpha on CPAN as well (the final  
1.6.1 should be out this week).

chris

On Sep 22, 2009, at 11:44 AM, Roy Chaudhuri wrote:

> 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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