[Bioperl-l] Fwd: about get_all_tags BioPerl method

Chris Fields cjfields at uiuc.edu
Fri May 23 13:18:36 EDT 2008


We can probably hack this in fairly easily; just need to think about  
the best way to do it.  Maybe a way of generating the SeqFeature  
string via a callback (which would allow some customization)?

chris

On May 23, 2008, at 11:44 AM, Jason Stajich wrote:

>
> resending from correct addr.
>
> Begin forwarded message:
>
>>
>> Date: May 23, 2008 9:44:18 AM MDT
>> To: Mgavi Brathwaite <lsbrath at gmail.com>
>> Cc: bioperl list <bioperl-l at lists.open-bio.org>
>> Subject: Fwd: about get_all_tags BioPerl method
>>
>> Mgavi -
>> you'd have to change the module to accept a custom sort function I  
>> suppose. I don't have any time to help hack it though, but others  
>> in the project may so it is important to ask on the list as I've CC- 
>> ed.
>>
>> -jason
>>
>> Begin forwarded message:
>>
>>> From: "Mgavi Brathwaite" <lsbrath at gmail.com>
>>> Date: May 23, 2008 8:07:10 AM MDT
>>> Subject: Re: about get_all_tags BioPerl method
>>>
>>> Hi Jason!
>>>
>>> I have a genbank file and I want to arrange the feature qualifiers  
>>> for CDS in a particular format. Presently the output is:
>>>
>>> CDS             join(34018..34488,35055..35136,35636..35757)
>>>                     /db_xref="CCDS:CCDS15306.1"
>>>                     /db_xref="MGI:Myog"
>>>                     /protein_id="ENSMUSP00000027730"
>>>                     /gene="ENSMUSG00000026459"
>>>                     /note="transcript_id=ENSMUST00000027730"
>>>
>>> I want it to be:
>>>
>>> CDS             join(34018..34488,35055..35136,35636..35757)
>>>                     /note="transcript_id=ENSMUST00000027730"
>>>                    /protein_id="ENSMUSP00000027730
>>>                     /gene="ENSMUSG00000026459
>>>                     /db_xref="CCDS:CCDS15306.1"
>>>                     /db_xref="MGI:Myog"
>>>
>>> How can I control the format and output?
>>>
>>> Thanks,
>>> Mgavi
>>>
>>> On Thu, May 22, 2008 at 4:10 PM, Jason Stajich > wrote:
>>> I don't understand what you want - can you be more specific?
>>>
>>> On May 22, 2008, at 1:31 PM, Mgavi Brathwaite wrote:
>>>
>>>> Hi Jason,
>>>>
>>>> You commented on the get_all_tags method:
>>>> # added a sort so that tags will be returned in a predictable order
>>>> # I still think we should be able to specify a sort function
>>>> # to the object at some point
>>>> # -js
>>>>
>>>> Would u be willing to share that code with me?
>>>>
>>>> M
>>>
>>>
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Marie-Claude Hofmann
College of Veterinary Medicine
University of Illinois Urbana-Champaign






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