[Bioperl-l] Fwd: about get_all_tags BioPerl method

Jason Stajich jason at bioperl.org
Fri May 23 12:44:57 EDT 2008


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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