[Bioperl-l] Phyloxml SeqI without actual sequence

Hilmar Lapp hlapp at gmx.net
Tue Jul 29 14:58:33 EDT 2008


I think that would be good. -hilmar

On Jul 29, 2008, at 2:00 PM, Jason Stajich wrote:

> I guess making a sequence is fine - maybe we can add a flag like - 
> nowarnonempty => 1 to not warn when the sequence is empty (in  
> Bio::PrimarySeq new() code ?
>
> -jason
> On Jul 29, 2008, at 10:31 AM, miraceti wrote:
>
>> sometimes the clade looks like.
>>
>>               <sequence>
>>                  <annotation>
>>                     <desc>alcohol dehydrogenase</desc>
>>                     <confidence type="probability">0.99</confidence>
>>                  </annotation>
>>               </sequence>
>>
>> sometimes the clade looks like.
>>
>>                 <sequence>
>>                  <symbol>ADHX</symbol>
>>                  <accession source="UniProtKB">P81431</accession>
>>                  <name>Alcohol dehydrogenase class-3</name>
>>
>> <mol_seq>TDATGKPIKCMAAIAWEAKKPLSIEEVEVAPPKSGEVRIKILHSGVCHTD</mol_seq>
>>                  <annotation ref="EC:1.1.1.1"/>
>>                  <annotation ref="GO:0004022"/>
>>               </sequence>
>>
>> Do you think it's better not to create the SeqI in the first case?.
>>
>>
>> On Tue, Jul 29, 2008 at 12:51 PM, Jason Stajich <jason at bioperl.org>  
>> wrote:
>>
>>> So why would you create the sequence in the first place when it is  
>>> empty?
>>> Shouldn't you just not create a sequence if there isn't one? Can  
>>> you provide
>>> sample data so we understand better - maybe there is sequence name  
>>> but no
>>> data?  Maybe we can specify an option to not warn when creating a  
>>> sequence
>>> if a specific flag is provided to the Seq initialization routine.
>>>
>>> -jason
>>>
>>>
>>> On Jul 29, 2008, at 9:13 AM, Han, Mira wrote:
>>>
>>>
>>>> Another phyloxml parsing question.
>>>> We have <Sequence> tags that sometimes have actual molecular  
>>>> sequences and
>>>> sometimes don't.
>>>> I decided to create a SeqI object and link it to AnnotatableNode.
>>>> But when it doesn't have actual sequence
>>>> It gives warning that the sequence is empty.
>>>> I don't think it's a big problem,
>>>> And I'd prefer having consistency than having two different  
>>>> solutions for
>>>> the same tag.
>>>> But I'd like to hear people's opinion on this as well.
>>>> Thank you
>>>>
>>>> Mira Han
>>>>
>>>>
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>>>
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>
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-- 
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: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
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