[Bioperl-l] Phyloxml SeqI without actual sequence

Jason Stajich jason at bioperl.org
Tue Jul 29 14:00:09 EDT 2008


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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