[Bioperl-l] Phyloxml SeqI without actual sequence

miraceti miraceti at gmail.com
Tue Jul 29 13:31:57 EDT 2008


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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