[Bioperl-l] Bio::AnnotatableI function annotation()

Fri Mar 27 19:02:14 UTC 2009

Right now SeqFeatureI doesn't inherit AnnotatableI, even though the  
note about the deprecated *_tag_* methods imply that it does.  We  
should probably add back the abstract (unimplemented) tag methods to  
Bio::SeqFeatureI and either remove them from Bio::AnnotatableI or  
activate the deprecation (they have no place with annotations).  This  
shouldn't hurt things (FLW).

Not sure if we really need to add AnnotatableI to SeqFeatureI; I think  
that would be up to the SeqFeatureI implementation, and it doesn't  
hurt leaving it out.

chris

On Mar 27, 2009, at 1:14 PM, Hilmar Lapp wrote:

> $feature->annotation() is a legitimate method call (it implements  
> AnnotatableI).
>
> SeqFeature::Generic has indeed two mechanism to store annotation,  
> the tag system and the annotation collection. This is because it  
> inherits from SeqFeatureI (which brings in the tag/value annotation)  
> and from AnnotatableI (which brings in annotation()).
>
> I agree this can be confusing from a user's perspective. As a rule  
> of thumb, SeqIO parsers will almost universally populate only the  
> tag/value system, because typically they will (or should) assume not  
> more than that the feature object they are dealing with is a  
> SeqFeatureI.
>
> Once you have the feature objects in your hands, you can add to  
> either tag/values or annotation() to your heart's content. Just be  
> aware that nearly all SeqIO writers won't use the annotation()  
> collection when you pass the sequence back to them since typically  
> they won't really know what to do with feature annotation that isn't  
> tag/value (unlike as for sequence annotation).
>
> If in your code you want to treat tag/value annotation in the same  
> way as (i.e., as if it were part of) the annotation that's in the  
> annotation collection then use SeqFeature::AnnotationAdaptor. That's  
> in fact what Bioperl-db does to ensure that all annotation gets  
> serialized to the database no matter where it is.
>
> Hth,
>
> 	-hilmar
>
> On Mar 27, 2009, at 1:44 PM, Govind Chandra wrote:
>
>> Hi Mark,
>> Will it be unfair to say that the documentation as well as the
>> implementation are confusing. SeqFeature::Generic should cause an  
>> error
>> when annotation() is called on it if it cannot do the right thing.  
>> For
>> the time being I will stick with the old ways (has_tag etc.). Good to
>> know they are not deprecated in the way I intend to use them (via
>> SeqFeature::Generic).
>> Cheers
>> Govind
>>
>>
>>
>> On Fri, 2009-03-27 at 13:30 -0400, Mark A. Jensen wrote:
>>> Hey Govind--
>>> You're right-- SeqFeature::Generic object inherits from
>>> AnnotatableI-- but the *_tags_* methods are now
>>> SeqFeature::Generic methods--ie, you can use these
>>> on features, and they are no longer hitting AnnotableI.
>>> It appears that the feature's AnnotationCollection doesn't
>>> even get loaded now.
>>> [developer out there like to chime in?]
>>> cheers,
>>> Mark
>>> ----- Original Message -----
>>> From: "Govind Chandra" <govind.chandra at bbsrc.ac.uk>
>>> To: "Mark A. Jensen" <maj at fortinbras.us>
>>> Cc: <bioperl-l at lists.open-bio.org>
>>> Sent: Friday, March 27, 2009 1:09 PM
>>> Subject: [Bioperl-l] Bio::AnnotatableI function annotation()
>>>
>>>
>>>> Thanks Mark,
>>>>
>>>> Sorry for not putting a proper subject in the last post.
>>>>
>>>> What you suggest is what I have been doing for a long time. I am  
>>>> just
>>>> trying to alter my code to conform to the latest bioperl version  
>>>> and ran
>>>> into this issue. I could be wrong (I am more a user rather than  
>>>> writer
>>>> of modules) but since $feature->annotation() does not result in  
>>>> an error
>>>> I think $feature is-a Bio::AnnotatableI as well.
>>>>
>>>> Cheers
>>>>
>>>> Govind
>>>>
>>>>
>>>>
>>>> On Fri, 2009-03-27 at 12:17 -0400, Mark A. Jensen wrote:
>>>>> Hi Govind-
>>>>>
>>>>> As near as I can tell, the *_tags methods are deprecated for
>>>>> Bio::AnnotatableI objects, but these methods are available
>>>>> off the SeqFeatureI objects themselves: i.e., rather than
>>>>>
>>>>>> $ac=$feature->annotation();
>>>>>> $temp1=$ac->get_Annotations("locus_tag");
>>>>>
>>>>> do
>>>>>
>>>>> $temp1 = $feature->get_tag_values("locus_tag");
>>>>>
>>>>> directly.
>>>>>
>>>>> hope it helps -
>>>>> Mark
>>>>>
>>>>> ----- Original Message -----
>>>>> From: "Govind Chandra" <govind.chandra at bbsrc.ac.uk>
>>>>> To: <bioperl-l at lists.open-bio.org>
>>>>> Sent: Friday, March 27, 2009 11:26 AM
>>>>> Subject: Re: [Bioperl-l] Bioperl-l Digest, Vol 71, Issue 15
>>>>>
>>>>>
>>>>>> Hi,
>>>>>>
>>>>>> The code below
>>>>>>
>>>>>>
>>>>>> ====== code begins =======
>>>>>> #use strict;
>>>>>> use Bio::SeqIO;
>>>>>>
>>>>>> $infile='NC_000913.gbk';
>>>>>> my $seqio=Bio::SeqIO->new(-file => $infile);
>>>>>> my $seqobj=$seqio->next_seq();
>>>>>> my @features=$seqobj->all_SeqFeatures();
>>>>>> my $count=0;
>>>>>> foreach my $feature (@features) {
>>>>>> unless($feature->primary_tag() eq 'CDS') {next;}
>>>>>> print($feature->start(),"   ", $feature->end(), "
>>>>>> ",$feature->strand(),"\n");
>>>>>> $ac=$feature->annotation();
>>>>>> $temp1=$ac->get_Annotations("locus_tag");
>>>>>> @temp2=$ac->get_Annotations();
>>>>>> print("$temp1   $temp2[0] @temp2\n");
>>>>>> if($count++ > 5) {last;}
>>>>>> }
>>>>>>
>>>>>> print(ref($ac),"\n");
>>>>>> exit;
>>>>>>
>>>>>> ======= code ends ========
>>>>>>
>>>>>> produces the output
>>>>>>
>>>>>> ========== output begins ========
>>>>>>
>>>>>> 190   255   1
>>>>>> 0
>>>>>> 337   2799   1
>>>>>> 0
>>>>>> 2801   3733   1
>>>>>> 0
>>>>>> 3734   5020   1
>>>>>> 0
>>>>>> 5234   5530   1
>>>>>> 0
>>>>>> 5683   6459   -1
>>>>>> 0
>>>>>> 6529   7959   -1
>>>>>> 0
>>>>>> Bio::Annotation::Collection
>>>>>>
>>>>>> =========== output ends ==========
>>>>>>
>>>>>> $ac is-a Bio::Annotation::Collection but does not actually  
>>>>>> contain any
>>>>>> annotation from the feature. Is this how it should be? I cannot  
>>>>>> figure
>>>>>> out what is wrong with the script. Earlier I used to use  
>>>>>> has_tag(),
>>>>>> get_tag_values() etc. but the documentation says these are  
>>>>>> deprecated.
>>>>>>
>>>>>> Perl is 5.8.8. BioPerl version is 1.6 (installed today). Output  
>>>>>> of uname
>>>>>> -a is
>>>>>>
>>>>>> Linux n61347 2.6.18-92.1.6.el5 #1 SMP Fri Jun 20 02:36:06 EDT  
>>>>>> 2008
>>>>>> x86_64 x86_64 x86_64 GNU/Linux
>>>>>>
>>>>>> Thanks in advance for any help.
>>>>>>
>>>>>> Govind
>>>>>>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> Bioperl-l mailing list
>>>>>> Bioperl-l at lists.open-bio.org
>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>
>>>>>>
>>>>>
>>>>
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>>>>
>>
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>
> -- 
> ===========================================================
> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
> ===========================================================
>
>
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