[Bioperl-l] Bio::AnnotatableI function annotation()
Mark A. Jensen
maj at fortinbras.us
Fri Mar 27 20:09:22 UTC 2009
Probably folks just starting to use 1.6 will be shunted in the
right direction by the docs, but those making the switch
might reasonably get confused (resulting in this thread, e.g.).
If someone tries to do $feature->annotation->getAnnotations('locus_tag')
when $feature->annotation is undef, then probably that user is
not hip to $feature->get_tag_values('locus_tag'), and would appreciate
something like
"Annotation property undefined. Did you mean $feature->get_tag_values?"
(not nec. that specific, but you get my drift?)
MAJ
----- Original Message -----
From: "Chris Fields" <cjfields at illinois.edu>
To: "Mark A. Jensen" <maj at fortinbras.us>
Cc: "Hilmar Lapp" <hlapp at gmx.net>; "Govind Chandra"
<govind.chandra at bbsrc.ac.uk>; <bioperl-l at lists.open-bio.org>
Sent: Friday, March 27, 2009 3:49 PM
Subject: Re: [Bioperl-l] Bio::AnnotatableI function annotation()
> What exactly would the hint be? I'm not sure, but I don't think there is any
> documentation indicating that one should use anything other than tag methods
> to retrieve generic data. We *could* possibly add in code to check the
> feature's Bio::Annotation::Collection for the same tag name, then add any
> returned AnnotationI::display_text to the array of returned values.
>
> This all depends on:
>
> 1) whether you want to mix your 'peanut butter' with your 'chocolate' or keep
> them separate (amazingly, some people don't like Reese's peanut butter cups),
> and
> 2) whether you want to automatically check for the empty collection each time
> (the Collection is lazily created on the fly if one isn't supplied, so it may
> slow things down by creating the instance for every has_tag check).
>
> chris
>
> On Mar 27, 2009, at 1:29 PM, Mark A. Jensen wrote:
>
>> Thanks Hilmar-- so there isn't really a bug, but would it
>> be useful if the object warned a user who attempts to access an empty
>> $feature->annotation with a hint encapsulating
>> your discussion below?
>> MAJ
>> ----- Original Message ----- From: "Hilmar Lapp" <hlapp at gmx.net>
>> To: "Govind Chandra" <govind.chandra at bbsrc.ac.uk>
>> Cc: "Mark A. Jensen" <maj at fortinbras.us>; <bioperl-l at lists.open-bio.org
>> >
>> Sent: Friday, March 27, 2009 2:14 PM
>> Subject: Re: [Bioperl-l] Bio::AnnotatableI function annotation()
>>
>>
>>> $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 :
>>> ===========================================================
>>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
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