[Bioperl-l] Bio::AnnotatableI function annotation()
Chris Fields
cjfields at illinois.edu
Fri Mar 27 15:49:26 EDT 2009
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
>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Bioperl-l mailing list
>>>>> Bioperl-l at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>
>>>>>
>>>
>>> _______________________________________________
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>> --
>> ===========================================================
>> : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net :
>> ===========================================================
>>
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