[Bioperl-l] Bio::AnnotatableI function annotation()
Mark A. Jensen
maj at fortinbras.us
Fri Mar 27 18:29:17 UTC 2009
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 :
> ===========================================================
>
>
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