[Bioperl-l] Bio::DB::SeqFeature treamtent of tags and annotations

Cook, Malcolm MEC at stowers-institute.org
Fri Feb 2 16:47:08 EST 2007


Lincoln,
 
I don't think that adding this directive is a good idea after all
either.
 
But, I see that you remap the ID= to a load_id attribute which is
preserved in the Bio::DB::SeqFeatureStore database.
 
And then it gets squelched during GFF production by
NormalizedFeature::format_attributes.
 
However, if ID is prone to clashes, then certainly simply renaming the
attribute to be load_id does not preclude clashes from happening, and
only courts disaster.  Don't you think?
 
I'm a little blurry on the GFF3Loader, but it looks like you're using
load_id to facilitate loading parent/child features out of order.  Is
that right?  If so, I suggest you delete all load_id features
immediately after performing a load.  It has not further use.
 
Or, you might consider instead of `round-trip-ids` directive, rather,
give the GFF3Loader  an IDAttribute option which would allow the use of
the loader to preserve the ID values, but to use a named
 
In my case, munging flybase gff,  I would then use it like this:
 
bp_seqfeature_load.PLS --fast --IDAttribute flybaseID
 
which would preserve the ID values in the database but under the
FlybaseID attribute for features so loaded.
 
---------------------------------------------
 
On a related topic:
I just committed this patch to Bio::DB::SeqFeature::NormalizedFeature

_create_subfeatures : ensure that subfeatures get the `source` of their
parent

While doing this I wonder: what is the -class that subfeatures are
getting from their parent...??? I left it in place. Please advise! Fix
my thinking....

----------------------------------------------

Further, I observe that Bio::Graphics::FeatureBase::new handles the
-segments option is to call add_segment.  So, when I create a new
Bio::DB::SeqFeature with -segments [[ 100,200 ] [300,400]], the
-segments option gets handled by Bio::Graphics::FeatureBase::new, which,
as mentioned, calls add_segment. The surprising thing to me when thrying
to trace through the class modules and understand what is going on is
that what gets run at this point is not
Bio::Graphics::FeatureBase::add_segment, but rather
Bio::DB::SeqFeature::add_segment, whose semantics is different in at
least one regard, namely, that it does not set the start and stop of the
parent feature from the min and max of the segments.

I have committed a patch to Bio::Graphics::FeatureBase with a comment to
this effect, and have also patched it's add_segment method to copy the
parent's source into the segment.

I hope my commits and suggestions further the cause.  Let me know if
not!
 
-- Malcolm
 


________________________________

	From: lincoln.stein at gmail.com [mailto:lincoln.stein at gmail.com]
On Behalf Of Lincoln Stein
	Sent: Tuesday, January 30, 2007 4:46 PM
	To: Cook, Malcolm
	Cc: bioperl list; lstein at cshl.org
	Subject: Re: Bio::DB::SeqFeature treamtent of tags and
annotations
	
	
	I've fixed the first issue in CVS. Sorry for the inconsistency.
add_tag_value(), delete_tag_value() and get_Annotations() now all work
as expected.
	
	The problem with the ID column is that it is supposed to be
LOCAL to the GFF3 file and is not intended to be stored in the database.
In contrast, Name can survive roundtripping. Perhaps the thing to do is
to add a flag to the GFF3 file that turns on ID round-tripping, e.g.
	
	##round-trip-ids: 1
	
	If you like this idea, I can implement it.
	
	Lincoln
	
	
	On 1/29/07, Cook, Malcolm < MEC at stowers-institute.org
<mailto:MEC at stowers-institute.org> > wrote: 

		Lincoln,
		 
		Thanks for your suggestions on approach to my problems
augmenting Flybase annotation.  I am trying to follow them and finding
the following oddities
		 
		The first issue relates to the intermix of 'annotations'
and 'tag values'.  I find that Bio::DB::SeqFeature implements some of
the 'tag' methods and some of the 'Annotation' methods.  Here is a perl
one-liner that shows values stored using add_tag_value are not retreived
with get_tag_values, but rather with get_Annotations.
		 
		> perl -MBio::DB::SeqFeature -e 'my
$f=Bio::DB::SeqFeature->new; $f->add_tag_value("x",666); print
"get_tag_values:\t" . $f->get_tag_values("x") . "\nget_Annotations:\t" .
$f->get_Annotations("x");'
		 
		whose output is:
		get_tag_values: 
		get_Annotations:    666
		 
		Tracing this shows me that this results from the fact
that:
		 
		
		Bio::DB::SeqFeature uses of Bio::Graphics::FeatureBase
(via Bio::DB::SeqFeature::NormalizedFeature) which does not support
-tags in ->new but rather -attributes, viz:
		 
		
		  -attributes   a hashref of tag value attributes, in
which the key is the tag
		                  and the value is an array reference of
values
		 
		
		And though Bio::Graphics::FeatureBase purports to
implement Bio::SeqFeatureI, it only partially implements the  'tag'
methods (now deprecated and relegated to Bio::AnnotatableI).  In
particular, the '*' methods Bio::SeqFeatureI are not implemented in
Bio::Graphics::FeatureBase 

		  has_tag
		*  add_tag_value
		  get_tag_values
		  get_all_tags
		*  remove_tag
		  get_tagset_values
		  get_Annotations

		As a result, add_tag_value and remove_tag are inherited
from different modules whose understanding of tags is not the same!

		This one-liner :

		>perl -MClass::ISA -MClass::Inspector
-MBio::DB::SeqFeature -e 'my @c =
Class::ISA::self_and_super_path("Bio::DB::SeqFeature"); foreach my $fn
qw(add_tag_value get_tag_values) {print "\n$fn:\t", join "\t", (grep
{Class::Inspector->function_exists($_, $fn)} @c)}'

		confirms that they are defined in different packages,
namely:

		add_tag_value: Bio::AnnotatableI 
		get_tag_values: Bio::Graphics::FeatureBase
Bio::AnnotatableI

		
		
		
		Proposed solution...  hmmmm ..... I dunno.... maybe the
following patch to Bio::Graphics::FeatureBase->add_tag_value :
		 
		sub add_tag_value {
		  my ($self,$tag, at vals) = @_;
		  push @{$self->{attributes}{$tag}}, @vals;
		}
		
		
		 
		
		It fixes my use case for now but I'm still concerned and
confused about this variety of methods.  
		 
		Suggestions?
		 

	
------------------------------------------------------------------------
-

		Also, I think that any "ID" in column 9 of GFF3 float
file should be preserved through a round-trip through a
Bio::DB::SeqFeature store, but this is not yet possible since any ID
attribute in GFF3 column 9 is being lost by GFF3Loader, causing me to
locally patch GFF3Loader::handle_feature method to add the following:

		  # mec at stowers-institute.org
<mailto:mec at stowers-institute.org>  , wondering why not all attributes
are
		  # carried forward, adds ID tag in particular service
of
		  # round-tripping ID, which, though present in database
as load_id
		  # attribute, was getting lost as itself
		  $unreserved->{ID}= $reserved->{ID}     if exists
$reserved->{ID}; 

		Poised to patch.... what d'you think?

		Malcolm Cook
		Stowers Institute for Medical Research - Kansas City,
Missouri
		  

		 
		
		

			
________________________________

			From: lincoln.stein at gmail.com [mailto:
lincoln.stein at gmail.com <mailto:lincoln.stein at gmail.com> ] On Behalf Of
Lincoln Stein
			Sent: Tuesday, December 19, 2006 3:58 PM
			To: Cook, Malcolm
			Cc: bioperl list; lstein at cshl.org
			Subject: Re: bp_seqfeature_load /
Bio::DB::SeqFeature::Store::GFF3Loader problems augmenting Flybase
annotation
			
			
			
			Hi Malcom,
			
			Your second guess was right. The use case of
augmenting an existing gene with additional splice forms isn't provided
for. You can get the functionality by making direct calls to
Bio::DB::SeqFeature::Store methods:
			
			my @genes =
$db->get_features_by_name('FBgn0017545');
			@genes == 1 or die "Didn't get exactly one
gene";
			my $parent = $genes[0];
			
			my $parent = $genes[0];
			my $chr    = $parent->seq_id;
			my $start  = $parent->start;
			my $end    = $parent->end;
			my $strand = $parent->strand;
			
			my $new_splice_form =
$db->new_feature(-primary_tag => 'mRNA',
			                       -source      => 'added',
			                       -seq_id   => '4r',
			                       -strand   => $strand,
			                       -start    => $start+10,
			                       -end      => $end,
			                       );
			$parent->add_SeqFeature($new_splice_form);
			
			for my $pos
([$start+10,$start+100],[$start+200,$end]) {
			  my ($e_start,$e_end) = @$pos;
			  my $exon =
Bio::DB::SeqFeature->new(-primary_tag => 'exon',
			                                      -store
=> $db,
			                      -seq_id      => '4r',
			                      -strand     => $strand,
			                      -start       => $e_start,
			                      -end         => $e_end);
			  $new_splice_form->add_SeqFeature($exon);
			}
			
			I found a bug in updating the seqfeature
database when I wrote this script, so you'll have to get the latest
biperl live. I think you can use this to write a splice form updating
script.
			
			In order to support the idea of adding new
splice forms to an existing gene using the GFF3 format, I will have to
either modify the loader, or write a separate script (probably better to
do the latter). It shouldn't be hard if you'd like to give it a try.
			
			Lincoln
			
			
			On 12/19/06, Cook, Malcolm
<MEC at stowers-institute.org <mailto:MEC at stowers-institute.org>  > wrote: 

				Lincoln and fellow Bio::DB::SeqFeature
travelers,
				
				I find that using bp_seqfeature_load.PLS
to load subfeatures of genes
				already loaded using
bp_seqfeature_load.PLS fails with
				
				------------- EXCEPTION  ------------- 
				MSG: FBgn0017545 doesn't have a primary
id
				STACK
	
Bio::DB::SeqFeature::Store::GFF3Loader::build_object_tree_in_tables
	
/home/mec/cvs/bioperl-live/Bio/DB/SeqFeature/Store/GFF3Loader.pm:682
				STACK
Bio::DB::SeqFeature::Store::GFF3Loader::build_object_tree 
	
/home/mec/cvs/bioperl-live/Bio/DB/SeqFeature/Store/GFF3Loader.pm:663
				STACK
Bio::DB::SeqFeature::Store::GFF3Loader::finish_load
	
/home/mec/cvs/bioperl-live/Bio/DB/SeqFeature/Store/GFF3Loader.pm:372
				STACK
Bio::DB::SeqFeature::Store::GFF3Loader::load_fh 
	
/home/mec/cvs/bioperl-live/Bio/DB/SeqFeature/Store/GFF3Loader.pm:345
				STACK
Bio::DB::SeqFeature::Store::GFF3Loader::load
	
/home/mec/cvs/bioperl-live/Bio/DB/SeqFeature/Store/GFF3Loader.pm:242
				STACK toplevel
	
/home/mec/cvs/bioperl-live/scripts/Bio-SeqFeature-Store/bp_seqfeature_lo

				ad.PLS:76
				
				Where FBgn0017545 is the ID of a gene
previously loaded.
				
				I am unsure how to remedy my situation
and welcome any advise on correct
				or improved approach to my problem.
				
				Here's some detail if it helps.  I am
developing a pipeline to design a 
				microarray probes capable of
distinguishing among splice variants in
				drosophila (using latest Flybase
dmel_r5.1 annotation).  So I
				
				1) load a filtered selection of Flybase
annotation using
				bp_seqfeature_load.  (for testing
purposes, I am using a single gene's 
				worth of annotation, FBgn0017545.gff,
attached).  This is done as
				follows:
				
				        > bp_seqfeature_load.PLS
--create FBgn0017545.gff
				
				2) analyze all the genes in the
database, and create GFF3 output each 
				feature of which has a 'Parent' that is
a previously loaded gene (i.e.
				FBgn0017545).  (These features represent
the unique introns, splice
				sites, and exonic design targets. Output
of this analysis,
				FBgn0017545_matd.gff, is also attached) 
				
				3) load these analysis results into the
same database, as follows:
				
				        > bp_seqfeature_load.PLS
FBgn0017545_matd.gff
				
				It is at this point that I get the above
error.
				
				However, I don't get any error and the
data loads fine if I load the two
				files together, as follows: 
				
				        > bp_seqfeature_load.PLS
--create <(cat FBgn0017545.gff
				FBgn0017545_matd.gff)
				
				So, I suspect that either I am
misunderstanding when/how to use
				bp_seqfeature_load.PLS or else this use
case has not yet arisen and must 
				be provided for somehow.
				
				I am running against bioperl-live
				
				Thanks for your thoughts and assistance,
				
				Malcolm Cook
				Database Applications Manager -
Bioinformatics
				Stowers Institute for Medical Research -
Kansas City, Missouri 
				
				




			-- 
			Lincoln D. Stein
			Cold Spring Harbor Laboratory
			1 Bungtown Road
			Cold Spring Harbor, NY 11724
			(516) 367-8380 (voice)
			(516) 367-8389 (fax)
			FOR URGENT MESSAGES & SCHEDULING, 
			PLEASE CONTACT MY ASSISTANT, 
			SANDRA MICHELSEN, AT michelse at cshl.edu
<mailto:michelse at cshl.edu>  




	-- 
	Lincoln D. Stein
	Cold Spring Harbor Laboratory
	1 Bungtown Road
	Cold Spring Harbor, NY 11724
	(516) 367-8380 (voice)
	(516) 367-8389 (fax)
	FOR URGENT MESSAGES & SCHEDULING, 
	PLEASE CONTACT MY ASSISTANT, 
	SANDRA MICHELSEN, AT michelse at cshl.edu 




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