[Bioperl-l] Handling discontiguous feature locations in Bio::DB::SeqFeature::Store -- proposed patch to Bio::Graphics::FeatureBase

Cook, Malcolm MEC at stowers-institute.org
Fri Apr 27 14:45:04 EDT 2007


Hi Lincoln,
 
Cool.
 
The principal of what I figured out I still think holds but the
implementation is slightly broke.  Improved patch forthoming next week.
 

Malcolm Cook
Database Applications Manager - Bioinformatics
Stowers Institute for Medical Research - Kansas City, Missouri
  

 


________________________________

	From: lincoln.stein at gmail.com [mailto:lincoln.stein at gmail.com]
On Behalf Of Lincoln Stein
	Sent: Friday, April 27, 2007 12:45 PM
	To: Cook, Malcolm
	Cc: lstein at cshl.org; bioperl list
	Subject: Re: Handling discontiguous feature locations in
Bio::DB::SeqFeature::Store -- proposed patch to
Bio::Graphics::FeatureBase
	
	
	Hi Malcom,
	
	This is absolutely ok and you can go ahead and commit. Thanks
for figuring this out!
	
	Lincoln
	
	
	On 4/26/07, Cook, Malcolm < MEC at stowers-institute.org
<mailto:MEC at stowers-institute.org> > wrote: 

		Lincoln, et al,
		
		I find that the gff3_string for Bio::DB::SeqFeature
objects retreived 
		from a Bio::DB::SeqFeature::Store that were initially
created with
		-seqments (i.e. whose location was discontiguous) does
not display any
		other attributes in column 9 than "Name".
		
		What do you think of the following patch to
Bio::Graphics::FeatureBase, 
		whose effect is to "contrive to return (duplicated)
common group values"
		(which otherwise get lost when "collapsing" "homogenous"
parent/child
		features)
		
		Another approach would be to copy the attributes from
the parent to the 
		children when the -seqments are first created.
		
		Another approach would be to use
Bio::SeqFeature::Generic  as the db's
		-seqfeature_class and save with -location being a
Bio::Location::Split,
		but this was wrougth with other problems. 
		
		Any other suggestions?  Do you want me to commit this
patch?
		
		Cheers,
		
		Malcolm
		
		Patch follows:
		
		
		
		
		Index: FeatureBase.pm
	
=================================================================== 
		RCS file:
	
/home/repository/bioperl/bioperl-live/Bio/Graphics/FeatureBase.pm,v
		retrieving revision 1.29
		diff -c -r1.29 FeatureBase.pm
		*** FeatureBase.pm      16 Apr 2007 19:55:33 -0000
1.29
		--- FeatureBase.pm       26 Apr 2007 16:30:23 -0000
		***************
		*** 581,587 ****
		      foreach (@children) {
		        s/Parent=/ID=/g;
		      } # replace Parent tag with ID
		!     return join "\n", at children;
		    }
		
		    return join("\n",$p, at children);
		--- 581,589 ----
		      foreach (@children) {
		        s/Parent=/ID=/g;
		      } # replace Parent tag with ID
		!     #return join "\n", at children; 
		!     # Instead of above, additionally, contrive to
return (duplicated)
		common group values
		!     return(join("$group\n", at children) . $group);
		    }
		
		    return join("\n",$p, at children); 
		




	-- 
	Lincoln D. Stein
	Cold Spring Harbor Laboratory
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