[Bioperl-l] GBroswe2 - feature details

[Smithies, Russell]

For the first part of your question, you can use a sub to access values in your annotations:

balloon hover = sub{my $f = shift;
			my %a = $f->attributes;
			my $name = $f->name;
			my $seq = $a{'BS_Seq'};
			return "<font size=small color=red>Motif name: $name, Sequence: $seq</font>" if defined $seq;
			return "<font size=small color=red>Motif name: $name, No sequence defined</font>";
			}


For the second bit, here's the formatting rules I'm using to create hyperlinks:

[Dbxref:DETAILS]
URL = sub {
      my ($tag,$value)=@_;
      if ($value =~ /NCBI_gi:(.+)/){
       return "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=$1";
       }
      if ($value =~ /NCBI_Gene:(.+)/){
       return "http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=gene&list_uids=$1";
       }
       return;
     }

And this is what the gff looks like:
BTA10	refseq	mRNA	10011147	10176454	0	-	.	ID=NM_001076052;Name=NM_001076052;Index=1;Alias=HOMER1;Note=homer homolog 1 (Drosophila);Dbxref=NCBI_gi:115496957;Dbxref=NCBI_Gene:535311;
BTA10	refseq	mRNA	10241506	10301142	0	+	.	ID=NM_001046361;Name=NM_001046361;Index=1;Alias=PAPD4,MGC138008;Note=PAP associated domain containing 4;Dbxref=NCBI_gi:114052221;Dbxref=NCBI_Gene:533862;

Hopefully, this will get you going :-)


Russell Smithies 

Bioinformatics Applications Developer 
T +64 3 489 9085 
E  russell.smithies at agresearch.co.nz 

Invermay  Research Centre 
Puddle Alley, 
Mosgiel, 
New Zealand 
T  +64 3 489 3809   
F  +64 3 489 9174  
www.agresearch.co.nz 



> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Alper Yilmaz
> Sent: Saturday, 6 June 2009 6:51 a.m.
> To: BioPerl List
> Subject: [Bioperl-l] GBroswe2 - feature details
> 
> Dear all,
> 
> I have a question about utilizing the tag/value pairs that were used
> in 9th of GFF. If my 9th column is like this:
> 
> ID=BS_1;BS_Seq=cacatg;BS_Color=Purple;Name=AtMYC2 BS in RD22
> 
> How can I use BS_Seq, BS_Color tags, say, in a balloon? If want to
> print name and sequence of a BindingSite, what do I need to replace
> question marks below?
> 
> balloon hover = <font size=small color=red>Motif name: $name,
> Sequence: ???????</font>
> 
> 
> The manual is mentioning that it's possible to use user defined
> tag/value pairs, but I couldn't figure out how. The manual is
> mentioning:
>  [feature_type:details]
>  tag1 = formatting rule
>  tag2 = formatting rule
>  tag3 = formatting rule
> 
> can be used to adjust formatting of a tag, but I don't how this can be
> used to assign value to a tag? I tried ;
> [cis-elements:details]
> bs_seq = <b>$value</b>     (I didn't use BS_Seq, since it was
> mentioned, tags are case-insensitive)
>  OR
> $bs_seq = <b>$value</b>
> 
> but, I cannot use $bs_seq in hover link option after doing this. What
> am I doing wrong?
> 
> thanks,
> 
> Alper Yilmaz
> Post-doctoral Researcher
> Plant Biotechnology Center
> The Ohio State University
> 1060 Carmack Rd
> Columbus, OH 43210
> (614)688-4954
> www.grassius.org
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
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