[Bioperl-l] Bio::Annotations::Collection confusion

Scott Markel SMarkel at accelrys.com
Thu Apr 30 15:56:40 EDT 2009


Kevin,

I believe the extra text was added for readability when printing
to the console.  In our code we just add the following post-
processing step.

        (my $text = $annotation->as_text()) =~ s/(Comment|Value): //;

Scott

Scott Markel, Ph.D.
Principal Bioinformatics Architect  email:  smarkel at accelrys.com
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> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Kevin Brown
> Sent: Thursday, 30 April 2009 12:27 PM
> To: BioPerl List
> Subject: [Bioperl-l] Bio::Annotations::Collection confusion
> 
> So, I'm parsing Genbank sequences to pull out the various exons. I found
> the way to get the NCBI Exon number from each feature, but am confused
> about one of the methods. When I do annotation->as_text I'm expecting to
> get back 1 from the feature, but instead get back Value: 1 ??!? Why is
> the value from the NCBI file getting that text tagged onto it?
> 
> http://www.ncbi.nlm.nih.gov/nuccore/73622129
> exon            1..774
>                 /gene="BOLA2"
>                 /gene_synonym="BOLA2A; My016"
>                 /inference="alignment:Splign"
>                 /number=1
> 
> print ($f->annotation->get_Annotations('number'))[0]->as_text;
> Value: 1
> 
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