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

[Kevin Brown]

OK. Can't see that method in the Deobfuscator which might explain why I
didn't know about it.

http://bioperl.org/cgi-bin/deob_interface.cgi?Search=Search&module=Bio%3
A%3AAnnotation%3A%3ACollection&sort_order=by+method&search_string=Bio%3A
%3AAnnotation%3A%3ACollection 

> -----Original Message-----
> From: Jason Stajich [mailto:jason.stajich at gmail.com] On 
> Behalf Of Jason Stajich
> Sent: Thursday, April 30, 2009 1:24 PM
> To: Kevin Brown
> Cc: BioPerl List
> Subject: Re: [Bioperl-l] Bio::Annotations::Collection confusion
> 
> Seems like you just want $annotation->value ?
> 
> 
> =head2 as_text
> 
>   Title   : as_text
>   Usage   : my $text = $obj->as_text
>   Function: return the string "Value: $v" where $v is the value
>   Returns : string
>   Args    : none
> 
> 
> =cut
> 
> =head2 display_text
> 
>   Title   : display_text
>   Usage   : my $str = $ann->display_text();
>   Function: returns a string. Unlike as_text(), this method 
> returns a  
> string
>             formatted as would be expected for te specific  
> implementation.
> 
>             One can pass a callback as an argument which 
> allows custom  
> text
>             generation; the callback is passed the current instance  
> and any text
>             returned
>   Example :
>   Returns : a string
>   Args    : [optional] callback
> 
> =cut
> 
> =head2 value
> 
>   Title   : value
>   Usage   : $obj->value($newval)
>   Function: Get/Set the value for simplevalue
>   Returns : value of value
>   Args    : newvalue (optional)
> 
> 
> =cut
> 
> On Apr 30, 2009, at 1:01 PM, Kevin Brown wrote:
> 
> > That's nice in some regards, but makes it hard to use the 
> function in
> > code without having to always process the result, which seems to be
> > counter to what one would expect.
> >
> > E.g. Bio::Seq->seq returns the sequence, not "Seq: sequence".
> >
> > Is there a better way to get the number directly without having to  
> > strip
> > off the text that never existed in the first place?
> >
> >> -----Original Message-----
> >> From: Scott Markel [mailto:SMarkel at accelrys.com]
> >> Sent: Thursday, April 30, 2009 12:57 PM
> >> To: Kevin Brown; BioPerl List
> >> Subject: RE: Bio::Annotations::Collection confusion
> >>
> >> 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 = $annotation->as_text()) =~ 
> s/(Comment|Value): //;
> >>
> >> Scott
> >>
> >> Scott Markel, Ph.D.
> >> Principal Bioinformatics Architect  email:  smarkel at accelrys.com
> >> Accelrys (SciTegic R&D)             mobile: +1 858 205 3653
> >> 10188 Telesis Court, Suite 100      voice:  +1 858 799 5603
> >> San Diego, CA 92121                 fax:    +1 858 799 5222
> >> USA                                 web:    http://www.accelrys.com
> >>
> >> http://www.linkedin.com/in/smarkel
> >> Vice President, Board of Directors:
> >>    International Society for Computational Biology
> >> Co-chair: ISCB Publications Committee
> >> Associate Editor: PLoS Computational Biology
> >> Editorial Board: Briefings in Bioinformatics
> >>
> >>
> >>> -----Original Message-----
> >>> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> >>> bounces at lists.open-bio.org] On Behalf Of Kevin Brown
> >>> Sent: Thursday, 30 April 2009 12:27 PM
> >>> To: BioPerl List
> >>> Subject: [Bioperl-l] Bio::Annotations::Collection confusion
> >>>
> >>> So, I'm parsing Genbank sequences to pull out the various
> >> exons. I found
> >>> the way to get the NCBI Exon number from each feature, but
> >> am confused
> >>> about one of the methods. When I do annotation->as_text I'm
> >> expecting to
> >>> get back 1 from the feature, but instead get back Value: 1
> >> ??!? Why is
> >>> the value from the NCBI file getting that text tagged onto it?
> >>>
> >>> http://www.ncbi.nlm.nih.gov/nuccore/73622129
> >>> exon            1..774
> >>>                /gene="BOLA2"
> >>>                /gene_synonym="BOLA2A; My016"
> >>>                /inference="alignment:Splign"
> >>>                /number=1
> >>>
> >>> print ($f->annotation->get_Annotations('number'))[0]->as_text;
> >>> Value: 1
> >>>
> >>> _______________________________________________
> >>> Bioperl-l mailing list
> >>> Bioperl-l at lists.open-bio.org
> >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >>
> >
> > _______________________________________________
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> > Bioperl-l at lists.open-bio.org
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> 
> Jason Stajich
> jason at bioperl.org
> 
> 
> 
>