[Bioperl-l] Bio::Annotations::Collection confusion
Smithies, Russell
Russell.Smithies at agresearch.co.nz
Thu Apr 30 21:28:39 UTC 2009
It's buried in Bio::Annotation::SimpleValue I think
http://bioperl.org/cgi-bin/deob_interface.cgi?Search=&module=&sort_order=by+method&search_string=Bio%3A%3AAnnotation%3A%3ASimpleValue&Filter=Submit+Query
> -----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: Friday, 1 May 2009 8:45 a.m.
> Cc: BioPerl List
> Subject: Re: [Bioperl-l] Bio::Annotations::Collection confusion
>
> 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
> > >>
> > >
> > > _______________________________________________
> > > Bioperl-l mailing list
> > > Bioperl-l at lists.open-bio.org
> > > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
> > Jason Stajich
> > jason at bioperl.org
> >
> >
> >
> >
>
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