[Bioperl-l] Bio::AnnotatableI function annotation()

[Govind Chandra]

Thanks to Mark for pursuing the discussion arising out of my initial
post so far. It soon got too technical for me to participate in actively
but I have followed it as well as I could. And thanks to everybody who
participated / commented.

I have been using BioPerl every working day for the last 8 years and I
will probably use it for the rest of my working life. It is a fantastic
resource thanks to all those who help maintain and develop it.

Cheers

Govind



On Sun, 2009-03-29 at 23:11 -0400, Mark A. Jensen wrote:
> Hi all-
> 
> On the wiki, I've attempted to codify and add exegesis to the 
> ideas discussed in this thread. Have a look at 
> 
> http://www.bioperl.org/wiki/Features_vs._Annotations
> 
> in the new 'Metadata' subcat of the Scrapbook
> (http://www.bioperl.org/wiki/Category:Scrapbook)
> 
> (Thanks Govind for stimulating this discussion!)
> 
> cheers, 
> Mark
> 
> ----- Original Message ----- 
> From: "Govind Chandra" <govind.chandra at bbsrc.ac.uk>
> To: "Mark A. Jensen" <maj at fortinbras.us>
> Cc: <bioperl-l at lists.open-bio.org>
> Sent: Friday, March 27, 2009 1:09 PM
> Subject: [Bioperl-l] Bio::AnnotatableI function annotation()
> 
> 
> > Thanks Mark,
> > 
> > Sorry for not putting a proper subject in the last post.
> > 
> > What you suggest is what I have been doing for a long time. I am just
> > trying to alter my code to conform to the latest bioperl version and ran
> > into this issue. I could be wrong (I am more a user rather than writer
> > of modules) but since $feature->annotation() does not result in an error
> > I think $feature is-a Bio::AnnotatableI as well.
> > 
> > Cheers
> > 
> > Govind
> > 
> > 
> > 
> > On Fri, 2009-03-27 at 12:17 -0400, Mark A. Jensen wrote:
> >> Hi Govind-
> >> 
> >> As near as I can tell, the *_tags methods are deprecated for
> >> Bio::AnnotatableI objects, but these methods are available
> >> off the SeqFeatureI objects themselves: i.e., rather than
> >> 
> >> >  $ac=$feature->annotation();
> >> >  $temp1=$ac->get_Annotations("locus_tag");
> >> 
> >> do
> >> 
> >>  $temp1 = $feature->get_tag_values("locus_tag");
> >> 
> >> directly.
> >> 
> >> hope it helps -
> >> Mark
> >> 
> >> ----- Original Message ----- 
> >> From: "Govind Chandra" <govind.chandra at bbsrc.ac.uk>
> >> To: <bioperl-l at lists.open-bio.org>
> >> Sent: Friday, March 27, 2009 11:26 AM
> >> Subject: Re: [Bioperl-l] Bioperl-l Digest, Vol 71, Issue 15
> >> 
> >> 
> >> > Hi,
> >> >
> >> > The code below
> >> >
> >> >
> >> > ====== code begins =======
> >> > #use strict;
> >> > use Bio::SeqIO;
> >> >
> >> > $infile='NC_000913.gbk';
> >> > my $seqio=Bio::SeqIO->new(-file => $infile);
> >> > my $seqobj=$seqio->next_seq();
> >> > my @features=$seqobj->all_SeqFeatures();
> >> > my $count=0;
> >> > foreach my $feature (@features) {
> >> >  unless($feature->primary_tag() eq 'CDS') {next;}
> >> >  print($feature->start(),"   ", $feature->end(), " 
> >> > ",$feature->strand(),"\n");
> >> >  $ac=$feature->annotation();
> >> >  $temp1=$ac->get_Annotations("locus_tag");
> >> >  @temp2=$ac->get_Annotations();
> >> >  print("$temp1   $temp2[0] @temp2\n");
> >> >  if($count++ > 5) {last;}
> >> > }
> >> >
> >> > print(ref($ac),"\n");
> >> > exit;
> >> >
> >> > ======= code ends ========
> >> >
> >> > produces the output
> >> >
> >> > ========== output begins ========
> >> >
> >> > 190   255   1
> >> > 0
> >> > 337   2799   1
> >> > 0
> >> > 2801   3733   1
> >> > 0
> >> > 3734   5020   1
> >> > 0
> >> > 5234   5530   1
> >> > 0
> >> > 5683   6459   -1
> >> > 0
> >> > 6529   7959   -1
> >> > 0
> >> > Bio::Annotation::Collection
> >> >
> >> > =========== output ends ==========
> >> >
> >> > $ac is-a Bio::Annotation::Collection but does not actually contain any
> >> > annotation from the feature. Is this how it should be? I cannot figure
> >> > out what is wrong with the script. Earlier I used to use has_tag(),
> >> > get_tag_values() etc. but the documentation says these are deprecated.
> >> >
> >> > Perl is 5.8.8. BioPerl version is 1.6 (installed today). Output of uname
> >> > -a is
> >> >
> >> > Linux n61347 2.6.18-92.1.6.el5 #1 SMP Fri Jun 20 02:36:06 EDT 2008
> >> > x86_64 x86_64 x86_64 GNU/Linux
> >> >
> >> > Thanks in advance for any help.
> >> >
> >> > Govind
> >> >
> >> >
> >> >
> >> > _______________________________________________
> >> > Bioperl-l mailing list
> >> > Bioperl-l at lists.open-bio.org
> >> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >> >
> >> > 
> >> 
> > 
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> > 
> >