[Bioperl-l] Bioperl-l Digest, Vol 71, Issue 15

[Mark A. Jensen]

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
>
>
>
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