[Bioperl-l] Odd problem with get_tag_values

[Brian Osborne]

Adlai,

You are absolutely sure that every single CDS feature has a "gene" tag inside it?

If this is not the case then you have to use the "if ($cds_feature->has_tag("gene")) …" type of logic.

Brian O.

On Feb 24, 2012, at 3:43 PM, Adlai Burman wrote:

> I have come across a perplexing problem with trying to parse sequence features into hashes from gb records. This is the minimal code which shows my problem:
> 
> #!/usr/bin/perl                                                                                                     
> use strict;
> use warnings;
> use IO::String;
> use Bio::Perl;
> use Bio::SeqIO;
> use IO::String;
> 
> my @files = </Users/adlai/Dropbox/atrsh/*>;
> foreach my $file(@files){
> 
> 
> my @cds_features = grep {$_->primary_tag eq 'CDS' } Bio::SeqIO->new(-file => $file)->next_seq->get_SeqFeatures;
> my %strands = map {$_->get_tag_values('gene'), $_->strand} @cds_features; ##This Is The Culprit. 
> .
> .
> .
> #do nifty stuff
> }
> 
> For some files this approach works just fine.
> For others the script dies immediately with the error message:
> 
> ------------- EXCEPTION -------------
> MSG: asking for tag value that does not exist gene
> STACK Bio::SeqFeature::Generic::get_tag_values /Users/adlai/Downloads/BioPerl-1.6.1/Bio/SeqFeature/Generic.pm:517
> STACK toplevel tosend.pl:16
> -------------------------------------
> 
> The difference in the files that parse and those that don't seems to be that the files that crash have "intron" and "exon" tags. They ALL have "gene" tags.
> Does anyone know why this is a problem and what can be done to circumvent it?
> 
> Thanks,
> Adlai
> 
> 
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