[Bioperl-l] Odd problem with get_tag_values

Jason Stajich jason.stajich at gmail.com
Fri Feb 24 16:21:07 EST 2012


not all CDS will be annotated with a 'gene' tag, this is due to variation in how annotation is done and that there is not a requirement that there be a gene tag for all CDS features.

You can protect your query - we often do this when dealing with data from the wild by testing for has_tag first.

my %strands;
for my $cds ( grep {$_->primary_tag eq 'CDS' } Bio::SeqIO->new(-file => $file)->next_seq->get_SeqFeatures ) {
 if( $cds->has_tag('gene') ) {
	my ($gene) = $cds->get_tag_values('gene'); # get the 1st one, this returns a list
	$strands{$gene} = $cds->strand; 
 } else { # look in alternative places for a name, e.g. locus, 
  ...
 }
}

An alternative is to loop through your list of tags in order of preference

my %strands;
for my $cds ( grep {$_->primary_tag eq 'CDS' } Bio::SeqIO->new(-file => $file)->next_seq->get_SeqFeatures ) {
 for my $tag ( qw(gene locus name product accession note) ) {  
   if( $cds->has_tag($tag) ) {
	my ($name) = $cds->get_tag_values($tag); # get the 1st one, this returns a list
	$strands{$name} = $cds->strand;
        $seen = 1;
        last;
 }
 if( ! $seen ) { 
	warn("not tag found for feature at ", $cds->location->to_FTstring, "\n");
 }
}

On Feb 24, 2012, at 12:43 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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Jason Stajich
jason.stajich at gmail.com
jason at bioperl.org




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