[Bioperl-l] Small bug in Bio::Tools::GFF.pm - Target output

Brian Osborne bosborne11 at verizon.net
Fri Apr 20 15:47:30 EDT 2007


Applied.


On 4/19/07 1:38 PM, "Don Gilbert" <gilbertd at cricket.bio.indiana.edu> wrote:

> 
> I'm not sure what kind of test data would have bad Target strings,
> but this should clear up those warnings -- insert the '+' line:
> 
>   sub _gff3_string:
>     for my $tag ( @all_tags ) {
>        ##dgg.patch.was# next if $tag eq 'Target';
>       if ($tag eq 'Target'
>          and ! $origfeat->isa('Bio::SeqFeature::FeaturePair'))
>        {  
>        my($target_id, $b,$e,$strand)= $feat->get_tag_values($tag);
> +       next unless(defined($e) && defined($b) && $target_id);
>        ($b,$e)= ($e,$b) if(defined $strand && $strand<0);
>        $target_id =~ s/([\t\n\r%&\=;,])/sprintf("%%%X",ord($1))/ge;
>        push @groups, sprintf("Target=%s %d %d", $target_id,$b,$e);
>        next;
>        }
> 
> -- Don
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