[Bioperl-l] Error parsing genbank file

[Fields, Christopher J]

On Aug 13, 2013, at 12:12 PM, "Koul, Sunita" <sunita at pathology.wustl.edu> wrote:

> All,
> I am trying to retrieve some gene information from genbank file.
> Part of the code is to ignore the pseudo genes
> 
> 
> if( $featobj->primary_tag eq 'gene' )
>                                             {
>                                               print "$geneID\n";
> 
> 
>                                                            if(scalar($featobj->get_tag_values('pseudo')) > 0)
>                                    {
>                                                                           $pseudo{$geneID} = 1;
> 
>                                                                           next;
>                                                            }
> }
> 
> This throws me an error
> 
> What is the reason for this error
> 
> 
> 
> MSG: asking for tag value that does not exist pseudo
> STACK: Error::throw
> STACK: Bio::Root::Root::throw /usr/local/share/perl5/Bio/Root/Root.pm:472
> STACK: Bio::SeqFeature::Generic::get_tag_values /usr/local/share/perl5/Bio/SeqFeature/Generic.pm:522

As the message implies, there is no tag for 'pseudo' for the feature in question, you need to use 'if ($featobj->has_tag('pseudo'))' as a check prior to working on the feature.

Frankly, this is a stricture that I don't like (e.g. dying if the tag isn't present), but it has been in place for quite a long time.  I wouldn't be opposed to removing or making it less death-y.

> If I comment out the above code -I get another error for this part of the error with the message that
> MSG: asking for tag value that does not exist 'db_xref'
> 
> 
>                              foreach my $featobj ($seqobj->all_SeqFeatures() )
>                              {
>                                             my $geneID;
> 
>                                             for my $value ($featobj->get_tag_values('db_xref'))
>      {
>               if ($value =~ /GeneID:(.*)/)
>               {
>                              $geneID = $1;
>               }
>      }
> 
> Please help me understand what is wrong in this code

Same problem, you are asking for a tag in the feature that doesn't exist.

chris