[Bioperl-l] Error parsing genbank file

[Koul, Sunita]

Thanks -I added the  "has->tag" option before working on the features and it is working fine now


-----Original Message-----
From: Fields, Christopher J [mailto:cjfields at illinois.edu]
Sent: Tuesday, August 13, 2013 1:23 PM
To: Koul, Sunita
Cc: bioperl-l at lists.open-bio.org
Subject: Re: [Bioperl-l] Error parsing genbank file


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


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