[Bioperl-l] Accessing /gene and /note fields in a GenBank file

[Mick Watson]

To get all the "tags" in a feature table, try something like:

foreach my $feat (@features)
     {
      my @tags = $feat->all_tags;
      foreach $tag (@tags) {
            my @values = $feat->each_tag_value($tag);
      }
     }

If I understand you correctly, /gene and /note will be in the tags array
somewhere if they exist.  I think $feat also has a has_tag($string) method (or
something similar) if you only want particular tags

Thanks
Mick



Adam Witney wrote:

> Hi, just been trying to write a GenBank parser for a GenBank file containing
> a whole genome
>
> How do I get access to the /gene and /note fields of each gene? I have this
> so far
>
> my $gbk_obj = Bio::SeqIO->new('-file' => "gbk_file",
>                               '-format' => 'GenBank');
>
> while (my $seq = $gbk_obj->next_seq())
>   {
>    my @features = $seq->all_SeqFeatures;
>
>    foreach my $feat (@features)
>      {
>       print $feat->primary_tag."\n";
>
>       print $feat->start.' - '.$feat->end."\t".$feat->strand."\n";
>
>       my $seq_obj = $feat->seq;
>
>       print $seq_obj->seq."\n";
>
>      }
>
> Thanks
>
> adam
>
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