[Bioperl-l] Extracting sequences from Genbank files

[Liam Elbourne]

Hi Brian,

Check out:

http://www.bioperl.org/wiki/HOWTO:Feature-Annotation#Getting_the_Features

But I think get_tag_values is the method you require.

Regards,
Liam Elbourne. 



On 24/05/2012, at 8:27 PM, Brian Forde <b.m.forde at umail.ucc.ie> wrote:

> Hello,
> 
> I have been modifying a script which extracts all the protein sequences
> from a genbank file and saves them in a multi-fasta file.
> 
> I wish the fasta header to have both the locus_tag of the protein and the
> product. However I cannot get the  product tag to write to the fasta header
> 
> this is the relevant section of the script
> 
> $s->display_id($f->has_tag('locus_tag') ? join(',',sort
> $f->each_tag_value('locus_tag')) :
>                           $f->has_tag('product') ?
> join(',',$f->each_tag_value('product')):
>                           $s->display_id);
> 
> is "product" not an actual tag
> 
> regards
> 
> Brian
> 
> 
> 
> -- 
> Brian Forde
> Microbiology Dept.
> Bioscience Institute. Room 4.11
> University College Cork
> Cork
> Ireland
> tel:+353 21 4901306
> email: b.m.forde at umail.ucc.ie
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