[Bioperl-l] annotating existing Seq objects

[Jason Stajich]

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On Fri, 1 Jun 2001, Stephen Henderson wrote:

> I have used the BioPerl tools to write some simple scripts for retrieving
> batches of Ref_sequences from Genbank (in Fasta flat file format). I have a
> slight problem in that some of the retrieved sequence objects:
> 
> $seq= $gb->get_Seq_by_id($ets[$i])

All methods (and then some) that one can initialize on in a constructor
are available through get/set methods.  To achieve what you are asking
just use the following:

 $seq->display_id($ets[$i]);

> 
> have a distinct display_id from that which I have retrieved them with e.g I
> put in X98048, and I get back HS408N23 (I'm not exactly sure why?)

LOCUS is what we put into display_id();

However, in your example I get back EHPAKMCM3 NOT 'HS408N23'
EHPAKMCM3 is the LOCUS name.

If you wanted to the existing display_id just do
$seq->display_id($seq->display_id() . ' ' . $ets[$i] );

> 
> Anyway to work round this I simply want to append my initial query to the
> end of the display_id in the fasta comment line, and then save the files.
> The documentation here shows good examples of creating new Seq objects, or
> returning various properties of seq objects, but are there simple methods to
> append/change Seq features such as accession_id, display_id themselves
> without recourse to creating new objects.
> _______________________________________________
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> Bioperl-l@bioperl.org
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> 

Jason Stajich
jason@chg.mc.duke.edu
Center for Human Genetics
Duke University Medical Center 
http://www.chg.duke.edu/ 


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