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Gmane
From: Fields, Christopher J <cjfields <at> illinois.edu>
Subject: Re: Bio::PrimarySeq obj?
Newsgroups: gmane.comp.lang.perl.bio.general
Date: Friday 21st June 2013 02:13:04 UTC (over 3 years ago)
On Jun 20, 2013, at 6:27 PM, Bob Freeman 
wrote:

> Hoping for an easy answer on this…
> 
> Using Bio::DB::Fasta to retrive a seqobj with get_Seq_by_id. I can print
the raw sequence with seqobj->seq(), but when I try to change and set the
raw sequence data (e.g. seqobj->seq("ACTT"), the change is ignored (as
evidenced when writing out to new FASTA file).
> 
> Looking under the hood with the Perl debugger, it appears that the object
returned is a Bio::PrimarySeq::FASTA, which points to the whole (indexed)
FASTA file; not what I had expected.
> 
> Is the PrimarySeq obj that is returned immutable?

Right; the object is a lightweight representation IIRC and is designed to
be immutable, I'm sure b/c the data in the 'database' (file) can't be
changed.

> If so, is there an easy way to 'copy' the object so that I can change the
sequence and then write this out to a different file?
> 
> Tx,
> B

I would copy them to a new Bio::PrimarySeq; it's lighter that a full
Bio::Seq and will work with Bio::SeqIO.  Might be worth adding a method to
Bio::DB::Fasta to do this for convenience.

chris

> -----------------------------------------------------
> Bob Freeman, Ph.D.
> Acorn Worm Informatics, Kirschner lab
> Dept of Systems Biology, Alpert 524
> Harvard Medical School
> 200 Longwood Avenue
> Boston, MA  02115
> 617/432.2294, vox
> 
> "Sorry I'm late. Oh, God, that sounded insincere. I'm late."
> 	-- Karen Walker, from Will and Grace
> 
> 
> 
> 
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