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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 13:38:35 UTC (over 3 years ago)
You're officially invited to be part of the development team.  It is
open-source, after all :)

chris

On Jun 21, 2013, at 7:12 AM, "Freeman, Robert M."
 wrote:

> Yeah, that's what I figured I'd have to do.
> 
> Thanks, Jason and Chris, for the helpful replies!!
> 
> (Now what do I have to do to get on the dev team?)
> 
> -b
> 
> Sent from my iPhone
> 
> On Jun 21, 2013, at 1:27 AM, "Jason Stajich"
<[email protected]> wrote:
> 
> I believe this is what you need - I do this all the time to write an
updated version of one that comes from the DB::Fasta DB.
> 
> my $newseq = Bio::PrimarySeq->new(-seq => $oldseq->seq, -id =>
$oldseq->id, -description => $oldseq->description);
> 
> On Jun 20, 2013, at 4:27 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? 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
> 
> -----------------------------------------------------
> 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
> 
> 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> [email protected]
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> Jason Stajich
> [email protected]
> [email protected]
> 
> 
> _______________________________________________
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