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Gmane
From: Freeman, Robert M. <Bob_Freeman <at> hms.harvard.edu>
Subject: Re: Bio::PrimarySeq obj?
Newsgroups: gmane.comp.lang.perl.bio.general
Date: Friday 21st June 2013 12:12:09 UTC (over 3 years ago)
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




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Jason Stajich
[email protected]
[email protected]


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