Freeman, Robert M. | 21 Jun 14:12 2013
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Re: Bio::PrimarySeq obj?

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"
<jason.stajich <at> gmail.com<mailto:jason.stajich <at> gmail.com>> 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
<Bob_Freeman <at> hms.harvard.edu<mailto:Bob_Freeman <at> hms.harvard.edu>> 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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