[Bioperl-l] Bio::PrimarySeq obj?

[Fields, Christopher J]

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." <Bob_Freeman at hms.harvard.edu> 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" <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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> Jason Stajich
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