Jason Stajich | 21 Jun 07:27 2013

Re: Bio::PrimarySeq obj?

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> 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
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Jason Stajich
jason.stajich <at> gmail.com
jason <at> bioperl.org