21 Jun 2013 15:38
Re: Bio::PrimarySeq obj?
Fields, Christopher J <cjfields <at> illinois.edu>
2013-06-21 13:38:35 GMT
2013-06-21 13:38:35 GMT
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 > > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l <at> lists.open-bio.org<mailto:Bioperl-l <at> lists.open-bio.org> > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > Jason Stajich > jason.stajich <at> gmail.com<mailto:jason.stajich <at> gmail.com> > jason <at> bioperl.org<mailto:jason <at> bioperl.org> > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l <at> lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l