Jason Stajich | 22 Jun 01:09 2013

Re: Bio::PrimarySeq obj?

fork, change, commit, issue pull request - it will be incorporated.  Lincoln wrote the module to support
gbrowse in the first iteration - I think I have been annoyed by the same problems as you but found it was
easier for me to just create a new object most of the time rather than try to worry about some of the speed
things that it does under the hood.  I think adding the warnings is your best bet though rather than
retooling it to allow objects to be mutable. 

On Jun 21, 2013, at 5:08 AM, "Freeman, Robert M." <Bob_Freeman <at> hms.harvard.edu> wrote:

> So, a number of things bother me about this:
> - why is BioPerl deciding that I can't change this?
> - no warning is thrown when I try to change any value of the object 
> - documentation does not indicate the object is immutable 
> - documentation does not indicate that a PrimarySeq is returned.
> - Worse (at the time), the object is tied to the DB file, so when I dumped the object in the debugger, it
started dumping the whole DB Index. Not sure why this decision was made. 
> LOL! Are these bugs or features?
> Yeah, an option at fetch time would be nice.
> -b
> Sent from my iPhone
>> On Jun 20, 2013, at 10:13 PM, "Fields, Christopher J" <cjfields <at> illinois.edu> wrote:
>>> On Jun 20, 2013, at 6:27 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?
>> Right; the object is a lightweight representation IIRC and is designed to be immutable, I'm sure b/c the
data in the 'database' (file) can't be changed.
>>> 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
>> I would copy them to a new Bio::PrimarySeq; it's lighter that a full Bio::Seq and will work with
Bio::SeqIO.  Might be worth adding a method to Bio::DB::Fasta to do this for convenience.
>> chris
>>> -----------------------------------------------------
>>> Bob Freeman, Ph.D.
>>> Acorn Worm Informatics, Kirschner lab
>>> Dept of Systems Biology, Alpert 524
>>> Harvard Medical School
>>> 200 Longwood Avenue
>>> Boston, MA  02115
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Jason Stajich
jason.stajich <at> gmail.com
jason <at> bioperl.org