[Bioperl-l] Bio::SeqFeature::Generic and Inheritance Question

Scott Cain scott at scottcain.net
Fri Oct 29 10:03:54 EDT 2010


Hi Daniel,

I cc'ed the bioperl mailing list back in and attached your tarball.  I
don't really know what it is you want to do, and you already know that
your code compiles and runs, so I'm not sure what advice you're
looking for.

Scott

On Fri, Oct 29, 2010 at 9:28 AM, Daniel Standage
<daniel.standage at gmail.com> wrote:
> I don't see how to attach files to the mailing list, so I'm just going to
> reply to you. Sorry if that is against the protocol.
>
> I have attached a working implementation of what I think you were
> suggesting. I have a parser class that subclasses Bio::Tools::GFF, and it
> has a method that will return objects of my class that subclasses
> Bio::SeqFeature::Generic. This is a rough test and I still need to clean
> things up and add the rest of the functionality that I originally needed, I
> just wanted to make sure that there aren't going to be any problems with the
> approach I'm taking.
>
> If you unpack and run './temptest' it should print out 7 valid features and
> 1 invalid feature.
>
> Thanks for your suggestions!
>
> Daniel
>
> On Thu, Oct 28, 2010 at 10:41 PM, Scott Cain <scott at scottcain.net> wrote:
>>
>> Hi Daniel,
>>
>> It seems like the easiest thing to do would be to subclass
>> Bio::Tools::GFF.  BSFGeneric is only mentioned explicitly a few times
>> (maybe only once), so subclassing and having it use your class instead
>> would probably be the easiest thing to do.
>>
>> Also, about having it produce GFF3: make sure you're actually getting
>> valid GFF3.  Bio::Tools::GFF is fairly old, and I am sure you could
>> give it valid SeqFeature objects and get invalid GFF3 out in some
>> circumstances.
>>
>> Scott
>>
>>
>> On Thu, Oct 28, 2010 at 10:45 PM, Daniel Standage
>> <daniel.standage at gmail.com> wrote:
>> > I am using the Bio::Tools::GFF parser to process and store GFF3 data
>> > in an application. Calls to next_feature() return
>> > Bio::SeqFeature::Generic objects. I have written a class that extends
>> > the Bio::SeqFeature::Generic class, but I still want to use the
>> > Bio::Tools::GFF class to do the initial parsing of the data.
>> >
>> > Is there a way for me to tell the Bio::Tools::GFF parser that I want
>> > it to give me objects from my custom class? Or should I just re-bless
>> > the objects it gives me? Will I run into garbage collection problems
>> > if I re-bless the Bio::SeqFeature::Generic objects to my custom class
>> > (that extends the Bio::SeqFeature::Generic class)?
>> >
>> > Thanks!
>> >
>> > Daniel
>> > _______________________________________________
>> > Bioperl-l mailing list
>> > Bioperl-l at lists.open-bio.org
>> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> >
>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain
>> dot net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> Ontario Institute for Cancer Research
>
>
>
> --
> Daniel S. Standage
> Graduate Research Assistant
> Bioinformatics and Computational Biology Program
> Iowa State University
>
>



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research
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