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

Daniel Standage daniel.standage at gmail.com
Fri Oct 29 10:34:41 EDT 2010


I guess my concern is that I haven't used inheritance much in Perl and I'm
unclear about the possible consequences of the approach I've taken. I've
seen people warning against re-blessing objects, and I just wanted to make
sure that the approach that I seem to have working now isn't going to cause
any problems down the line.

Sorry I wasn't clear. Thanks for your help.

Daniel

On Fri, Oct 29, 2010 at 9:21 AM, Scott Cain <scott at scottcain.net> wrote:

> Hi all,
>
> I'm resending this because it seems that some mail clients don't like
> having executable files hidden inside of a tarball, so I removed the
> executable bit.
>
> Scott
>
>
> On Fri, Oct 29, 2010 at 10:03 AM, Scott Cain <scott at scottcain.net> wrote:
> > 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
> >
>
>
>
> --
> ------------------------------------------------------------------------
> 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


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