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

Scott Cain scott at scottcain.net
Fri Oct 29 10:21:51 EDT 2010


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
-------------- next part --------------
A non-text attachment was scrubbed...
Name: temp.tar.gz
Type: application/x-gzip
Size: 1888 bytes
Desc: not available
URL: <http://lists.open-bio.org/pipermail/bioperl-l/attachments/20101029/7f79ea59/attachment.gz>


More information about the Bioperl-l mailing list