[Bioperl-l] Re: [Bioperl-guts-l] bioperl commit

Aaron J. Mackey amackey at pcbi.upenn.edu
Wed Jul 14 10:37:30 EDT 2004

On Jul 13, 2004, at 12:42 PM, Chris Mungall wrote:

>>> +  $gffio->features_attached_to_seqs_toggle(1)
>> Again, $gffio->attach_features(1) seems sufficient ...
> OK; although one might be led to expect that the argument for a method
> with that name would be a list of SeqFeatures. Is the BP method name
> syntax enshrined anywhere, or is it more a general set of principles
> shared by the authors?

You're right.  No, there is no shrine, I think it's like the difference 
between art and pornography; we know it when we see it.  Perhaps 
"$gffio->features_attached_to_seqs(1)" is the necessarily-long-but-best 

> So perhaps I should reeingineer it a bit so that it rejects anything 
> that
> doesn't follow the spec. This makes it easier to use the FASTA parser.

I think that'd be great, and should simplify matters a bit.

Thanks again,


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