[Bioperl-l] GSoC proposal
cjfields at illinois.edu
Tue Apr 14 14:21:43 EDT 2009
On Apr 12, 2009, at 6:10 AM, Oleksii Nikolaienko wrote:
> Hi all!
> My name is Oleksii, I`m PhD student and I`d like to receive your
> comments on
> my proposal for Google summer of code. It`s called
> "bioperl-live::Bio::Restriction::* - implementing missing features"
> and I`m
> going to:
> 1) add support for reading and writing different file formats for
> module Bio::Restriction::IO
You should specify which formats you intend on working with. It's
known that several formats don't carry all data, for instance
prototype information, vendors, etc. so that should be documented for
end-users. You should probably suggest a workaround for getting at
missing data (i.e. a format that carries all info, retrieving
prototype data separately, etc).
> 2) add support for multicut/multisite enzymes
Agreed, though you should be more specific on how you intend to
implement this. From the Bio::Restriction::Enzyme documentation the
sequence site is supposed to be a Bio::PrimarySeq (though I would
probably change that internally so it creates these on the fly from
the stored string). Multicut/multisite implies list context return,
so it may become an API issue (and using wantarray as a workaround is
fraught with problematic API traps that I suggest avoiding if at all
> 3) add information on recommended buffers, restriction
> sensitivity to methylation, etc and corresponding new methods
Much of this should probably be outlined in the corresponding
interface class prior to implementation.
> 4) update documentation for Bio::Restriction::* modules
Yes, completely agree. This should be bumped closer to the top of the
priority list (and outlined in the interface classes).
> Thanks in advance for your suggestions.
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