[Bioperl-l] SimpleAlign - get_seq_by_id
cjfields at illinois.edu
Sat Oct 25 13:32:54 EDT 2008
Issues with naming each_* vs get_* vs next_* have been raised in the
past, though I can't find them on the mail list archives. I have
similar issues with num_* vs no_*.
Maybe we should come up with some basic coding guidelines in a HOWTO
(tests, method names, etc). We already have some basic documentation
for coding standards with some suggestions (best practices, advanced
bioperl, etc), so maybe these should be consolidated into a single
resource and revised by the core devs to reflect what we expect.
BTW, I think an API cleanup is worth doing, but I don't see it getting
done before a 1.6 release until we agree on some simple coding
conventions. However, for SimpleAlign, we could run a simple cleanup
by moving non-AlignI (utility) methods to the Bio::Align::Utilities
module and deprecating use of the Bio::SimpleAlign versions (i.e. warn
and delegate to the Utilities versions in the meantime, then remove
On Oct 25, 2008, at 10:47 AM, Jason Stajich wrote:
> you're right - it should be rolled back. I guess each_seq_xxx gets
> the job done.
> We have a real problem with each vs get for our API mixture. I think
> there had been some logic there at one point but I think it is
> confusingly mixed now.
> Perhaps a cleaned up API with deprecated aliases would be okay way
> to at some point move towards more standardized.
> It would make sense to also see about implementing Gblocks style
> filtering method as well (but not in SimpleAlign give then number of
> methods already as you mention!).
> On Oct 24, 2008, at 3:05 AM, Heikki Lehvaslaiho wrote:
>> Spoke too soon: each_seq_with_id() already exists. Is there really
>> a need for
>> A more general observation: Bio::SimpleAlign with its 83 methods
>> has grown too
>> big to keep all the code (3055 lines total) in one file. Any
>> volunteers to
>> break it up into more manageable chunks?
>> The methods in the current file have already been categorised which
>> should help
>> in the task:
>> =head1 Modifier methods
>> =head1 Sequence selection methods
>> =head1 Create new alignments
>> =head1 Change sequences within the MSA
>> =head1 MSA attributes
>> =head1 Alignment descriptors
>> =head1 Alignment positions
>> =head1 Sequence names
>> The helper modules should go into Bio::Align name space.
>> On Friday 24 October 2008 08:32:49 Heikki Lehvaslaiho wrote:
>>> The main reason it has not been Bio::SeqAlign is that sequence ID
>>> necessarily a unique identifier in a MSA. Multiple regions of the
>>> defined by one ID can be in one.
>>> The current code returns only the more or less randomly selected
>>> Bio::LocatebleSeqI object with that ID. Should we make it context
>>> and return an array of sequences in array context?
>>> That brings up an other question: After the change, the
>>> will behave differently from all other instances of that method,
>>> so should
>>> it be renamed to reflect that?
>>> On Thursday 23 October 2008 21:29:20 Jason Stajich wrote:
>>>> I added get_seq_by_id to Bio::SimpleAlign to allow retrieval of a
>>>> particular sequence from the alignment by ID. Not sure why this
>>>> exist before.
>>>> Jason Stajich
>>>> jason at bioperl.org
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>> ______ _/ _/
>> _/ _/
>> _/ _/ _/ Heikki Lehvaslaiho heikki at_sanbi _ac _za
>> _/_/_/_/_/ Senior Scientist skype: heikki_lehvaslaiho
>> _/ _/ _/ SANBI, South African National Bioinformatics Institute
>> _/ _/ _/ University of Western Cape, South Africa
>> _/ Phone: +27 21 959 2096 FAX: +27 21 959 2512
>> ___ _/_/_/_/_/
>> Bioperl-l mailing list
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> Jason Stajich
> jason at bioperl.org
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
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College of Veterinary Medicine
University of Illinois Urbana-Champaign
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