[Bioperl-l] Another Taxonomy modules to CPAN
miguel.pignatelli at uv.es
Fri Nov 5 05:31:46 EDT 2010
In the perl module-authors list I have been suggested two nice alternatives:
If the devs don't have any objection/preference I will follow the first one.
Hilmar Lapp wrote:
> I agree - Bio:: isn't exclusive to BioPerl, but in choosing module name
> and namespace, as well as in documentation, try to minimize potential
> confusion for users.
> On Nov 3, 2010, at 10:34 PM, Chris Fields wrote:
>> (Caveat: You should also ask this on the perl module-authors list,
>> just in case: http://lists.perl.org/list/module-authors.html)
>> Not sure how the other devs feel, but I personally don't think the
>> Bio* namespace is reserved only for BioPerl modules (see Bio::Phylo,
>> for example). It's a fairly generic top-level name. The only worry I
>> have is if these are too similar to current BioPerl modules;
>> Bio::Taxonomy and Bio::DB::Taxonomy already have namespaces in CPAN
>> related to BioPerl modules.
>> Saying that, tagging them as *::Lite might be fine, as long as the
>> documentation indicated these are not related to BioPerl. Anyone else
>> want to chime in? Maybe releasing them as a top-level Taxonomy?
>> On Nov 3, 2010, at 4:42 AM, Miguel Pignatelli wrote:
>>> Hi all,
>>> I have written a couple of modules that overlap certain functionality
>>> with Bio::DB::Taxonomy and Bio::Taxon. I had to write them because
>>> certain constraints in the environment I had to run it (GRID) made
>>> impossible to use a bioperl based solution.
>>> The main features of these modules are:
>>> + No dependencies of non-standard Perl modules
>>> + NCBI and RDP based taxonomies supported
>>> + Very fast and low memory footprint -- orders of magnitude faster
>>> than Bioperl modules (for the tasks they are designed for --).
>>> Of course, they do not compete with Bio::DB::Taxonomy and Bio::Taxon
>>> in completeness or integration with other tools (e.g. rest of bioperl
>>> suit) but they are handy for mapping very large datasets (for example
>>> blast results) with the NCBI or RDP Taxonomy.
>>> The modules are:
>>> Taxonomy::Base -- Finds ancestors, ranks, converts between
>>> names, ranks and IDs, etc...
>>> Taxonomy::RDP -- Reads the taxonomic tree from the RDP xml file
>>> Taxonomy::NCBI -- Reads the taxonomic tree from flat NCBI files
>>> (nodes.dmp and names.dmp)
>>> (Similar to Bio::DB::Taxonomy::flatfile)
>>> Taxonomy::NCBI::Gi2taxid -- Converts very fast and efficiently
>>> NCBI GIs to Taxids.
>>> Uses a binary lookup table.
>>> These modules are being used by several groups now -- mainly working
>>> with large metagenomics datasets -- and I am considering uploading
>>> them to CPAN, but I am not clear on where these modules should be
>>> placed there.
>>> How do you think I should name these modules? (e.g. where these
>>> modules should live in CPAN?) Their natural place could be under
>>> Bio::DB::Taxonomy, maybe Bio::DB::Taxonomy::Lite /
>>> Bio::DB::Taxonomy::Lite::NCBI / etc...? Is this possible (and
>>> convenient) without being part of Bioperl? Any other suggestions?
>>> Thank you very much in advance,
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
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