[Bioperl-l] Another Taxonomy modules to CPAN

Miguel Pignatelli miguel.pignatelli at uv.es
Fri Nov 5 05:31:46 EDT 2010

Hi all,

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.
>     -hilmar
> On Nov 3, 2010, at 10:34 PM, Chris Fields wrote:
>> Miguel,
>> (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?
>> chris
>> 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,
>>> M;
>>> ----------------------------------------------------
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