[Bioperl-l] Another Taxonomy modules to CPAN

[Hilmar Lapp]

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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>
>
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-- 
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: Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
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