[Bioperl-l] Another Taxonomy modules to CPAN

Miguel Pignatelli miguel.pignatelli at uv.es
Thu Dec 9 07:05:59 EST 2010


Hi all,

I have uploaded these modules into CPAN a couple of weeks ago.

Bio::LITE::Taxonomy
Bio::LITE::Taxonomy::NCBI
Bio::LITE::Taxonomy::NCBI::Gi2taxi
Bio::LITE::Taxonomy::RDP

Feel free to test them and see if they fit your needs.

Remember: They are not part of Bioperl, just alternatives. See the 
documentation for (not many... but improving) details.

Any feedback is highly welcome

Regards,

M;


On 11/03/2010 10:42 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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