[Bioperl-l] Another Taxonomy modules to CPAN
hlapp at drycafe.net
Thu Nov 4 12:12:04 EDT 2010
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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: Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
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