bp_local_taxonomydb_query - query a local TaxonomyDB for species or taxonid
This script provides an example implementation of access to a local Taxonomy database implemented with Berkeley DB (DB_File module is needed).
Usage:
bp_local_taxonomydb_query.PLS: [-v] --nodes nodes.dmp --names names.dmp "Genus1 species1" "Genus2 species2"
Providing the nodes.dmp and names.dmp files from the NCBI Taxonomy dump (see Bio::DB::Taxonomy::flatfile for more info) is only necessary on the first time running. This will create the local indexes and may take quite a long time. However once created, these indexes will allow fast access for species to taxon id OR taxon id to species name lookups.
To install BioPerl, copy and paste the appropriate command in to your terminal.
cpanm
cpanm BioPerl
CPAN shell
perl -MCPAN -e shell install BioPerl
For more information on module installation, please visit the detailed CPAN module installation guide.