Man page - bp_local_taxonomydb_query(1)
Packages contas this manual
- bp_process_sgd(1)
- bp_genbank2gff3(1)
- bp_make_mrna_protein(1)
- bp_search2alnblocks(1)
- bp_seqret(1)
- bp_fetch(1)
- bp_seqretsplit(1)
- bp_mrtrans(1)
- bp_index(1)
- bp_extract_feature_seq(1)
- bp_seqcut(1)
- bp_nexus2nh(1)
- bp_aacomp(1)
- bp_gccalc(1)
- bp_unflatten_seq(1)
- bp_local_taxonomydb_query(1)
- bp_dbsplit(1)
- bp_process_gadfly(1)
- bp_oligo_count(1)
- bp_nrdb(1)
- bp_seqpart(1)
- bp_tree2pag(1)
- bp_taxonomy2tree(1)
- bp_filter_search(1)
- bp_bioflat_index(1)
- bp_taxid4species(1)
- bp_split_seq(1)
- bp_find-blast-matches(1)
- bp_mask_by_search(1)
- bp_mutate(1)
- bp_seqconvert(1)
- bp_search2gff(1)
- bp_fastam9_to_table(1)
- bp_seq_length(1)
- bp_biogetseq(1)
- bp_translate_seq(1)
- bp_search2table(1)
- bp_sreformat(1)
- bp_revtrans-motif(1)
- bp_search2tribe(1)
Package: bioperl
apt-get install bioperl
apt-get install bioperl
Manuals in package:
Documentations in package:
Manual
| BP_LOCAL_TAXONOMYDB_QUERY(1p) | User Contributed Perl Documentation | BP_LOCAL_TAXONOMYDB_QUERY(1p) |
NAME
bp_local_taxonomydb_query - query a local TaxonomyDB for species or taxonid
DESCRIPTION
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.
| 2021-08-15 | perl v5.32.1 |