/usr/bin/bp_local_taxonomydb_query is in bioperl 1.6.923-1.
This file is owned by root:root, with mode 0o755.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 | #!/usr/bin/perl
eval 'exec /usr/bin/perl -S $0 ${1+"$@"}'
if 0; # not running under some shell
use strict;
use warnings;
use Bio::DB::Taxonomy;
use strict;
use Getopt::Long;
my $verbose = 0;
my $plain = 0;
my ($nodesfile,$namesfile);
my $idx_dir = '/tmp/idx';
GetOptions('v|verbose' => \$verbose,
'nodes:s' => \$nodesfile,
'names:s' => \$namesfile,
'idx:s' => \$idx_dir,
'h|help' => sub{ exec('perldoc',$0);
exit(0)
} );
unless( @ARGV || $nodesfile || $namesfile ) {
exec('perldoc',$0);
exit(0);
}
mkdir($idx_dir) unless -d $idx_dir;
my $db = new Bio::DB::Taxonomy(-source => 'flatfile',
-nodesfile => $nodesfile,
-namesfile => $namesfile,
-directory => $idx_dir);
foreach my $sp ( @ARGV ) {
my $node = $db->get_Taxonomy_Node(-name => $sp);
if( defined $node ) {
print "id is ", $node->id, "\n"; # 9606
print "rank is ", $node->rank, "\n"; # species
print "scientific name is ", $node->scientific_name, "\n"; # Homo sapiens
print "division is ", $node->division, "\n"; # Primates
} else {
warn("no node found for query $sp");
}
}
=head1 NAME
bp_local_taxonomydb_query - query a local TaxonomyDB for species or taxonid
=head1 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.
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