/usr/bin/bp_query_entrez_taxa 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 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 | #!/usr/bin/perl
eval 'exec /usr/bin/perl -S $0 ${1+"$@"}'
if 0; # not running under some shell
# This is a -*-Perl-* file (make my emacs happy)
=head1 NAME
bp_query_entrez_taxa - query Entrez taxonomy database and print out information
=head1 USAGE
bp_query_entrez_taxa "Homo sapiens" "Saccharomyces cerevisiae" Rhizopus Metazoa
bp_query_entrez_taxa -gi 28800981 -gi 54301680 -db nucleotide
bp_query_entrez_taxa -gi 71836523 -db protein
Provide the genus and species name in quotes, you can also query for
a non-species node like Family or Order
Command-line options:
-v or --verbose : print verbose debugging info
-gi : one or many GI numbers to lookup taxon id for
-db : the sequence db (nucleotide or protein) the GI is for
other arguments are assumed to be species names to lookup in taxonomy db
=head1 AUTHOR
Jason Stajich jason-at-bioperl-dot-org
=cut
use strict;
use warnings;
use Bio::DB::Taxonomy;
use Getopt::Long;
my $verbose = 0;
my (@gi, $dbname);
GetOptions('v|verbose' => \$verbose,
'gi:i' => \@gi,
'db:s' => \$dbname);
my $db = new Bio::DB::Taxonomy(-source => 'entrez', -verbose => $verbose);
if( @gi ) {
my @nodes= $db->get_Taxonomy_Node(-gi => \@gi,
-db => $dbname);
for my $node ( @nodes ) {
my $gi = shift @gi;
print " for gi $gi:\n";
print " taxonid is ",$node->ncbi_taxid,"\n";
print " node is ", join(", ",$node->classification), "\n";
print " species is ", $node->species,"\n";
print " parent is ", $node->parent_id, "\n";
print " rank is ", $node->rank, "\n";
print " genetic_code ", $node->genetic_code, "\n";
print " mito_genetic_code ", $node->mitochondrial_genetic_code, "\n";
print " scientfic name is ", $node->binomial, "\n";
}
}
print "\n\n";
for my $name ( @ARGV ) {
my $taxonid = $db->get_taxonid($name);
my $node = $db->get_Taxonomy_Node(-taxonid => $taxonid);
print "taxonid is $taxonid\n";
print " node is ", join(", ",$node->classification), "\n";
print " species is ", $node->species,"\n";
print " parent is ", $node->parent_id, "\n";
print " rank is ", $node->rank, "\n";
print " genetic_code ", $node->genetic_code, "\n";
print " mito_genetic_code ", $node->mitochondrial_genetic_code, "\n";
print " scientfic name is ", $node->binomial, "\n";
print " common name is ", $node->common_name, "\n";
print " create date is ", $node->create_date, "\n";
print " update date is ", $node->update_date, "\n";
print " pub date is ", ($node->pub_date || ''), "\n";
print " variant is ", $node->variant, "\n";
print " sub_species is ", $node->sub_species, "\n";
print " organelle is ", $node->organelle, "\n";
print " division is ", $node->division, "\n";
}
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