get_taxid_for_gi.pl

#!/usr/bin/env perl
use strict;
use warnings;

use Bio::DB::Taxonomy;

my @gis;
while(<>) {
    chomp;
    push @gis, $_;
}

my $remote_entrez_tax_db = Bio::DB::Taxonomy->new(-source => "entrez");
my @matching_nodes = $remote_entrez_tax_db->get_Taxonomy_Node( -gi => \@gis );

for my $node ( @matching_nodes ) {
    print $node->ncbi_taxid, "\n";
}