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#!/usr/bin/env perl
# Copyright © 2011, Battelle National Biodefense Institute (BNBI);
# all rights reserved. Authored by: Brian Ondov, Nicholas Bergman, and
# Adam Phillippy
#
# See the LICENSE.txt file included with this software for license information.
use strict;
my ($taxonomy) = @ARGV;
my %data;
# load scientific names for each tax ID
open NAMES, "<$taxonomy/names.dmp" or die "Couldn't open names.dmp";
while ( my $line = <NAMES> )
{
my ($id, $name, $uniqueName, $class) = split /\t\|\t/, $line;
if ( $class =~ /scientific name/ )
{
if ( ! defined $data{$id} )
{
$data{$id} = ();
}
$data{$id}->{'name'} = $name;
}
}
close NAMES;
# load parents and ranks for each tax ID
open NODES, "<$taxonomy/nodes.dmp" or die "Couldn't open nodes.dmp";
while ( my $line = <NODES> )
{
$line =~ /(\d+)\t\|\t(\d+)\t\|\t([^\t]+)/;
my $id = $1;
if ( ! defined $data{$id} )
{
$data{$id} = ();
}
$data{$id}->{'parent'} = $2;
$data{$id}->{'rank'} = $3;
}
close NODES;
open OUT, ">$taxonomy/taxonomy.tab" or die "Couldn't write to taxonomy.tab";
foreach my $id ( sort {$a <=> $b} keys %data )
{
print OUT join "\t",
(
$id,
depth($id),
getParent($id),
$data{$id}->{'rank'},
$data{$id}->{'name'}
);
print OUT "\n";
}
close OUT;
sub depth
{
my ($id) = @_;
if ( $id == 1 )
{
return 0;
}
else
{
return depth(getParent($id)) + 1;
}
}
sub getParent
{
my ($id) = @_;
return $data{$id}->{'parent'};
}
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