add_taxonomy_info.pl

#=============================================================================
#     FileName: add_taxonomy_info.pl
#         Desc: Add taxonomy information for a blast nt/nr table file.
#       Author: tanhao
#        Email: tanhao2013@gmail.com
#     HomePage: http://buttonwood.github.io
#      Version: 0.0.1
#   LastChange: 2013-05-05 11:35:12
#      History:
#=============================================================================

#! /usr/bin/perl -w
use strict;


die("Usage:\n\tperl $0 blast.table gi_colum\n")unless(@ARGV >= 1);

my $dir = `dirname $0`;
chop($dir);

my %gi_hash;
my %gi_tax_hash;
my %tax_name_hash;
my %node_hash;

my $blast_result    = "$ARGV[0]";
my $gi_tax          = "$dir/gi_taxid_nucl.dmp";
my $tax_name        = "$dir/names.dmp";
my $node            = "$dir/nodes.dmp";
my $gi_colum        = ($ARGV[1] - 1) || 1;
my $outfile         = $blast_result + ".info";


open (BL,"$blast_result") or die ("can not open $blast_result\n");
while(<BL>){
	chomp;
	my @line= split /\t/;
	$gi_hash{$1} = $2 if( $line[$gi_colum] =~ /gi\|(\d+)\|.+\|*(.+)\|/);
}
close BL;

if ($gi_tax=~/\.gz$/){
    open (GT,"gzip -dc $gi_tax |") or die ("can not open $gi_tax\n");
}else{
    open (GT,"$gi_tax ") or die ("can not open $gi_tax\n");
}
while(<GT>){
	chomp;
	my @line= split /\t/;
	$gi_tax_hash{$line[0]} = $line[1] if(exists $gi_hash{$line[0]});
}
close GT;

open (TN, "$tax_name");
while(<TN>){
	chomp;
	my @line= split /\t\|\t/;
	$line[3] =~ s/\t\|//g;
	$tax_name_hash{$line[0]} = $line[1] if($line[3] eq "scientific name");
}
close TN;

open (NOD,"$node");
while(<NOD>){
	chomp;
	my @line = split /\t\|\t/;
	$node_hash{$line[0]}= $line[1];
}
close NOD;

open (BL,"$blast_result");
open (NAM,">>$outfile");
while(<BL>){
	chomp;
	my @line = split /\t/;
	$line[$gi_colum] =~ /gi\|(\d+)\|.+\|*(.+)\|/;
	my $gi=$1; my $id= $2;
	my $tax= $gi_tax_hash{$gi};
	my $pretax= $node_hash{$tax};
	if(!$tax){$tax=0; $pretax=1;}
	my @alltax;
	push @alltax, $tax;
	while($pretax!=1){
		push @alltax, $pretax;
		$pretax= $node_hash{$pretax};
	}
	foreach my $ele (@line){ print NAM "$ele\t";} 
	foreach my $tele (@alltax){print NAM "$tax_name_hash{$tele}|";}
	print NAM "\n";
}
close BL;

taxnomy_nt.sh

wget -r ftp://ftp.ncbi.nih.gov/pub/taxonomy/

I've developed another version of fetching taxonomy id from gi which improved searching algorithm in Node.js.
https://github.com/shinout/gitax
Thanks for your idea and implementation.

@shinout You‘ve done a nice work!