[zwc2101|login2] ~/TALL/ref/HomoloGene $ head homologene.data 
3	9606	34	ACADM	187960098	NP_001120800.1
3	9598	469356	ACADM	114557331	XP_524741.2
3	9615	490207	ACADM	73960161	XP_547328.2
3	9913	505968	ACADM	115497690	NP_001068703.1
3	10090	11364	Acadm	6680618	NP_031408.1
3	10116	24158	Acadm	8392833	NP_058682.1
3	7955	406283	acadm	47085823	NP_998254.1
3	7227	38864	CG12262	24660351	NP_648149.1
3	7165	1276346	AgaP_AGAP005662	58387602	XP_315683.2
3	6239	181757	acdh-10	17569725	NP_510788.1


##</code><code>##

 #!/usr/bin/perl -w
use strict;
open (FILEHANDLE,"$ARGV[0]") || die("Could not open OnlyNormal file");
   my @homo = <FILEHANDLE> ;
 close (FILEHANDLE);
   
 open (FILEHANDLE, "$ARGV[1]") || die("Could not open input file");
    my @file = <FILEHANDLE> ;
 close (FILEHANDLE);   
     foreach my $line (@homo)
     {
        chomp $line;
        (my $GroupID)=split(/\t/,$line);
        foreach my $Gene(@file)
        {
              chomp $Gene;
              if ($line =~m/\t$Gene\t/ && $line =~m/9606/) #Human Gene name and Human Taxid
                    {
                     foreach my $LINE(@homo)
                        {
                           (my @drosophila)=split(/\t/,$LINE);
                           if ($LINE =~m/^$GroupID\t/ && $line =~m/7227/) # Gene group ID and Drosophila Tax ID
                               {
                                 print $Gene . "\t". $drosophila[3] . "\n"; # [3] is the Drosophila Gene name at the group ID determined above
                               }
                        
                        }
                    }
         }
     }