http://www.perlmonks.org?node_id=377857
BioGeek has asked for the wisdom of the Perl Monks concerning the following question:

Hey All, I have 2 ArrayOfArrays, one with a gene name and its score, like this:
@gene_score = ( [ "gene_name_0", "score_0" ], [ "gene_name_1", "score_1" ], ... [ "gene_name_400", "score_400" ] );
and, one with a gene name and its start and stop positions on a chromosone:
@gene_start_stop_chr = ( [ "gene_name_0", "start_0", "stop_0", "chr_0" ], [ "gene_name_1", "start_1", "stop_1", "chr_1" ], ... [ "gene_name_30000", "start_30000", "stop_30000", "chr_30000 +" ] );
And of course I want to match the scores with the positions, using the gene names, so that I end with an array:
@results = ( [ "gene_name_0", "score_0", "start_0", "stop_0", "chr_0" ], [ "gene_name_1", "score_1", "start_1", "stop_1", "chr_1" ], ... [ "gene_name_400", "score_400", "start_400", "stop_400", "chr +_400" ], );
The code I've written so far is (@gene_start_stop_chr abbreviated till @gssc):
for (my $a = 0; $a < scalar @gene_score; $a++) { for (my $b = 0; $b < scalar @gssc; $b++) { if ("$gene_score[$a][0]" eq "$gssc[$b][0]") { print "$gene-score[$a][0]\t$gene_score[$a][1]\t$gssc[$ +b][1]\t$gssc[$b][2]\t$gssc[$b][3]\n"; } } }
Which works, but is very slow, as I am comparing each of the 400 gene names of my first array with every of the 30000 gene names in the second array. So I was wondering of there are changes I could make to speed things up.
Thanks in advance.