Hello Monks, may I request your consummate wisdom on a wee question I have?

I have a hash, where the key is a unique ID tag and the value is the genetic data for the gene corresponding to that ID. In the kinds of analyses I do I am generally dealing with relatively large hashes, maybe ~15000 key/value pairs kinda thing. I want to extract the sequence information for a given subset of genes for which I have the ID's stored in an array. I can do it with the following code, which works pretty well (it uses a bit of BioPerl...):

#!/usr/bin/perl

use strict;
use warnings;
use Bio::Seq;
use Bio::SeqIO;

my $uniqueFile = $ARGV[0];
my $goodProteinsFile = $ARGV[1];

## imports a bunch of gene IDs 
open (FILE, $uniqueFile);
my @data_in = <FILE>;
close FILE;

## create lookup hash; key = ID, val = sequence
my %goodProteins_hash;
my $in = Bio::SeqIO->new(-file=>$goodProteinsFile, -format=>'Fasta');
while (my $seq = $in -> next_seq() ) {
  my $id = $seq -> display_id();
  my $seq_string = $seq -> seq();
  $goodProteins_hash{$id} = $seq_string;
}

my $file_out = "strainSpecific_seqData.protein.fasta";

## iterate thru @data_in; if $id eq $_ then get at the value in 
## %goodProteins hash and store it in %strSpec... takes a while!
my %strSpec;
foreach (@data_in) {  
  chomp ($_);
  while (my ($id, $seq) = each %goodProteins_hash) {  
    if ($_ =~ /($id)$/) {  
      $strSpec_protein_hash{$id} = $seq;
    }
  }   
}

open (OUT, ">strainSpecific_seqData.protein.fasta");
while (my ($k, $v) = each %strSpec) {  ## print to file
  print OUT "\>$k\n$v\n";
}    
close OUT;
print "- Finished\n";

[download]

So I am getting to the sequence data for the IDs I want by looping through the '@data_in' array, then using a 'while each' on the %goodProteins_hash followed by an if... Perhaps not surprisingly this takes quite a long time per input ID, and if I want to get out a lot of sequences it takes ages!

So my question is: is there a quicker and more efficient way of doing something like this?? I tried playing around with grep and exists etc but I couldn't get it to do what I wanted...

Your responses, as always, are very much appreciated!

Thanks :-)

In reply to search and extract from a large hash by reubs85

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