Hey everyone, I am trying to rename a very large dataset, approx. 260,000. The script below, which as I am no perl expert is possibly quite amature, performs the required task but is slow. I was wondering if anyone had any sugestions on how to increase the performance of this script. The reason to rename one file like another is that they are matching FASTA and QUALITY files for genetic sequencing reactions and it is preferable if they have the same name but under different directories. The FASTA files were renamed using information contianed inside the file itself but this is not possible with the quality files. the usage of the script is  ./qual_renamer.pl fasta ./QUAL qual Any ideas on how to increase the performance would be appreciated. thanks, wayne 
#! /usr/bin/perl -w

use strict;
use Data::Dumper;

my $fasta_file = $ARGV[0];
my $directory = $ARGV[1];
my $qual_file = $ARGV[2];

sub make_file_hash
{
  my ($file) = @_;
  my %file_hash;

  open(FH, "< $file");
  while (my $line = <FH>) {
    chomp($line);
    my @parts = split(/\//,$line);
    my $name = $parts[3];
    if ($name =~ /(^.{3})([0-9]{4})(F|P|R)/) {
        my $key = $2 . "." . lc($3);
        $file_hash{$key} = $name;
    }
    elsif ($name =~ /(^.{2})([0-9]{8})(F|P|R)/) {
        my $key = $2 . "." . lc($3);
        $file_hash{$key} = $name;
    }
    else {
      print $name . " is crap\n";
    }
  }
  return %file_hash;
}

sub rename
{
  my ($file, $hash_ref, $dir) = @_;
  my %hash = %$hash_ref;
  #print Dumper(%hash);
  if ($file =~ /([0-9]{4,8})(.f|r|p)(.*)/) {
    my $key = $1 . $2;
    if (exists $hash{$key}) {
      my $filename = $hash{$key};
      `mv $file $dir/$filename`;
    }
    else {
      print "no key $key\n";
    }
  }
}

my %tmp_hash = &make_file_hash($fasta_file);

open(FH2, "< $qual_file");
while( my $file = <FH2>) {
  chomp($file);
  &rename($file, \%tmp_hash, $directory)
}

[download]
./FASTA/LO-leaves_drought/LO45829460F
./FASTA/LO-leaves_drought/LO45815650F
./FASTA/LO-leaves_drought/LO45852136R
./FASTA/LO-leaves_drought/LO45987989F
./FASTA/LO-leaves_drought/LO45959830F
./FASTA/LO-leaves_drought/LO45982398F
./FASTA/LO-leaves_drought/LO45990585F
./FASTA/LO-leaves_drought/LO46021000F
./FASTA/LO-leaves_drought/LO45815528R
./FASTA/LO-leaves_drought/LO45994910F
./FASTA/LO-leaves_drought/LO45925816F
./FASTA/LO-leaves_drought/LO45938935F
./FASTA/LO-leaves_drought/LO45782339F
./FASTA/LO-leaves_drought/LO46006257F
./FASTA/LO-leaves_drought/LO46018733F
./FASTA/LO-leaves_drought/LO45815795F
./FASTA/LO-leaves_drought/LO46006601F
./FASTA/LO-leaves_drought/LO45893249F
./FASTA/LO-leaves_drought/LO45953120F
./FASTA/LO-leaves_drought/LO46053350F
./FASTA/LO-leaves_drought/LO45978413F
./FASTA/LO-leaves_drought/LO45866607F
./FASTA/LO-leaves_drought/LO46017397F

[download]
./QUAL/48743192.f_a09_1.fasta.qual
./QUAL/51455741.f_b20_1.fasta.qual
./QUAL/42595949.f_n02_1.fasta.qual
./QUAL/51293480.f_g04_2.fasta.qual
./QUAL/42188856.f_h02_2.fasta.qual
./QUAL/51477163.f_m12_2.fasta.qual
./QUAL/42219670.f_d02_1.fasta.qual
./QUAL/46911125.f_p06_1.fasta.qual
./QUAL/44656731.f_c24_1.fasta.qual
./QUAL/BNP3104.p.scf.qual
./QUAL/42063951.f_p22_1.fasta.qual
./QUAL/42939137.f_j20_1.fasta.qual
./QUAL/42824374.f_k16_2.fasta.qual
./QUAL/49426321.f_h08_2.fasta.qual
./QUAL/48869367.r_k07_2.fasta.qual
./QUAL/48637192.f_h15_1.fasta.qual
./QUAL/45574303.f_d17_1.fasta.qual
./QUAL/46189823.f_n05_2.fasta.qual
./QUAL/BNP0977.p.scf.qual
./QUAL/49408758.f_i10_1.fasta.qual
./QUAL/50040300.f_a20_1.fasta.qual
./QUAL/48690145.f_l05_2.fasta.qual
./QUAL/46242796.f_g23_1.fasta.qual

[download]

In reply to performance problems with renaming multiple files using another file name by mav3067

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