I reversed the hash to get a unique list of the "numbers". Then opened that many files and put the file handles in another hash. This eliminates some of the "if" logic. Using different record separator does help, but a slight bit of fiddling is required.

update: See how different filehandles are used in the print below. Also if what reverse is unclear add a print Dumper(\%rhash); statement. 

#!/usr/bin/perl -w
use strict;
use Data::Dumper;


my %hash = (aw1 => 10, qs2 => 20, dd3 => 30,
            de4 => 10, hg5 => 30, dfd6 => 20,
            gf4 => 20, hgh5 => 30, hgy3 => 10);
            
my %rhash = reverse %hash;
my %fh;
foreach my $num (keys %rhash)
{
    open ($fh{"$num.txt"} , '>', "$num.txt") or die ;
}

$/ = '>';
while (<DATA>)
{
   my $tag = (m/^(\w+)/)[0];   #"blank" rec at beginning
   next unless defined $tag;
   s/>$//;

   my $filename = "$hash{$tag}.txt";
   my $handle = $fh{$filename};
   print $handle ">$_";   
}


__DATA__
>aw1
ATGCTAGATGCTAGCTAGCTAGCACTGAT
CGATGCTAGCGTAGTCAGCTGATGCTGTA
CGATGCTAGTCGTACG
>qs2
CGAGCTAGTCGTAGTCGTGATGCTGATTA
CGATGCTAGTCGTAGCTAGCTGATGCTGC
CGATGCTAGTCGTAGTC
>dd3
CGTAGTCGTAGTCGTAGTCGATGCTGATG
GCTAGTCGATGCTAGCTAGTCGATGCTGG
CGATGCTGAT
>de4
CGTAGTCGTAGTCGTACGTAGTCGTGAGT
CGATTATTTAGGAGGGACAAGGATAGTA
>hg5
CGTAGTCGTAGTCTAGTCGTGATGCTAGA
>dfd6
CGATGCTACGTACGTAGTCAGTCGTGATG
AATTAGAGCAGATAGAGGGGGAAAGGGTT
AAACCCC
>gf4
CGTAGTCAGTCTAGCTGATGTCGATGCTG
>hgh5
CATGCTAGTCGTAGTCGTAGTCGATGCTT
TTTTAAGGGAACCCCC
>hgy3
CCCCGGGTTTGGGAAAAGGGGGGGGATAG

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In reply to Re: Compare hash with arrays and print by Marshall
in thread Compare hash with arrays and print by ad23

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