A while loop always prints keys in the order they appear in the hash. To get the keys in the right order, you need a slightly different technique: (a) extract the keys (b) sort them (c) use a foreach loop to visit each key (d) for each key query the hash to get the value. The code to print out the hash would look something like this:

# keys %foo:  extracts the keys from hash %foo
#             and returns them as an array
#
# sort @foo:  sorts the elements of array @foo
#
# foreach:    loops through the 

my @aKeys = sort(keys(%hSequences));
foreach my $k (@aKeys) {
  my $v = $hSequences{$k};  #get value
  $k =~ s/ / gid=/;
  print ">$k\n" . join("\n", sort @$v) . "\n";
}
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For more information, see keys and sort.

I'm assuming the number of keys is a lot less than 2G and that you have enough memory to hold the keys and sort them. If not, there are some other things that can be done to sort a super large key list, but see first you can do without getting fancy.

Good luck and great work!

Best, beth

hi elisheva, thank u so much. my work is done. it took 10 seconds only to process a 300 MB file. i did some changes to modify the program according to the input file. i used a different technique to sort the sequence before seeing your last post.anyways, i still used the sorting the hash part for arranging the headers in the right order :)

#use local so that the setting doesn't interfere with
#other places you might want to read in data.
local $/='>';
open(DATA,"seq.txt") or die "cannot not open";
#load sequences
my %hSequences;
while (my $line = <DATA>) {
  chomp $line;
  next if $line eq '';
  
  #extract data from record
  #  -- s at end of regex needed so that . matches new lines
  my ($subs, $xon, $gid, $sSequences)
    = $line
      =~ /^(\d+)_(\d+)\s+gid(\d+)\s+\d+\s+\d+\s+len=\d+\s+(.*)$/;

  #populate hash
  my $sKey="$gid $subs";
  my $aSequences = $hSequences{$sKey};
  $hSequences{$sKey} = $aSequences = []
    unless defined($aSequences);
  push @$aSequences, split(/\s+/, $xon.$sSequences);
}

my @aKeys = sort(keys(%hSequences));
foreach my $k (@aKeys) {
  my $v = $hSequences{$k};  #get value
  $k =~ s/^/gid/;
  $single=join("", sort @$v);
  $single=~s/[0-9]//g;
  print ">$k\n" . $single . "\n";
}
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