Using a hash is probably a better way to do it. Something like this may be what you want:

use warnings;
use strict;

my %Ids;
open (IDS, "$ARGV[0]") or die "unable to open file $!\n";

while (<IDS>)
  {
  chomp;
  $Ids {$_} = undef;
  }
  
close IDS;

open (GENES, "$ARGV[1]") or die "unable to open file $!\n";
my @genes;
while (<GENES>)
  {
  if (/^>/)
    {
    unshift @genes, substr "$_ ", 1;
    }
  else
    {
    $genes[0] .= $_;
    }
  }
close GENES;

foreach my $gene (@genes)
  {
  my ($id) = $gene =~ /^(.*?)[,\s]/g;
  next if ! defined $id;
  ++$Ids{$id};
  }
  
foreach (sort keys %Ids)
  {
  print "$_\n" if defined $Ids{$_};
  }

[download]

Assumes sample data given in original node.

dbj|BA000040|:2701685-2702539
gi|11995001:156374-156649

[download]
Perl is Huffman encoded by design.

In reply to Re: pattern matching and array comparison by GrandFather
in thread pattern matching and array comparison by Anonymous Monk

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