Y 39 1jpeA
Y 40 1jpeA
L 41 1jpeA
Y 42 1jpeA
R 43 1jpeA
K 44 1jpeA
Q 45 1jpeA
L 72 1gtiA
G 73 1gtiA
R 74 1gtiA
S 75 1gtiA
L 76 1gtiA
etc ...1jpe,0,TYR,A,42


##</code><code>##

1jpe,0,CYS,A,109
1jpe,0,CYS,A,103
1jpe,0,TYR,A,42
1jpe,0,ASP,A,68
1jpe,0,TYR,A,71
1jpe,0,PHE,A,70
etc ...

##</code><code>##

1jpeA 42

##</code><code>##

Y 42 1jpeA (from file 1)
1jpe,0,TYR,A,42 (from file 2)

##</code><code>##

#!/usr/local/bin/perl

use strict;
use warnings;

my $aa;
my $num;
my $str;
my $hashlookup;

my $pdb;
my $csanum;
my $chain;

my $resfile = shift;
my $csafile = shift;

my %hash;

open(RESFILE, "$resfile") or die "unable to open $resfile: $!\n";
open(CSAFILE, "$csafile") or die "unable to open $csafile: $!\n";

#my @resarray = <RESFILE>;

#close(RESFILE);

my @csaarray = <CSAFILE>;

close(CSAFILE);

#for (my $i = 0; $i < @resarray; $i++)
while(<RESFILE>)
{
    #my @array = split /\s+/, $resarray[$i];

    my @array = split /\s+/, $_;

    # lets do a test print

    $aa = $array[0];
    $num = $array[1];
    $str = $array[2];

    $str = substr($str, 0, 5);

    #print "test $str $num $aa\n";

    for (my $j = 0; $j < @csaarray; $j++)
   {
       my @fields = split /\,/, $csaarray[$j];
       
       $pdb = $fields[0];
       $csanum = $fields[4];
       $chain = $fields[3];
       
       #print "test2 $pdb $csanum $chain\n";
       
       
       my $pdbchain = "$pdb" . "$chain";
       
       if("$str" eq "$pdbchain")
       {
	   
	   if (!$hash{$str}{$csanum})
	   {
	       $hash{$str}{$csanum}++;
	       
	       print "$str $csanum\n";
	   }
	   
       }
       
   }
    
}