#!/usr/bin/perl

use strict;
use Data::Dumper;

my %temp_record;

my $file_1 =<<FILE_1;
385#19126!NM_167210@[1103;1104]    2
386#19127!NM_167211@[1103;1104]    2
387#19128!NM_167212@[1103;1104]    2
438#1781!NM_135492@[1337]    1
442#1794!NM_001042886@[1349]    1
FILE_1

open( my $fh, '<', \$file_1 )
  or die( "Cannot open $file_1" );

while (<$fh>) {
    my ($key, $value) = /\!(\w+)\@\S.*\s+(\d)/;
    $temp_record{$key} = $value;
}

close( $fh );

my %record;
while (<DATA>) {
    my ($key, $value) = /(\S+)\s+(\S+)/;
    for my $i (keys %temp_record) {
        $record{$key} = $temp_record{$i} if ( $i eq $value );
    }
}

print Dumper \%record;

__DATA__
CG32694-RD    NM_167211
CG32694-RC    NM_167210
CG32694-RA    NM_167209
CG32694-RB    NM_167212
CG33557-RA    NM_001014730

##</code><code>##

$VAR1 = {
          'CG32694-RD' => '2',
          'CG32694-RB' => '2',
          'CG32694-RC' => '2'
        };