Hello mao9856,

Just to add some minor ideas here on the answer of the fellow monk toolic. I would also add a regex to skip the blank lines with next, where it seems to exist on your file(s) with data.

Also I would change the die statements of close file to warn. For me it is not necessary to stop the whole script in case a file can not close but I would like to know it, this is why I would use warn and not die.

I would also suggest mao9856 to read this article Don't Open Files in the old way.

Sample of code including output based on all the minor modifications:

#!/usr/bin/perl
use strict;
use warnings;

my (%patts, $f2_rec, $f2_field);
my $f1 = $ARGV[0];
my $f2 = $ARGV[1];

open(my $fh1,"<", $f1)
    or die "Failled to open '$f1' $!";

while (<$fh1>) {
    chomp;
    next if /^\s*$/;
    $patts{substr $_, 0, 3} = 1;
}

close($fh1)
    or warn "Failled to close '$f1' $!";

open(my $fh2,"<", $f2)
    or die "Failled to open '$f2' $!";

while (defined ($f2_rec = <$fh2>)) {
    chomp $f2_rec;
    next if $f2_rec =~ /^\s*$/;
    $f2_field = (split(/ /,$f2_rec))[1];
    $f2_field = substr $f2_field, 0, 3;
    if(exists($patts{$f2_field})) {
        print "$f2_rec\n";
    }
}

close($fh2)
    or warn "Failled to close '$f2' $!"; # update changing open to clo
+se thank to Laurent_R for pointing out

__END__

$ perl test.pl file1.txt file2.txt
ID121 ABC14
ID122 EFG87
ID145 XYZ43
ID157 TSR11
ID181 ABC31
ID529 EFG56
ID684 TSR07
[download]

Hope this helps, BR.

Update: Thanks to fellow monk Laurent_R for noticing a typo I have update the sample of code.