Well you're doing a lot of work, searching though a large array for each entry in another large array.

but there are a few things you can try.

You don't need to extract the positions unless it's a line your interested in, so swap the order of those tests :-

foreach $line (@data) {
    if ( $line =~ /$one/  && $line =~ /$two/ ) {
        if ( $line =~ /(.*?)\s+(.*?)\s+(.*?)\s+(.*)+/ ) {
            $chr  = $1;
            $pos1 = $2;
            $pos2 = $3;
        }
     ...
    }
}

[download]

Try using index instead of a regex to match $one & $two, it's usually quicker.

if (index($line,$one) != -1 && index($line,$two) != -1) {
...
}

[download]

Profile your code to find out where the time is going, and measure the difference each change makes.

In reply to Re: how to speed up pattern match between two files by RichardK
in thread how to speed up pattern match between two files by Anonymous Monk

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