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copied!<ol> <li><p>Avoid naked handles when possible; use $fh (filehandle) instead of FH</p></li> <li><p>You can use until instead of unless, and skip the redo:</p> <pre><code>print "Enter the file name\n"; my $file_a = <STDIN>; chomp $file_a; my $fh_a; until(open $fh_a, '<', $file_a) { print "Re-enter the file name or 'n' to cancel\n"; $file_a = <STDIN>; chomp $file_a; if($file_a eq 'n') { exit; } } </code></pre></li> <li><p>You can (should) use an array instead of all those individual column variables: <code>my @cols_a = split /\t/, $line;</code></p></li> <li><p>You should read file B into an array, once, and then search that array each time you need to: <code>my @file_b = <$fh_b>;</code></p></li> <li><p>The result will look something like this:</p> <pre><code>#Assume we have opened both files already . . . my @file_b = <$fh_b>; chomp @file_b; while(my $line = <$fh_a>) { chomp $line; my @cols_a = split /\t/, $line; #Remember, most arrays (perl included) are zero-indexed, #so $cols_a[1] is actually the SECOND column. my $range = ($cols_a[1] + length $cols_a[3]); foreach my $line_b (@file_b) { #This loop will run once for every single line of file A. #Not efficient, but it will work. #There are, of course, lots of optimisations you can make #(starting with, for example, storing file B as an array of array #references so you don't have to split each line every time) my @cols_b = split /\t/, $line_b; if($cols_b[3] > $cols_a[2] && $cols_b[3] < ($cols_a[2] + $range)) { #Do whatever here } } } </code></pre></li> </ol>

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