In the above code, you are limited to the length of the shortest file. Instead, you can read each line separately into a hash with the key being the line number. You can do a single pass comparison for the same key in each hash.

Example: 
# read in file one and place into a hash
my $line_number = 1;
while ( <$infile1> ) {
    chomp;
    $hash1{$line_number} = $_;
    $line_number++;
}
# read in file 2 and place in a hash
$line_number = 1;
while (<$infile2>) {
    chomp;
    $hash2{$line_number) = $_;
    $line_number++;
}
# determine the file with the largest number of keys
my @keys1 = keys %hash1;
my @keys2 = keys %hash2;
my $NoK1 = @keys1;
my $NoK2  @keys2;
 
if ($NoK1 > $NoK2) {
    for $key (sort {$a <=> $b} keys %hash1) {
        if (!defined $hash2{$key}) {
            next;
        }
        elsif ($hash1{$key} eq $hash2{$key}) {
            #do nothing?
            next;
        }
        else {
            print "Line number $key in both files is different";
        }
    }
    # the rest of the code you can figure out from here
    ...

[download]
Hope that helps!

Bioinformatics

In reply to Re: Reading concurrently two files with different number of lines by bioinformatics
in thread Reading concurrently two files with different number of lines by frogsausage

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