in reply to Reading concurrently two files with different number of lines

If you don't want to read in the file, then you can use  or in your original code above. You'll need an if statement to catch when either of the two $lineX values is undefined, and make the comparison otherwise. The code can increase in complexity as you decide whether you want to see if things are offset in a file, rather than if the same lines have the same values.

Bioinformatics