Thanks graff the code takes around :- 4115 wallclock secs (4112.37 usr + 0.28 sys = 4112.65 CPU) for running one methylome file that is similar to file2 in the above comments.

I have been programming for quite some time but I have mostly used cookbook solutions to make things work and that seem to have stunted my learning in perl or programming as a whole of solutions like indexing. What would be a good way to learn such tricks as indexing e.t.c. Thanks again for all your help

In reply to Re^4: Comparing and getting information from two large files and appending it in a new file by perlkhan77
in thread Comparing and getting information from two large files and appending it in a new file by perlkhan77

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