If the total data size will sensibly -fit- in memory at the same time, then you can use a hash as you are doing now. Otherwise sort the files identically and write code that compares the two sorted files. Or ... put the data into an SQLite database file, which is a flat-file requiring no server at all, and use queries.

In reply to Re: renaming 1000's of FASTA files by Anonymous Monk
in thread renaming 1000's of FASTA files by garyboyd

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