Is the file too big to slurp into an array? If not...something like the following from the Cookbook should work:
open(FILE,"peptides.txt");
@peptides=<FILE>;
%seen=();
@unique=grep{! $seen{$_} ++} @peptides;

[download]
Your unique peptides will now be in @unique
-Jason

In reply to Re: finding and deleting repeated lines in a file by insensate
in thread finding and deleting repeated lines in a file by Becky

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