in reply to comparing two fasta files

basic approach (in "pseudocode"):
open the first file (the one with 1000-something names) while reading one record at a time save the "name" part of the line is as a "hash key" open the second file while reading one record at a time check for the "name" portion (e.g. use a regular expression to "capture" the name) if the name exists as a key in the hash, print this record
That's it. You just need to work out how to read a record at a time, how identify and capture the "name" part of each record using a regex, and how to use a hash. The resources cited in the first reply will be helpful.

Try it out, and if you have trouble with code you've tried, show us the code. You'll learn more that way.

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Re^2: comparing two fasta files
by nemo2 (Initiate) on Jul 29, 2008 at 08:10 UTC
    thanks a lot for your time and help. many thanks!!!