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

[download]
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.

In reply to Re: comparing two fasta files by graff
in thread comparing two fasta files by nemo2

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