If you have two plain text files where one file looks like this:

key1
key3
key4
key6
...
[download]

and the other file looks like this:

key2
key3
key4
key5
...
[download]

then you might try downloading this script that I posted here under "Code/Utilities". To find the keys that are common to both files, the command line is:

cmpcol -i file1 file2
[download]

To find the union:

cmpcol -u file1 file2
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To find the keys that are unique to file1 (or file2):

cmpcol -x1 file1 file2  # what's uniq to file1
cmpcol -x2 file1 file2  # what's uniq to file2
cmpcol -x  file1 file2  # all uniq items, tagged by source -- i.e.:
key1 <1
key2 <2
key5 <2
key6 <1
[download]

It also handles multi-column data (use "file1:4" to use column 4 of file1 as the key field in that file), and supports perl regex field delimiters (e.g. -d '[\s:;,.]+' to split each line of each file at any combination of whitespace and/or punctuation).

It has more bells and whistles... I hope it helps.