Load the values of your first file into a hash rather than an array, lookup will be easier and performance much faster.
Then read the second file and check if the values can be found in the hash.
Provide some sample data if you need more help.
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So here is an example of some of may data:
GLU 66 PRO 436 9.116044197 Blank Asterisk
GLU 67 ASN 427 9.34269896 Asterisk Asterisk
What I would like it to do is if column 2 matches a number in the hash (or array), and the value in column 4 is within a given range of numbers, and column 7 matches a search phrase such as "Asterisk" it would print the entire matching line to a new file, and then for it to continue searching until the end of the document.
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