You might like to read How do i extract only contigs of interest, from today. To quote choroba from that thread: 

Searching for information taken from one file in another file is quite
+ a common task. The usual solution is to hash the identifiers, then i
+terate over the second file and check the hash for the existence of t
+he identifier.

[download]

The way forward always starts with a minimal test.

In reply to Re^3: How to do a reciprocal matching statement by 1nickt
in thread How to do a reciprocal matching statement by ajl412860

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