Fast alternative to grep -f

Question

file.contain.query.txt

ENST001

ENST002

ENST003

file.to.search.in.txt

ENST001  90

ENST002  80

ENST004  50

Answer 1

This may be a little dated, but is tailor-made for simple UNIX utilities. Given:

• keys are fixed-length (here 7 chars)
• files are sorted (true in the example) allowing the use of fast merge sort

Then:

$ sort -m file.contain.query.txt file.to.search.in.txt | tac | uniq -d -w7

ENST002  80

ENST001  90

Variants:

To strip the number printed after the key, remove tac command:

$ sort -m file.contain.query.txt file.to.search.in.txt | uniq -d -w7

To keep sorted order, add an extra tac command at the end:

$ sort -m file.contain.query.txt file.to.search.in.txt | tac | uniq -d -w7 | tac