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i have two files, file1 have a column with ~600 row and file2 have ~20 columns and ~3000 row. i want to find patterns form file1 that are common in file2.

file1:

K00001 K00002 K00003 K00006 K00013 K00025 K00089

file2:

TRINITY_DN102283_c0_g1 KEGG:xtr:496432`KO:K16860 TRINITY_DN42420_c0_g1 KO:K01762 TRINITY_DN52581_c0_g1 KEGG:zma:732844`KO:K13523 TRINITY_DN36387_c0_g2 KEGG:zma:732811`KO:K00089 TRINITY_DN54650_c4_g1 KEGG:zma:542598`KO:K00025 TRINITY_DN93494_c0_g1 KEGG:zma:542598`KO:K00025 TRINITY_DN36051_c0_g1 KEGG:zma:542598`KO:K00025

i would like obtain a result like this:

K00025 K00089
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  • yes i want ti find common words Commented May 5, 2016 at 18:29

2 Answers 2

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comm -12 <(grep -oP '\w+' a|sort -u) <(grep -oP '\w+' b|sort -u)

where:

  • grep -oP '\w+' a|sort -u gets a sorted list o words in file a
  • the some for file b
  • comm -12 outputs common lines
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You can do this with the following snippet

grep -f file1 -o file2 | sort -u K00025 K00089
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