perl : load perl

-nE : 

$1 stands for : ([^\(]+) for example Metan1_4283 in Metan1_4283(Metac1_3189)

$2 stands for : \n((.*)\) for example (Metac1_3189) in Metan1_4283(Metac1_3189)

$1 ne $2 : Means if first pattern does not match second pattern.

++ $seen{$2} : 

< 2 : less than 2.

say "$1 : $2"' : prints out into two columns.

raw_data.txt : path to file goes here.