Cut for variable delimiter - Bash

Question

I want to get the second column of a file where separator between column 1 and column 2 is of variable length. For example:

A1_KOG1494_________AAMFAARSFSERK
A2_KOG1494_______AAKFALRSFSERK
A3_KOG1494___________AAKFALRSFSCCK

Thank's for your help

@fedorqui That `tr` trick is not foolproof here. What if input string is: `A1KOG1494_______ABCD`? — anubhava, May 15 '14 at 10:46
@anubhava oh that's is different from what I understood. So column1 is everything up to "at least two __"? In that case, please reopen the question because I got it wrong. — fedorqui, May 15 '14 at 10:47
Wrong dupe closure. Here OP wants to find 2nd field when delimiter is 2 or more underscores. Neither the dupe target question or none of the answers address this. — anubhava, Jul 13 '21 at 20:05

score 8 · Accepted Answer · answered May 15 '14 at 10:24

You can use awk with custom field separator:

s='A1_KOG1494_________AAMFAARSFSERK'
awk -F '_{2,}' '{print $2}' <<< "$s"
AAMFAARSFSERK

awk -F '_' '{print $NF}' <<< "$s"
AAMFAARSFSERK

Another example:

awk -F '_{2,}' '{print $2}' <<< "A3_KOG1494___________AAKFALRSFSCCK"
AAKFALRSFSCCK

1 Answers1