Grabbing only text/substring between 4th and 7th underscores in all lines of a file

Question

I have a list.txt which contains the following lines.

Primer_Adapter_clean_KL01_BOLD1_100_KL01_BOLD1_100_N701_S507_L001_merged.fasta
Primer_Adapt_clean_KL01_BOLD1_500_KL01_BOLD1_500_N704_S507_L001_merged.fasta
Primer_Adapt_clean_LD03_BOLD2_Sessile_LD03_BOLD2_Sessile_N710_S506_L001_merged.fasta

Now I would like to grab only the substring between the 4th underscore and 7th underscore such that it will appear as below

BOLD1_100_KL01
BOLD1_500_KL01
BOLD2_Sessile_LD03

I tried the below awk command but I guess I've got it wrong. Any help here would be appreciated. If this can be achieved via sed, I would be interested in that solution too.

awk -v FPAT="[^__]*" '$4=$7' list.txt

score 2 · Answer 1 · answered Jun 20 '20 at 01:13

2

I feel like awk is overkill for this. You can just use cut to select just the fields you want:

$ cut -d_ -f5-7 list.txt
BOLD1_100_KL01
BOLD1_500_KL01
BOLD2_Sessile_LD03

answered Jun 20 '20 at 01:13

Shawn

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score 0 · Accepted Answer · answered Jun 20 '20 at 00:02

0

awk 'BEGIN{FS=OFS="_"} {print $5,$6,$7}' file

Output:

BOLD1_100_KL01
BOLD1_500_KL01
BOLD2_Sessile_LD03

answered Jun 20 '20 at 00:02

Cyrus

84,225
14
89
153

Grabbing only text/substring between 4th and 7th underscores in all lines of a file

2 Answers2