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# 1  
Old 11-15-2018
awk and seen to report duplicates
I have this file:
Code:
@Muestra-1
agctgcgagctgcgacccgggttatataggaagagacacacacaccccc
+
!@$#%^&*()@^#&HH!&*(@&#*(FT^%$&*()*&^%@
@Muestra-2
agctgcgagctgcgacccgggttatataggaagagacacacacaccccc
+
!@$#%^&*()@^#&HH!&*(@&#*(FT^%$&*()*&^%@
@Muestra-3
agctgcgagctgcgacccgggttatataggaagagacacacacaccccc
+
!@$#%^&*()@^#&HH!&*(@&#*(FT^%$&*()*&^%@
@Muestra-4
agctgcgagctgcgacccgggttatataggaagagacacacacaccccc
+
!@$#%^&*()@^#&HH!&*(@&#*(FT^%$&*()*&^%@
@Muestra-5
agctgcgagctgcgacccgggttatataggaagagacacacacaccccc
+
!@$#%^&*()@^#&HH!&*(@&#*(FT^%$&*()*&^%@

And I would like to use this code to output the entries with identical nucleotide sequences (second line for every forth one). I thought did would do the job but obviously didnt:
Code:
awk 'BEGIN{ RS="^@"; FS="\n" } !x[$2]++ '

I am not quite sure what I am doing wrong here
Last edited by Xterra; 11-15-2018 at 01:58 PM..
# 2  
Old 11-15-2018
and what's the desired output based on your sample input?
Kind of hard to understand the explanation - maybe the output would help.
# 3  
Old 11-15-2018
Always four lines per record? Try
Code:
awk '{for (i=1; i<=3; i++) {getline X; $0 = $0 "\n" X}} !x[$2]++' file
@Muestra-1
agctgcgagctgcgacccgggttatataggaagagacacacacaccccc
+
 !@$#%^&*()@^#&HH!&*(@&#*(FT^%$&*()*&^%@




Or adapt your code like
Code:
awk 'BEGIN{ RS="\n@" } !x[$2]++ ' file

This User Gave Thanks to RudiC For This Post:
Xterra
# 4  
Old 11-15-2018
Rudy
Thanks a TON! Quick question, why BEGIN{ RS="^@"; FS="\n" } would not work?
# 5  
Old 11-15-2018
Can't tell. Although man awk says
Quote:
... mawk interprets RS as a regular expression ...
, it might be it doesn't like the caret for begin-of-line. When I modified your code snippet like in post#3, it seems to work.
This User Gave Thanks to RudiC For This Post:
Xterra
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