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[SOLVED] remove lines that have duplicate values in column two

 
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Top Forums UNIX for Dummies Questions & Answers [SOLVED] remove lines that have duplicate values in column two
# 1  
Old 09-26-2012
[SOLVED] remove lines that have duplicate values in column two
Hi, I've got a file that I'd like to uniquely sort based on column 2 (values in column 2 begin with "comp").

I tried
Code:
sort -t -nuk2,3 file.txt

But got:
sort: multi-character tab `-nuk2,3'

"man sort" did not help me out

Any pointers?

Input:
Quote:
gi|328725975|ref|XP_003248692.1| comp47911_c0_seq1 82.02 367 66 0 1 367 78 1178 0 603
gi|328718720|ref|XP_001946259.2| comp110820_c0_seq1 46.85 111 59 0 422 532 2 334 1.00E-31 120
gi|193617875|ref|XP_001945312.1| comp110820_c0_seq1 45.13 113 62 0 535 647 2 340 7.00E-31 119
gi|328698003|ref|XP_001947254.2| comp1227639_c0_seq1 89.36 141 15 0 3 143 3 425 5.00E-82 247
gi|328725151|ref|XP_001951585.2| comp142443_c0_seq1 53.33 75 32 2 49 122 240 22 1.00E-16 73.2
gi|328725427|ref|XP_001948141.2| comp143768_c0_seq1 89.49 257 25 1 1 257 147 911 3.00E-171 483
gi|328717989|ref|XP_003246356.1| comp143768_c0_seq1 91.42 303 26 0 132 434 3 911 0 587
gi|328712467|ref|XP_001948906.2| comp143768_c0_seq1 69.81 308 87 3 69 375 3 911 1.00E-153 443
gi|328698003|ref|XP_001947254.2| comp143768_c0_seq1 94.12 102 6 0 147 248 3 308 1.00E-62 203
Output:
Quote:
gi|328725975|ref|XP_003248692.1| comp47911_c0_seq1 82.02 367 66 0 1 367 78 1178 0 603
gi|328718720|ref|XP_001946259.2| comp110820_c0_seq1 46.85 111 59 0 422 532 2 334 1.00E-31 120
gi|328698003|ref|XP_001947254.2| comp1227639_c0_seq1 89.36 141 15 0 3 143 3 425 5.00E-82 247
gi|328725151|ref|XP_001951585.2| comp142443_c0_seq1 53.33 75 32 2 49 122 240 22 1.00E-16 73.2
gi|328725427|ref|XP_001948141.2| comp143768_c0_seq1 89.49 257 25 1 1 257 147 911 3.00E-171 483
# 2  
Old 09-26-2012
try this

Code:
awk '!x[$2]++' file

Last edited by pamu; 09-26-2012 at 01:44 PM.. Reason: missed +
# 3  
Old 09-26-2012
I'm not sure sort can reject non-unique lines like that. But you forgot to actually tell sort which character you wanted to sort by after -t there.

Since it appears to be a single space, you don't need -t anyway.

This will use awk to reject duplicates before sorting.
Code:
awk '!($2 in X) { X[$2]++; print }' inputfile | sort -k 2,3

This User Gave Thanks to Corona688 For This Post:
pathunkathunk
# 4  
Old 09-26-2012
Pamu thanks for taking a look at this, but your suggestion did not work, it did not seem to affect the file.

Corona688, your solution worked. Thanks!
# 5  
Old 09-26-2012
pamu's solution looks like my solution in brief. I think he fixed a typo after you saw it.
# 6  
Old 09-26-2012
Quote:
Originally Posted by Corona688
pamu's solution looks like my solution in brief. I think he fixed a typo after you saw it.
Just missed ++...Smilie

Now corrected...Smilie
 
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