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I am doing some sorting with uniq -d command. it's not getting me the desired results.

My file is like:

>TCONS_00000066 174     206  33
>TCONS_00000066 210     281  72
>TCONS_00000066 227     316  90
>TCONS_00000066 285     338  54
>TCONS_00000066 335     373  39
>TCONS_00000066 342     377  36
>TCONS_00006042 493     552  60
>TCONS_00006042 562     606  45
>TCONS_00006042 630     686  57
>TCONS_00006042 622     699  78
>TCONS_00006042 614     724  111
>TCONS_00006042 696     767  72

I want to remove duplicates in column 1

output:

     >TCONS_00000066
     >TCONS_00006042

but I get a blank file everytime I do

uniq -d file > newfile

is there any other way?

  • 1
    You want to remove duplicates, or output duplicates? Your Question says remove but your example shows output. – roaima Mar 18 '15 at 9:40
3

You can use awk:

awk '!x[$1]++ { print $1 }' file
3

uniq -d lists only duplicated lines from its input; since your file contains no duplicate lines (considered in their entirety), it outputs nothing.

To get the result you're after, you need to extract the first column, and filter that:

cut -d\  -f1 file | uniq

assuming your file is sorted (uniq only filters duplicate adjacent lines); otherwise

cut -d\  -f1 file | sort -u

Or you can do it with awk as pointed out by taliezin, with a slight variant to only output the first column:

awk '!x[$1]++ { print $1 }' file
3

Uniq doesn't sort and it doesn't strip the rest of the line. uniq -d only shows duplicated lines, which is not the same as showing each line once (i.e. with -d it has to be in there twice, and consecutively to be shown)

First cut the non-interesting columns, then sort and then find the unique elements:

cut -d ' ' -f 1 your_file | sort | uniq

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