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Top Forums Shell Programming and Scripting Count of unique lines in field 4 Post 302960172 by cmccabe on Wednesday 11th of November 2015 05:42:20 PM
Old 11-11-2015
Count of unique lines in field 4

When I use the below awk to count the unique lines in $4 for the input it seems to work. The answer is 3 because $4 is only unique 3 times in all the entries. However, when I use the same on actual data I get 56,536 and I know the answer should be 56,548. My question is there a better way to count the unique lines? Thank you Smilie.

input
Code:
chr1    955543    955763    chr1:955543-955763    AGRN-6|gc=75    1    20
chr1    955543    955763    chr1:955543-955763    AGRN-6|gc=75    2    20
chr1    955543    955763    chr1:955543-955763    AGRN-6|gc=75    3    22
chr1    955543    955763    chr1:955543-955763    AGRN-6|gc=75    4    22
chr1    955543    955763    chr1:955543-955763    AGRN-6|gc=75    5    22
chr1    957571    957852    chr1:957571-957852    AGRN-7|gc=61.2    1    186
chr1    957571    957852    chr1:957571-957852    AGRN-7|gc=61.2    2    201
chr1    957571    957852    chr1:957571-957852    AGRN-7|gc=61.2    3    201
chr1    957571    957852    chr1:957571-957852    AGRN-7|gc=61.2    271    176
chr1    957571    957852    chr1:957571-957852    AGRN-7|gc=61.2    272    175
chr1    957571    957852    chr1:957571-957852    AGRN-7|gc=61.2    273    175
chr1    957571    957852    chr1:957571-957852    AGRN-7|gc=61.2    274    175
chr1    970621    970740    chr1:970621-970740    AGRN-8|gc=57.1    46    280
chr1    970621    970740    chr1:970621-970740    AGRN-8|gc=57.1    47    280

 

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UNIQ(1) 								FSF								   UNIQ(1)

NAME
uniq - remove duplicate lines from a sorted file SYNOPSIS
uniq [OPTION]... [INPUT [OUTPUT]] DESCRIPTION
Discard all but one of successive identical lines from INPUT (or standard input), writing to OUTPUT (or standard output). Mandatory arguments to long options are mandatory for short options too. -c, --count prefix lines by the number of occurrences -d, --repeated only print duplicate lines -D, --all-repeated[=delimit-method] print all duplicate lines delimit-method={none(default),prepend,separate} Delimiting is done with blank lines. -f, --skip-fields=N avoid comparing the first N fields -i, --ignore-case ignore differences in case when comparing -s, --skip-chars=N avoid comparing the first N characters -u, --unique only print unique lines -w, --check-chars=N compare no more than N characters in lines --help display this help and exit --version output version information and exit A field is a run of whitespace, then non-whitespace characters. Fields are skipped before chars. AUTHOR
Written by Richard Stallman and David MacKenzie. REPORTING BUGS
Report bugs to <bug-coreutils@gnu.org>. COPYRIGHT
Copyright (C) 2002 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICU- LAR PURPOSE. SEE ALSO
The full documentation for uniq is maintained as a Texinfo manual. If the info and uniq programs are properly installed at your site, the command info uniq should give you access to the complete manual. uniq (coreutils) 4.5.3 February 2003 UNIQ(1)
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