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Top Forums Shell Programming and Scripting awk to remove lines in file if specific field matches Post 302969069 by cmccabe on Thursday 17th of March 2016 04:14:10 PM
Old 03-17-2016
awk to remove lines in file if specific field matches

I am trying to remove lines in the target.txt file if $5 before the - in that file matches sorted_list. I have tried grep and awk. Thank you Smilie.

grep
Code:
grep -v -F -f targets.bed sort_list

Code:
grep -vFf sort_list targets

awk
Code:
awk -F, '
>   FILENAME == ARGV[1] {to_remove[$1]=1; next}
>   ! ($5 in to_remove) {print}
> ' sort_list targets

example:
sorted_list
Code:
AGRN
ABL
SCN1A

file2
Code:
chr1    955543  955763  chr1:955543-955763  AGRN-6|gc=75
chr1    957571  957852  chr1:957571-957852  AGRN-7|gc=61.2
chr1    970621  970740  chr1:970621-970740  BCR-8|gc=57.1
chr1    976035  976270  chr1:976035-976270  BCR-9|gc=74.5

desired output (AGRN removed as it is in file1)
Code:
chr1    970621  970740  chr1:970621-970740  BCR-8|gc=57.1
chr1    976035  976270  chr1:976035-976270  BCR-9|gc=74.5


Last edited by cmccabe; 03-17-2016 at 05:19 PM.. Reason: added additional grep
 

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ZGREP(1)                                                      General Commands Manual                                                     ZGREP(1)

NAME
zgrep - search possibly compressed files for a regular expression SYNOPSIS
zgrep [ grep_options ] [ -e ] pattern filename... DESCRIPTION
Zgrep invokes grep on compressed or gzipped files. These grep options will cause zgrep to terminate with an error code: (-[drRzZ]|--di*|--exc*|--inc*|--rec*|--nu*). All other options specified are passed directly to grep. If no file is specified, then the standard input is decompressed if necessary and fed to grep. Otherwise the given files are uncompressed if necessary and fed to grep. If the GREP environment variable is set, zgrep uses it as the grep program to be invoked. EXIT CODE
2 - An option that is not supported was specified. AUTHOR
Charles Levert (charles@comm.polymtl.ca) SEE ALSO
grep(1), gzexe(1), gzip(1), zdiff(1), zforce(1), zmore(1), znew(1) ZGREP(1)
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