I have two large files (~250GB) that I am trying to remove the where GT: 0/0 or 1/1 or 2/2 for both files. I was going to use a bash with the below awk, which I think will find each line but how do I remove that line is that condition is found? Thank you .
Input
Code:
20 60055 . A . 35 PASS DP=25;PF=20;MF=5;MQ=60;SB=0.800 GT:AD:DP:GQ:FL 0/0:25:25:99:PASS
20 60056 . G A. 35 PASS DP=25;PF=20;MF=5;MQ=60;SB=0.800 GT:AD:DP:GQ:FL 0/1:12,13:25:99:PASS,PASS
20 60057 . T . 35 PASS DP=26;PF=20;MF=6;MQ=60;SB=0.769 GT:AD:DP:GQ:FL 0/0:26:26:99:PASS
20 60058 . C T 35 PASS DP=25;PF=20;MF=5;MQ=60;SB=0.800 GT:AD:DP:GQ:FL 1/1:25:25:99:PASS
Code:
awk '$9~"^[012]"{$0=$0($9~"^(0/0|1/1|2/2)"?" hom
":" het")}1' input
Desired output
Code:
20 60056 . G A. 35 PASS DP=25;PF=20;MF=5;MQ=60;SB=0.800 GT:AD:DP:GQ:FL 0/1:12,13:25:99:PASS,PASS
Last edited by RudiC; 07-01-2016 at 12:38 PM..
Reason: corrected icode tags.
hey guys, I have two files both with two columns, I have already created an
awk code to ignore certain lines (e.g lines that start with 963) as they wou
ld begin with a certain string, however, the rest I have added together and
calculated the average.
At the moment the code also displays... (3 Replies)
Hi,
I came to know that using awk '!x++' removes the duplicate lines. Can anyone please explain the above syntax. I want to understand how the above awk syntax removes the duplicates.
Thanks in advance,
sudvishw :confused: (7 Replies)
Hello again, I am wanting to remove all duplicate blocks of XML code in a file. This is an example:
input:
<string-array name="threeItems">
<item>item1</item>
<item>item2</item>
<item>item3</item>
</string-array>
<string-array name="twoItems">
<item>item1</item>
<item>item2</item>... (19 Replies)
Hi,
I have a file with contents.
file1:
<2013 tttaaa
abc123
<2013 gggdddd
<2013 sssssss
<2013 eeeee
I need to remove the lines which do not have the word "tttaaa"
can some one help ? (7 Replies)
I have two files, a keepout.txt and a database.csv. They're unsorted, but could be sorted.
keepout:
user1
buser3
anuser19
notheruser27
database:
user1,2343,"information about",field,blah,34
user2,4231,"mo info",etc,stuff,43
notheruser27,4344,"hiya",thing,more thing,423... (4 Replies)
Hi all,
I am trying to delete all lines from a file in which the value in 'column 3' is not the value of 'column 1' + 4. The code below that I tried doesn't work.
awk '$3 == $1 + 4 {print}' input > output
Example Input:-
1 xxx 2
3 xxx 26
4 xxx 8
2 xxx 9
7 xxx 11
(input file... (9 Replies)
I have been searching and trying to come up with an awk that will perform the following on a
converted text file (original is a pdf).
1. Since the first two lines are (begin with) text they are removed
2. if $1 is a number then all text is merged (combined) into one line until the next... (3 Replies)
Hi,
A beginner one.
my input.tab (tab-separated):
h1 h2 h3 h4 h5
item1 grpA 2 3 customer1
item2 grpB 4 6 customer1
item3 grpA 5 9 customer1
item4 grpA 0 0 customer2
item5 grpA 9 1 customer2
objective:
output a file for each customer ($5) with the item number ($1) only if $2 matches... (2 Replies)
Discussion started by: beca123456
2 Replies
LEARN ABOUT CENTOS
igawk
IGAWK(1) Utility Commands IGAWK(1)NAME
igawk - gawk with include files
SYNOPSIS
igawk [ all gawk options ] -f program-file [ -- ] file ...
igawk [ all gawk options ] [ -- ] program-text file ...
DESCRIPTION
Igawk is a simple shell script that adds the ability to have ``include files'' to gawk(1).
AWK programs for igawk are the same as for gawk, except that, in addition, you may have lines like
@include getopt.awk
in your program to include the file getopt.awk from either the current directory or one of the other directories in the search path.
OPTIONS
See gawk(1) for a full description of the AWK language and the options that gawk supports.
EXAMPLES
cat << EOF > test.awk
@include getopt.awk
BEGIN {
while (getopt(ARGC, ARGV, "am:q") != -1)
...
}
EOF
igawk -f test.awk
SEE ALSO gawk(1)
Effective AWK Programming, Edition 1.0, published by the Free Software Foundation, 1995.
AUTHOR
Arnold Robbins (arnold@skeeve.com).
Free Software Foundation Nov 3 1999 IGAWK(1)
07-01-2016
.