CODEWITHSUNDEEP
bashawkgrep
Nicholas Smith
Nicholas Smith

Reputation: 3

How to grep a pattern followed by a number, only if the number is above a certain value

I actually need to grep the entire line. I have a file with a bunch of lines that look like this

1  123213 A T . stuff=1.232;otherstuf=34;morestuff=121;AF=0.44;laststuff=AV
4  223152 D L . stuff=1.122;otherstuf=4;morestuff=41;AF=0.02;laststuff=RV

and I want to keep all the lines where AF>0.1. So for the lines above I only want to keep the first line.

Upvotes: 0

Views: 334

Answers (5)

Ed Morton
Ed Morton

Reputation: 203324

$ awk -F= '$5>0.1' file
1  123213 A T . stuff=1.232;otherstuf=34;morestuff=121;AF=0.44;laststuff=AV

If that doesn't do what you want when run against your real data then edit your question to provide more truly representative sample input/output.

Upvotes: 1

anubhava
anubhava

Reputation: 785058

Using gnu-awk you can do this:

awk 'gensub(/.*;AF=([^;]+).*/, "\\1", "1", $NF)+0 > 0.1' file

1  123213 A T . stuff=1.232;otherstuf=34;morestuff=121;AF=0.44;laststuff=AV

This gensub function parses out AF=<number> from last field of the input and captures number in captured group #1 which is used for comparison with 0.1.

PS: +0 will convert parsed field to a number.

Upvotes: 2

Zlemini
Zlemini

Reputation: 4963

You could use awk with multiple delimeters to extract the value and compare it:

$ awk -F';|=' '$8 > 0.1' file

Upvotes: 1

hek2mgl
hek2mgl

Reputation: 157967

I would use awk. Since awk supports alphanumerical comparisons you can simply use this:

awk -F';' '$(NF-1) > "AF=0.1"' file.txt

-F';' splits the line into fields by ;. $(NF-1) address the second last field in the line. (NF is the number of fields)

Upvotes: 0

dimo414
dimo414

Reputation: 48804

Assuming that AF is always of the form 0.NN you can simply match values where the tens place is 1-9, e.g.:

grep ';AF=0.[1-9][0-9];' your_file.csv

You could add a + after the second character group to support additional digits (i.e. 0.NNNNN) but if the values could be outside the range [0, 1) you shouldn't try to match the field with regular expressions.

Upvotes: 1

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