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I have a csv file with the following headers - Interaction_ID, PDB_ID, First_Residue, First_Chain, Second_Residue, Third_Residue, Third_Chain & Pattern:

AM_AUTO_1,1cx0,A166,B,C118,B,G129,B,A-minor Type I ACG                            
AM_AUTO_2,1cx0,A165,B,C119,B,G128,B,A-minor Type II ACG                           
AM_AUTO_3,1cx0,A166,B,C119,B,G128,B,A-minor Type II ACG                           
AM_AUTO_4,1ddy,A25,A,C21,A,G8,A,A-minor Type I ACG                            
AM_AUTO_5,1e7k,A33,C,C28,C,G45,C,A-minor Type 0 AGC                            
AM_AUTO_6,1e7k,A33,D,C28,D,G45,D,A-minor Type 0 AAU

What I would like to do is delete rows in the csv file where Pattern = %Type 0% and then print the resulting csv file. The result should be like this:

AM_AUTO_1,1cx0,A166,B,C118,B,G129,B,A-minor Type I ACG                            
AM_AUTO_2,1cx0,A165,B,C119,B,G128,B,A-minor Type II ACG                           
AM_AUTO_3,1cx0,A166,B,C119,B,G128,B,A-minor Type II ACG                           
AM_AUTO_4,1ddy,A25,A,C21,A,G8,A,A-minor Type I ACG

How I can do this using awk?

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2 Answers 2

up vote 1 down vote accepted

With awk, you can do:

$ awk '$(NF-1)!=0' file
AM_AUTO_1,1cx0,A166,B,C118,B,G129,B,A-minor Type I ACG
AM_AUTO_2,1cx0,A165,B,C119,B,G128,B,A-minor Type II ACG
AM_AUTO_3,1cx0,A166,B,C119,B,G128,B,A-minor Type II ACG
AM_AUTO_4,1ddy,A25,A,C21,A,G8,A,A-minor Type I ACG

or using grep:

grep -v 'Type 0' file
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Just what I wanted. Thank you very much! –  Sri 23 hours ago
up vote 1 down vote

Using awk:

awk -F, '$9!~/Type 0/{print $0}' file
AM_AUTO_1,1cx0,A166,B,C118,B,G129,B,A-minor Type I ACG
AM_AUTO_2,1cx0,A165,B,C119,B,G128,B,A-minor Type II ACG
AM_AUTO_3,1cx0,A166,B,C119,B,G128,B,A-minor Type II ACG
AM_AUTO_4,1ddy,A25,A,C21,A,G8,A,A-minor Type I ACG

Explanation:

This causes awk to use , as delimiter (-F,). If the 9th field doesn't contain "Type 0" ($9!~/Type 0/), print the line ({print $0}).

And a sed solution:

sed '/,[^,]*Type 0[^,]*$/d' file
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