Shell Programming and Scripting

Hello,

I have a very large file for which I would like to remove all rows for which the value of columns 2-5 is zero.

For instance I would like this file:

Code:

contig1, 0, 0, 0, 0 
contig2, 1, 3, 5, 0 
contig3, 0, 0, 0, 0 
contig4, 0, 5, 6, 7

To become this file:

Code:

contig2, 1, 3, 5,0 
contig4, 0, 5, 6, 7

I'm aware that you can use 'Awk' to remove rows for which a particular column has a specific value, but I can't seem to figure out how to remove a row if multiple columns have to have a particular value (i.e zero).

Thanks!

Moderator's Comments:

Please use code tags when posting data and code samples!

Code:

 
awk -F, '!($2==0 && $3==0 && $4==0 && $5==0)' infile

Code:

awk '{n=0;for(i=2;i<=5;i++) if ($i+0!=0) n++}n' FS=',' myFile

When I run this script (from rdrtx1), it seems to have taken out all of the rows that have any zeros and not just rows for which all four columns have zeros. Also, is there a way to print the data following row removal into a new file?

just redirect the output to a new file....

When I run this script nothing seems to happen? Is the output being directed somewhere? Sorry for my ignorance.

you should see the output on your screen like so:

Code:

$ awk '{n=0;for(i=2;i<=5;i++) if ($i+0!=0) n++}n' FS=, myFile
contig2, 1, 3, 5, 0
contig4, 0, 5, 6, 7

(assuming myFile is the name of a file you're trying to parse)