Help with awk

[Vanisha]

Hi guys

My knowledge on shell linux/unix is pretty basic. I need some help with a command I don't think is working, it may be something simple, which I find is usually the case with informatics!

One line of my dataset looks like this:

"exonic","GPR153","synonymous SNV","NM_207370:c.A144G.T48T",,,0.68,0.81,0.60,rs11590458,,1,6237409,6237409,T,C,"het","204","49","60"

i want to pull out those lines which have values in columns 7, 8 and 9 (in this case the values in this line are 0.68,0.81,0.60,)

Is there a simple way of doing this using awk?

I initially tried matching those lines with no values in those columns with this command:

awk '{ if ($7=="" && $8=="" && $9=="" && $10=="") print $0'} | wc -l

but it doesn't work

Any advice is appreciated!

Cheers

[essvee]

There is a fairly simple way, you were on the right track.

try:

awk '{print $7,$8,$9}' FS="," < (filename)

and then you can redirect the stdout to a new file
Hopefully this helps!

[pj_oz]

You can also set the field separator within the awk code using 'BEGIN{FS=",";}' which can be helpful. Also, if you're checking for the presence of values, make sure to use !="" which checks that a value is not empty

awk 'BEGIN{FS=",";}{ if ($7!="" && $8!="" && $9!=""){print $0}}' input_filename > output_filename

Hope this helps!

[Vanisha]

That works, thanks guys!

[steven]

I'd have done this:
awk -F"," '$7 && $8 && $9' input > output

If only the condition is specified, the default action is already "print $0". Also, "$N" as a condition should only return FALSE if the column is empty (but will be TRUE even for a 0 or a space).

[husamia]

try
cut -f 7-9 inputfile > outputfile

where 7-9 means cut columns 7 8 and 9
if you want everything except those columns then use something like --complement

[steven]

try
cut -f 7-9 inputfile > outputfile

where 7-9 means cut columns 7 8 and 9
if you want everything except those columns then use something like --complement

I think vanisha wanted lines in output, not just columns ("i want to pull out those lines which have values in columns 7, 8 and 9").

[rahulvarma]

hi guys!
i am dealing with the problem where in single file 3 different columns are there.

eg:
1 7 -0.2567
2 8 -0.4321
2 10 -0.4560
3 12 -0.2210
4 12 -0.3243
5 11 -0.9870
5 15 -0.7860
6 16 -0.2345

description:whn (1) link with (7) its energy is [-0.2567]
same things follws

if u look at col 1
(2) is linked with (8) &(10) of column two and gives respective energy( -0.4321)& (-0.4560) .in those cases i would prefer the least energy say (-0.4321)

same case whn we look into coumn 2 value (12) two option exist like 3 (-0.2210) &
4( -0.3243).i would prefer least one as mention early (-0.2210)


so finally the result should something like below:

1 7 -0.2567
2 8 -0.4321
3 12 -0.2210
5 15 -0.7860
6 16 -0.2345

can any one hlep me to get this...
thanks in advance....

[pj_oz]

Hi rahulvarma,

Looking at your question, while it could be achieved by scripting in awk it is a more complex question than just pulling lines with a value in certain columns. You would need to script it according to the parameters you've set. Something like the following nearly works in awk, it currently gives the wrong results but it might give you a start in resolving your problem.

#!/usr/bin/awk
BEGIN{
        lastnumber1=0;
        lastnumber2=0
        energy=0;
        toprint=0;
        alreadydone=0;
}

{
        if (lastnumber1==$1) {
                if ($3>energy and lastnumber1 != 0) {
                        toprint = $0;
                }
        } else if (lastnumber2 == $2) {
                if ($3>energy and lastnumber2 != 0) {
                        toprint = $0;
                }
        } else {
                if (toprint != 0) {
                        print toprint;
                } else {
                        print lastline;
                }
                toprint = 0;
        }

        lastnumber1 = $1;
        lastnumber2 = $2;
        energy = $3;
        lastline = $0;
}

On your test set it gives the results:
1 7 -0.2567
2 10 -0.4560
4 12 -0.3243
5 15 -0.7860

Good luck!

[rahulvarma]

hi pj_oz,
thank you soo much for your effort.
appreciate your work.