UNIX for Dummies Questions & Answers

HI,

I need to filter my data based on 3 different columns.

Two of the columns are unique so it worked if u use something like

Code:

grep 'PASS.*HIGH|HIGH.*PASS' file.tsv

However the other column is not unique ..

So basically I want to extract out lines that match only match these 3 criteria : HIGH in column 1, PASS in column 2, 1 and 3 in column 3. Other columns also contain numbers that can include 1 and 3.

how can I use 'awk' on this ? the columns are separated by "\t"

Try:

Code:

awk -F'\t' '$1=="HIGH" && $2=="PASS" && ( $3==1 || $3==3 )' file

or do you mean:

Code:

awk -F'\t' '$1=="HIGH" && $2=="PASS" && $3~/1.*3|3.*1/' file

which could also be written as:

Code:

awk -F'\t' '$1=="HIGH" && $2=="PASS" && $3~/1/ && $3~/3/' file

or do you mean:

Code:

awk -F'\t' '$1=="HIGH" && $2=="PASS" && $3~/[13]/' file

which could also be written as:

Code:

awk -F'\t' '$1=="HIGH" && $2=="PASS" && ( $3~/1/ || $3~/3/ )' file

Hello and welcome to the forum.

Have you done any appoaches yet?
Maybe with other tools?
Or must it be awk?

Is this a homework question?

Thank you

Hi,

Thank you, the 4th code worked for me. No this is not a homework. Im a PhD student in cancer research and I'm analyzing sequencing result which is very big and normally excel would not be able to load this kind of data properly. As someone who has a very limited knowledge in programming, I tend to ask around which commands are useful to be applied in biological analysis. Cheers.

It usually pays off to post adequate, representative (mayhap abbreviated) samples helping to describe the problem in more detail, so solutions can be neatly tailored.