Extract column using grep

Question

I have a data frame with >100 columns each labeled with a unique string. Column 1 represents the index variable. I would like to use a basic UNIX command to extract the index column (column 1) + a specific column string using grep.

For example, if my data frame looks like the following:

Index  A  B  C...D  E  F p1     1  7  4   2  5  6 p2     2  2  1   2  .  3 p3     3  3  1   5  6  1 

I would like to use some command to extract only column "X" which I will specify with grep, and display both column 1 & the column I grep'd. I know that I can use cut -f1 myfile for the first bit, but need help with the grep per column. As a more concrete example, if my grep phrase were "B", I would like the output to be:

Index  B p1     7 p2     2 p3     3 

I am new to UNIX, and have not found much in similar examples. Any help would be much appreciated!!

Answer 1

You need to use awk:

awk '{print $1,$3}' <namefile> 

This simple command allows printing the first ($1) and third ($3) column of the file. The software awk is actually much more powerful. I think you should have a look at the man page of awk.

A nice combo is using grep and awk with a pipe. The following code will print column 1 and 3 of only the lines of your file that contain 'p1':

grep 'p1' <namefile> | awk '{print $1,$3}' 

If, instead, you want to select lines by line number you can replace grep with sed:

sed 1p <namefile> | awk '{print $1,$3}' 

Actually, awk can be used alone in all the examples:

awk '/p1/{print $1,$3}' <namefile> # will print only lines containing p1 awk '{if(NR == 1){print $1,$3}}' <namefile> # Will print only first line 

Answer 2

First figure out the command to find the column number.

columnname=C sed -n "1 s/${columnname}.*//p" datafile | sed 's/[^\t*]//g' | wc -c 

Once you know the number, use cut

cut -f1,3 < datafile  

Combine into one command

cut -f1,$(sed -n "1 s/${columnname}.*//p" datafile |     sed 's/[^\t*]//g' | wc -c) < datafile 

Finished? No, you should improve the first sed command when one header can be a substring of another header: include tabs in your match and put the tabs back in the replacement string.