UNIX for Dummies Questions & Answers

#!/bin/sh

I have a file matrix.pair.cols that contains numbers like shown below:

Code:

case1	17	18
case2	1	2
case3	4	5
case4 ..	..

I want to cut the column numbers mentioned in col2 and 3 from another file
I have tried the code below, but no avail.

Code:

#!/bin/sh
 
while read p q r
do
	cut -f "$q,$r" matrix > $p.cols
done < matrix.pair.cols

exit 0

Suggestions on what I need to do differently?

Thanks,
Guss

I suggest you first make sure your variables are set correctly. Try:

Code:

#!/bin/sh
 
while read p q r ; do
	echo p: \"$p\"    q: \"$q\"    r: \"$r\"
	echo "cut -f \"$q,$r\" matrix > $p.cols"
done < matrix.pair.cols

exit 0

It might be that your source file contains hidden formatting characters which will not show in the copy here but may interrupt the reading of your file. It never hurts to ascertain each step separately.

The next thing is to apply the printed cut-commands manually one by one and see if they work as expected. One problem might be that you need to specify a field-delimiter (see option "-d" of "cut") to parse the file "matrix" correctly (not all cut-versions will understand tabs instead of spaces, for instance).

Btw: in scripts i would - just to be 1000% sure - always write "${var}" instead of "$var". In most cases the latter works the same, but in some combinations (within complex statements) the former might avoid ambiguity. Therefore:

Code:

	echo "cut -f \"${q},${r}\" matrix > ${p}.cols"

I hope this helps.

bakunin

What exactly is going wrong?

Is the field delimiter in the file matrix a tab character? If not, you'll need to add a -d option to your cut command or convert your field numbers to character positions and use something other than the -f option.

Hello

#Don:

Code:

matrix

is a tab delimited file. I have used the

Code:

-d

option successfully for other delimiters

Code:

(space, ',').

#RudiC: I am just not getting an output as I ran it.

#bakunin: I tried running your code as well; no output here either.

Thank you for all your inputs!

~Guss

There is no output to expect. The script as you showed it writes a lot of output files and you will have to examine these for any output.

If there is no output (that is: none of the files to be expected) then your input file (matrix.pair.cols) isn't even read. Make sure the file is accessible, in the directory you expect it to be (in your script this is the current directory, regardless of where the script may be). Modify your script further to test this:

Code:

#!/bin/sh

input="matrix.pair.cols"

if [ ! -r $input ] ; then
     echo "ERROR: file $input not readable or not existing at all"
     exit 2
fi

while read p q r ; do
	echo p: \"$p\"    q: \"$q\"    r: \"$r\"
	echo "cut -f \"$q,$r\" matrix > $p.cols"
done < matrix.pair.cols

exit 0

I hope this helps.

bakunin