Bash script using "while read" to call two different variables from a file

Question

I'd be grateful for your help. I believe I need to use 'while read' to achieve what I am hoping to achieve here. I have looked in the forum for similar questions, but can't find an example where more than one variable is called from another file.

I have file.txt, which has two columns and is ~1000 lines long and looks like this:

1 rs3131962
3 rs12562034
2 rs4040617
8 rs79373928
2 rs11240779

I want to write a script, that for each line of file.txt, will take the variable from column 1 and column 2 and place them in different parts of my command. Now, I know that this syntax is completely wrong, but for illustrative purposes, I want it to look something like:

#!/bin/bash
filename='file.txt'
while read file.txt;
do 
./qctool -g chr"$1"_v3.bgen  -os chr"$1"_"$2".bgen -condition-on "$2"
done

..where $1 and $2 represent the variables in the first and second columns of each line in file.txt.

Essentially, I want it to read line 1 of file.txt and execute:

./qctool -g chr1_v3.bgen  -os chr1_rs3131962.bgen -condition-on rs3131962

And once that's done, to move onto line 2, and execute:

./qctool -g chr3_v3.bgen  -os chr3_rs12562034.bgen -condition-on rs12562034

and so on, for all ~1000 lines in file.txt

Could somebody please help me with the getting the syntax right for getting the variables from column 1 and column 2 separately into my script?

Apologies for the poverty of my attempt - any help warmly appreciated.

Tom Fenech · Accepted Answer · 2018-07-19 11:57:01Z

2

You just need to name your variables in your read command:

#!/bin/bash
filename='file.txt'
while read -r first second
do 
./qctool -g chr"$first"_v3.bgen  -os chr"$first"_"$second".bgen -condition-on "$second"
done < "$filename"

Also, read reads from standard input, so pass the contents of the file over standard input using < "$filename" after done.

By the way, I added the -r switch to read because it does no harm and stops the shell trying to do "clever" things with \s in the input that it reads.

answered Jul 19, 2018 at 11:57

Tom Fenech

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1 Comment

GB44444 Over a year ago

Tom Fenech, that's worked perfectly. Thank you very much for your help.

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