Execute commands from a single column of an input file

Question

I have very little experience with bash, but am attempting to put together a pipeline that reads in and executes commands line by line from an input file. The input file, called "seeds.txt", is set up like so

program_to_execute -seed_value 4496341759106 -a_bunch_of_arguments c(1,2,3) ; #Short_description_of_run
program_to_execute -seed_value 7502828106749 -a_bunch_of_arguments c(4,5,6) ; #Short_description_of_run

I separated the #Short_descriptions from the commands by a semi-colon (;) since the arguments contain commas (,). When I run the following script I get a "No such file or directory" error

#!/bin/bash

in="${1:-seeds.txt}"

in2=$(cut -d';' -f1 "${in}")

while IFS= read -r SAMP
    do
    $SAMP 

done < $in2

I know that seeds.txt is getting read in fine, so I'm not sure why I'm getting a missing file/directory message. Could anyone point me in the right direction?

If you have lots to do, you could get **GNU Parallel** to do them in parallel... — Mark Setchell, Feb 12 '20 at 16:09

score 2 · Answer 1 · answered Feb 13 '20 at 08:57

2

Using GNU Parallel it looks like this:

cut -d';' -f1 seeds.txt | parallel

answered Feb 13 '20 at 08:57

Ole Tange

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nullPointer · Accepted Answer · 2020-02-12T16:29:22.533

1

you can try as below with eval...not very safe though, see this for more info

while read line; do eval "$line" ; done < <(cut -d';' -f1 seeds.txt)

edited Feb 12 '20 at 16:29

answered Feb 12 '20 at 15:59

nullPointer

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Thank you, this does exactly what I want. In this case, where I'm the only one making the seeds.txt file, it seems like the safety concern with `eval` is less of an issue. – Jarl Feb 12 '20 at 17:20

score 1 · Answer 3 · answered Feb 13 '20 at 09:15

Just in case you want to avoid eval

while read -ra line; do command "${line[@]}"; done < <(cut -d';' -f1 seeds.txt)

Note this solution does not work if the program/utility is not an executable within your PATH, e.g. you wan to use a function or an alias. Not sure if the eval solution can do that too. Kudos to the cut solution!

Execute commands from a single column of an input file

3 Answers3