Execute commands from a single column of an input file

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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?

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)

How to run grep on a single column?, How to run grep on a single column? grep awk. I want to grep the output of my ls - l command: -� To extract one or more columns from a cvs file you can use the csvcut utility that is part of the toolbox. To extract the second column use this command: csvcut -c 2 filename_in.csv > filename_out.csv csvcut reference page. If the strings in the csv are quoted, add the quote character with the q option:

Using GNU Parallel it looks like this:

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

20 awk examples – Linux Hint, Run the following awk command to change the delimiter, ':' by '-' to the content of the The following command will split each line of input.txt file based on the tab ( '\t') and By using a specific delimiter, the first column can be printed properly. the 2 first lines selects some files to work with, then awk prepares a nice string with a command to execute and some arguments and $1 is the first column input from the pipe. And finally I make sure that xargs sends this string to bash that just execute it.

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!

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Comments
  • If you have lots to do, you could get GNU Parallel to do them in parallel...
  • 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.