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



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

while IFS= read -r 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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Shell tricks for one-liner bioinformatics, Example Linux/UNIX commands for quick bioinformatics analysis. To extract column number 4 from data.bim in awk , do: awk '{print $4}' data.bim. This will print the is the program, and it is run on every line of the input file. By default, awk� LAMMPS executes by reading commands from a input script (text file), one line at a time. When the input script ends, LAMMPS exits. Each command causes LAMMPS to take some action. It may set an internal variable, read in a file, or run a simulation.

4.4. Read HBase Shell Commands from a Command File, You can enter HBase Shell commands into a text file, one command per line, and pass Directing HBase Shell to Execute the Commands Also, though you see the output for each command, the commands themselves are not echoed to row1 column=cf:a, timestamp=1407130286968, value=value1 row2 column=cf:b, � One of my favorite ways to use the Unix awk command is to print columns of information from text files, including printing columns in a different order than they are in in the text file. Here are some examples of how awk works in this use case.

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  • 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.