How to send formatted print statement to shell command line?

Question

I have this bash script which prints out ~800 commands I would like to run on the command line:

paste abyss_names.txt abyss_quast.txt | while IFS="$(printf '\t')" read -r f1 f2
do
       printf 'python /quast-2.3/quast.py -o %s %s \n' "$f1 $f2"
done

How do I send the print output directly to the unix shell command line?

anubhava · Accepted Answer · 2015-06-23 14:43:55Z

2

You don't need to use printf. Just execute the command directly in the loop.

Try this script:

while IFS=$'\t' read -r f1 f2; do
       python /quast-2.3/quast.py -o "$f1" "$f2"
done < <(paste abyss_names.txt abyss_quast.txt)

edited Jun 23, 2015 at 14:43

answered Jun 22, 2015 at 21:08

anubhava

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3 Comments

sdemurjian Over a year ago

python /quast-2.3/quast.py -o file1 /path/to/file1, where file1 is from abyss_names.txt and the path is from abyss_quast.txt

anubhava Over a year ago

Then python /quast-2.3/quast.py -o "$f1" "$f2" should have worked right?

sdemurjian Over a year ago

Ah, it does work. Sorry about that. Thanks for your patience

Mike Atkins · Accepted Answer · 2015-06-22 21:09:55Z

0

how about:

paste abyss_names.txt abyss_quast.txt | while IFS="$(printf '\t')" read -r f1 f2
do
       $(printf 'python /quast-2.3/quast.py -o %s %s \n' "$f1 $f2")
done

answered Jun 22, 2015 at 21:09

Mike Atkins

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1 Comment

anubhava Over a year ago

$(...) is not needed as it will fork a sub-shell for every line in the loop and pipe after paste can also be avoided.

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