How to add output “non_assigned” when there is no match in grep?

Question

When I run a command (COMMAND) on one line of my input file (input.txt) I get an associated result where only one line is interesting, always starting by the world phylum.

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Answer 1

This will do the job:

for p in $(<input.txt)
do
    (COMMAND $p | grep -w "phylum") || echo "non_assigned"
done >> results.txt

This runs the command and the grep in a subshell. If the grep finds 'phylum', the RHS of the || is not run; if 'phylum' is not found, the echo is executed to output a suitable marker.

Notice that the redirection has been moved to after the done; it might be better to use > rather than >> now.

Beware the set option -o pipefail — if the command can fail, you might need to use set +o pipefail. However, it is disabled by default, so you'll probably be OK.