We can now run:
$ bash middle.sh pentane.pdb 15 5
ATOM 9 H 1 1.324 0.350 -1.332 1.00 0.00
ATOM 10 H 1 1.271 1.378 0.122 1.00 0.00
ATOM 11 H 1 -0.074 -0.384 1.288 1.00 0.00
ATOM 12 H 1 -0.048 -1.362 -0.205 1.00 0.00
ATOM 13 H 1 -1.183 0.500 -1.412 1.00 0.00
By changing the arguments to our command we can change our script’s behaviour:
$ bash middle.sh pentane.pdb 20 5
ATOM 14 H 1 -1.259 1.420 0.112 1.00 0.00
ATOM 15 H 1 -2.608 -0.407 1.130 1.00 0.00
ATOM 16 H 1 -2.540 -1.303 -0.404 1.00 0.00
ATOM 17 H 1 -3.393 0.254 -0.321 1.00 0.00
TER 18 1
This works,
but it may take the next person who reads middle.sh a moment to figure out what it does.
We can improve our script by adding some comments at the top:
$ nano middle.sh
# Select lines from the middle of a file.
# Usage: bash middle.sh filename end_line num_lines
head -n "$2" "$1" | tail -n "$3"
A comment starts with a # character and runs to the end of the line.
The computer ignores comments,
but they’re invaluable for helping people (including your future self) understand and use scripts.
The only caveat is that each time you modify the script,
you should check that the comment is still accurate:
an explanation that sends the reader in the wrong direction is worse than none at all.