Saturday 17 August 2019
Read last line of file in bash script when reading file line by line
Answer
Answer
I am writing a script to read commands from a file and execute a specific command. I want my script to work for either single input arguments or when an argument is a filename which contains the arguments in question.
My code below works except for one problem, it ignores the last line of the file. So, if the file were as follows.
file.txt
file1
file2
The script posted below only runs the command for file.txt
for currentJob in "$@"
do
if [[ "$currentJob" != *.* ]] #single file input arg
then
echo $currentJob
serverJobName="$( tr '[A-Z]' '[a-z]' <<< "$currentJob" )" #Change to lowercase
#run cURL job
curl -o "$currentJob"PisaInterfaces.xml http://www.ebi.ac.uk/msd-srv/pisa/cgi-bin/interfaces.pisa?"$serverJobName"
else #file with list of pdbs
echo "Reading "$currentJob
while read line; do
echo "-"$line
serverJobName="$( tr '[A-Z]' '[a-z]' <<< "$line" )"
curl -o "$line"PisaInterfaces.xml http://www.ebi.ac.uk/msd-srv/pisa/cgi-bin/interfaces.pisa?"$serverJobName"
done < "$currentJob"
fi
done
There is, of course, the obvious work around where after the while loop I repeat the steps for inside the loop to complete those commands with the last file, but this is not desirable as any changes I make inside the while loop must be repeated again outside of the while loop. I have searched around online and could not find anyone asking this precise question. I am sure it is out there, but I have not found it.
The output I get is as follows.
>testScript.sh file.txt
Reading file.txt
-file1
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 642k 0 642k 0 0 349k 0 --:--:-- 0:00:01 --:--:-- 492k
My bash version is 3.2.48
Answer
It sounds like your input file is missing the newline character after its last line. When read encounters this, it sets the variable ($line in this case) to the last line, but then returns an end-of-file error so the loop doesn't execute for that last line. To work around this, you can make the loop execute if read succeeds or it read anything into $line:
...
while read line || [[ -n "$line" ]]; do
...
EDIT: the || in the while condition is what's known as a short-circuit boolean -- it tries the first command (read line), and if that succeeds it skips the second ([[ -n "$line" ]]) and goes through the loop (basically, as long as the read succeeds, it runs just like your original script). If the read fails, it checks the second command ([[ -n "$line" ]]) -- if read read anything into $line before hitting the end of file (i.e. if there was an unterminated last line in the file), this'll succeed, so the while condition as a whole is considered to have succeeded, and the loop runs one more time.
After that last unterminated line is processed, it'll run the test again. This time, the read will fail (it's still at the end of file), and since read didn't read anything into $line this time the [[ -n "$line" ]] test will also fail, so the while condition as a whole fails and the loop terminates.
EDIT2: The [[ ]] is a bash conditional expression -- it's not a regular command, but it can be used in place of one. Its primary purpose is to succeed or fail, based on the condition inside it. In this case, the -n test means succeed if the operand ("$line") is NONempty. There's a list of other test conditions here, as well as in the man page for the test command.
Note that a conditional expression in [[ ... ]] is subtly different from a test command [ ... ] -- see BashFAQ #031 for differences and a list of available tests. And they're both different from an arithmetic expression with (( ... )), and completely different from a subshell with( ... )...
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