根据管道输出终止Bash脚本

Question

I have written the following shell script:

#!/bin/bash


counter=0

while [ $counter -lt 250 ]; do
        perl Cumulative_Percentage.pl TP53.lst T1_endo.maf >> OutFile
        perl Optimize_Panel.pl TP53.LST T1_endo.maf >> TP53.lst 
        let counter=counter+1
done

And it works well. The problem is that it often runs through far more loops than it needs to. The Perl script, Optimize_Panel.pl, prints a single line if the loop should continue or exits without printing if the loop should stop. I want the while loop to terminate if Optimize_Panel.pl exits instead of printing ... but how?

One possible solution I can imagine is to run

wc TP53.lst

at the beginning and end of the loop; first setting it to a variable then checking to see if it had increased then leading it to a premature done statement if TP53.lst had not been appended. I'm confident that this could work but it feels clunky and I suspect there is a much simpler way to modify the shell script.

Another way I can think of doing this would be to pipe the output of Optimize_Panel.pl into a temporary file then somehow check to see if that file was empty.

Any ideas?

Answer 1

You can capture the output in a variable, then break out of the loop if that variable is zero-length.

while [ $counter -lt 250 ]; do
    perl Cumulative_Percentage.pl TP53.lst T1_endo.maf >> OutFile
    output=$(perl Optimize_Panel.pl TP53.LST T1_endo.maf)
    [ -z "$output" ] && break
    echo "$output" >> TP53.lst 
    let counter=counter+1
done

Answer 2

Simple hack (in case the perl script doesn't produce meaningful exit status):

perl Optimize_Panel.pl TP53.LST T1_endo.maf | grep . >> TP53.lst || break

grep . matches any non-empty line, so it is a way of removing empty lines. But it is also a way of detecting whether there were any non-empty lines; it will fail precisely in the case where there weren't any. Of course, it would be much better if the perl script provided an appropriate exit status code (0 for success; non-zero for failure), in which case you could leave out the | grep . | grep . hack.)

By the way, you can use bash's arithmetic for statement to make your script possibly more readable:

for ((counter=0; counter < 250; ++counter)); do
    perl Cumulative_Percentage.pl TP53.lst T1_endo.maf >> OutFile
    perl Optimize_Panel.pl TP53.LST T1_endo.maf |
      grep . >> TP53.lst || break;
done