Problem with piped filehandle in perl
I am trying to run bp_genbank2gff3.pl
(bioperl package) from another perl script that
gets a genbank as its argument.
This does not work (no output files are generated):
my $command = "bp_genbank2gff3.pl -y -o /tmp $ARGV[0]";
open( my $command_out, "-|", $command );
close $command_out;
but this does
open( my $command_out, "-|", $command );
sleep 3; # why do I need to sleep?
close $command_out;
Why?
I thought that close
is supposed to block until the command is done:
Closing any piped filehandle causes the parent process to wait for the 开发者_StackOverflow中文版 child to finish... (see http://perldoc.perl.org/functions/open.html).
Edit
I added this as last line:
say "ret=$ret, \$?=$?, \$!=$!";
and in both cases the printout is:
ret=, $?=13, $!=
(which means close
failed in both cases, right?)
$? = 13
means your child process was terminated by a SIGPIPE
signal. Your external program (bp_genbank2gff3.pl
) tried to write some output to a pipe to your perl
program. But the perl
program closed its end of the pipe so your OS sent a SIGPIPE
to the external program.
By sleep
ing for 3 seconds, you are letting your program run for 3 seconds before the OS kills it, so this will let your program get something done. Note that pipes have a limited capacity, though, so if your parent perl
script is not reading from the pipe and if the external program is writing a lot to standard output, the external program's write operations will eventually block and you may not really get 3 seconds of effort from your external program.
The workaround is to read the output from the external program, even if you are just going to throw it away.
open( my $command_out, "-|", $command );
my @ignore_me = <$command_out>;
close $command_out;
Update: If you really don't care about the command's output, you can avoid SIGPIPE
issues by redirecting the output to /dev/null
:
open my $command_out, "-|", "$command > /dev/null";
close $command_out; # succeeds, no SIGPIPE
Of course if you are going to go to that much trouble to ignore the output, you might as well just use system
.
Additional info: As the OP says, closing a piped filehandle causes the parent to wait for the child to finish (by using waitpid
or something similar). But before it starts waiting, it closes its end of the pipe. In this case, that end is the read end of the pipe that the child process is writing its standard output to. The next time the child tries to write something to standard output, the OS detects that the read end of that pipe is closed and sends a SIGPIPE
to the child process, killing it and quickly letting the close
statement in the parent finish.
I'm not sure what you're trying to do but system is probably better in this case...
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