[Bioperl-l] Problem executing bp_genbank2gff3.pl from another perl script

David Breimann david.breimann at gmail.com
Fri Aug 13 09:01:10 EDT 2010


Hi,
I am rying to run bp_genbank2gff3.pl 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 though that close is supposed to block until the command is done:

Closing any piped filehandle causes the parent process to wait for the
child to finish... (see http://perldoc.perl.org/functions/open.html).

Thanks
Dave


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