[Bioperl-l] general perl question

Smithies, Russell Russell.Smithies at agresearch.co.nz
Wed Jun 2 01:00:33 EDT 2010

It's not really a BioPerl question, more one of reading the Perl documentation.

There's several ways of executing commands from Perl:
*  The exec() function executes a system command and never returns
*  system() exactly the same thing as exec(), except that a fork is done first, and the parent process waits for the child process to exit
*  backticks
   Eg. $date=`/usr/bin/date`;
* open() and parse
   Eg. open PS, "/usr/bin/ps -ef |";

Up to you which you use,


> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Dimitar Kenanov
> Sent: Wednesday, 2 June 2010 4:34 p.m.
> To: 'bioperl-l at bioperl.org'
> Subject: [Bioperl-l] general perl question
> Hi guys,
> firstly i am sorry ive sent this email first to the wrong
> email(bioperl-l-request at lists.open-bio.org).
> Secondly, i am sorry to bother you with such problem but i do not know
> how to google that one :)
> Here is the problem. I want to start several simultaneous processes
> through my script but i found i cant do that unless i start them as
> background processes because otherwise 'system' waits for the process to
> exit. Now i use something like this:
>      my @args=("$program $seqinput $$specname $eval &");
>      system(@args) == 0 or die "system @args failed: $!";
> But that is a bit weird when i want to terminate the program then all
> the processes are still running and i have to kill them manually.
> Is there a way to start several simultaneous processes without '&'?
> Thank you for your patience and help
> Greetings
> Dimitar
> --
> Dimitar Kenanov
> Postdoctoral research fellow
> Protein Sequence Analysis Group
> Bioinformatics Institute
> A*STAR, Singapore
> tel: +65 6478 8514
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> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
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