[Bioperl-l] Bio::Tools::Run::Alignment::Probcons

Andreas Kahari ak at ebi.ac.uk
Mon Feb 14 11:11:55 EST 2005

On Mon, Feb 14, 2005 at 04:49:38PM +0100, Albert Vilella wrote:
> Hi all,
> I have added a Probcons wrapper/caller to bioperl, so that
> probcons can be run as the other Bio::Tools::Run::Alignment::*
> available.
> There is a #FIXME in the module, because I'm not sure if in:
> "program input > output"
> The ">" pipe works in other OSes apart from *nixes,

Hi Albert,

Strictly speaking, it's not a pipe but a redirection.  It is
handled by the shell, not the OS (unless the shell is built into
the OS).

However, judging from the web site it looks like Probcons is a
Unix program.  This makes you concern somewhat unnecessary.  A
few lines further down, you also add a redirection of stderr to
/dev/null.  This would prevent the user from seeing any errors
produced by the probcons executable, which is bad since it will
mean that the user would be unaware of them.  In general, I
believe in letting the user decide what to see or not see.


Andreas Kähäri


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