[Bioperl-l] EMBOSS die/warn

Bernd Web bernd.web at gmail.com
Tue Sep 19 04:12:02 EDT 2006


Hi,

X11 on OS-X read hardcoded paths. This caused the absence of the path
to EMBOSS in a newly opened X-term. However, EMBOSS-factory does not
signal the absence of EMBOSS when the pathto EMBOSS is absent.
When I realized this, I thought to signal the absence of EMBOSS and
stumbled on something surprising. A small example follows below:
------------
use Bio::Factory::EMBOSS;

print "1\n";
#comment line below
my $fact = new Bio::Factory::EMBOSS;
print "2\n";
die "DIE STRING NOT PRINTED";
print "3\n";
--------------

Output:
1
2

So die does work but nothing is printed. When you comment the "my
$fact" line the die string is printed.  When EMBOSS cannot be found
die and warn do not print their strings anymore. I could not find why
this happens yet. So, the above happens when the path to emboss
binaries is not in $PATH.

regards,
bernd


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