[BiO BB] Bio::Factory::EMBOSS problem

Christopher Woelk cwoelk at popmail.ucsd.edu
Thu Sep 16 21:26:34 EDT 2004

I was looking for some help

I am under OS X 10.3.5 and I have bioperl-1.4 and EMBOSS-2.9.0 
installed.   I am trying to implement to following code: 	

use Bio::Factory::EMBOSS;

	# get an EMBOSS application object from the EMBOSS factory
	$factory = new Bio::Factory::EMBOSS;
   	$application = $factory->program('sixpack');
   	# run the application with an optional hash containing parameters
	%input = ( -sequence => $seqobj );

I get the error message:

Can't locate Bio/Factory/EMBOSS.pm in @INC (@INC contains: 
/Library/Perl/5.8.1/darwin-thread-multi-2level /Library/Perl/5.8.1 
/Library/Perl /Network/Library/Perl/5.8.1/darwin-thread-multi-2level 
/Network/Library/Perl/5.8.1 /Network/Library/Perl .) at 
./iterate_seqs.1.pl line 9.

I noticed that EMBOSS.pm does not exist in my Factory directory.  I 
then tried switching to emboss.pm in the AlignIO directory:

use Bio::AlignIO::emboss;

But got this error message

Can't locate object method "program" via package "Bio::AlignIO::emboss" 
at ./iterate_seqs.1.pl line 40, <GEN0> line 1.

Thanks for any help

Christopher Woelk, PhD

University California at San Diego
Department of Pathology
Stein Clinical Research Bldg.
9500 Gilman Drive
La Jolla CA 92093-0679
Tel: 858 642 1106
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