[Bioperl-l] basic questions

David Messina dmessina at wustl.edu
Tue Jun 12 12:11:36 EDT 2007

Hmm, it almost looks like you're having an issue with line breaks.

The 'swissprot stream with no ID' error made me think that perhaps  
Perl wasn't seeing the second argument to get_sequence. And then your  
new program has the error 'Can't use string  
("Bio::Restriction::EnzymeCollecti")' where the end of the word is  
cut off.

I don't know how ActivePerl handles Windows vs UNIX line breaks.  Are  
there any example scripts that come with ActivePerl? If there are,  
and they run correctly, perhaps you could look to see how the line  
breaks are done and make sure the your program does it the same way.

Other than that, I'm not seeing an obvious answer to your problem --  
anyone else have a suggestion?

Perhaps the easiest thing for you to do would be to reinstall BioPerl  
and make sure that you run the full test suite and that all of the  
tests pass. My guess is that something in your current setup is not  
quite right.


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