[Bioperl-l] basic questions
cjfields at uiuc.edu
Tue Jun 12 13:51:47 EDT 2007
This is an instance where 'use strict' would have shown the problem
right away. You left off your constructor call:
my $all_collection = Bio::Restriction::EnzymeCollection;
my $all_collection = Bio::Restriction::EnzymeCollection->new;
On Jun 12, 2007, at 12:17 PM, L Xu wrote:
> I reinstalled activePerl and BioPerl, now the activePerl is 5.8.8
> build 820.
> However, both scripts generated the same error with my computer. I
> the code in another WinXP computer with the same versions of
> activePerl and
> BioPerl, the one for the swissprot did work but the restriction enzyme
> generated the same error.
> = = = Original message = = =
> 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?
> 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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Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign
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