[Bioperl-l] basic questions

Chris Fields 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;

should be

my $all_collection = Bio::Restriction::EnzymeCollection->new;

chris

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  
> tested
> 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?  
> 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.
>
> Dave
>
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





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