[Bioperl-l] basic questions

L Xu ryanx07 at hotmail.com
Tue Jun 12 14:11:15 EDT 2007


Thank you very much, it did make the script advanced a bit but I got the 
following error:

C:\~Scripts>perl t9.pl
Can't locate object method "name" via package 
"Bio::Restriction::EnzymeCollectio
n" at t9.pl line 5, <DATA> line 532.

I checked the documentation , there is no "name" method for the package. 
Thanks.

= = = Original message = = =

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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