[Bioperl-l] hickup in SimpleAlign remove_gaps method

Chris Fields cjfields at uiuc.edu
Fri Oct 13 11:51:38 EDT 2006


You can check to see if it passes all tests.  I'm guessing  
SimpleAlign.t tests this method out in some way (though it's always  
safer to check).

Chris

On Oct 13, 2006, at 10:26 AM, Albert Vilella wrote:

> Hi all,
>
> While using the remove_gaps method in Bio::SimpleAlign I found out
> that if the alignment is (bad enough for) having no columns without
> any gap at all, the method will give a:
>
> Use of uninitialized value in split at this line in add_seq:
>
> map { $self->{'_symbols'}->{$_} = 1; } split(//,$seq->seq);
>
> So my idea was to tweak this line to something like:
>
> map { $self->{'_symbols'}->{$_} = 1; } split(//,$seq->seq || '');
>
> But I am unsure about any other side effects this may have.
>
> Anyone?
>
>     Albert.
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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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