[Bioperl-l] no_residues test in SimpleAlign.t

Chris Fields cjfields at uiuc.edu
Sun Oct 15 13:53:50 EDT 2006


Albert,

I get all 75 tests passing.  SimpleAlign.t was recently switched over  
to Test::More, so you should be seeing more explicit test  
descriptions.  It looks like test 27 is no_residues().  Were there  
any more that failed?

I usually run 'perl -I. t/test.t' from the main bioperl directory to  
check individual tests from the local directory.  Otherwise you are  
checking your installed version which may be older (and may not match  
tests and recent bug fixes).  Could that be the problem?

Chris

On Oct 15, 2006, at 6:08 AM, Albert Vilella wrote:

> Hi all,
>
> Can somebody check the SimpleAlign.t test?
>
> perl t/SimpleAlign.t
>
> I get a few errors, I am looking at one that deals with no_residues. I
> don't understand if this is suposed to work:
>
> sub no_residues {
>     my $self = shift;
>     my $count = 0;
>
>     foreach my $seq ($self->each_seq) {
> 	my $str = $seq->seq();
>
> 	$count += ($str =~ s/[^A-Za-z]//g);
>         #is this the same as:
>         # $str =~ s/[^A-Za-z]//g;
>         # $count += length($str);
>     }
>
> Cheers,
>
>     Albert.
>     return $count;
> }
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

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





More information about the Bioperl-l mailing list