[Bioperl-l] problems with clustalw

[Sendu Bala]

vdar at yorku.ca wrote:
> Yes, seems like it worked, now I am having the following error message which is
> not because of the errors in installation..right?
> 
> $ perl mult_align.pl
> Can't call method "isa" without a package or object reference at
> /opt/rocks/lib/perl5/site_perl/5.8.8//Bio/Tools/Run/Alignment/Clustalw.pm line
> 617.

You weren't passing sequence objects to align() due to another error in 
your script:

Instead of:
my @seq_array = qw/$seq_obj_on $seq_obj_too $seq_obj_thre/;
my $seq_array_ref = \@seq_array;
my $aln = $factory->align($seq_array_ref);

You can have:
my @seq_array = ($seq_obj_on, $seq_obj_too, $seq_obj_thre);
my $seq_array_ref = \@seq_array;
my $aln = $factory->align($seq_array_ref);

Or just:
my $aln = $factory->align([$seq_obj_on, $seq_obj_too, $seq_obj_thre]);