[Bioperl-l] errors when aligning

[Maurice Manning]

Hi Bioperl folks,

I am just getting started with bioperl and trying some
of the examples in the tutorial but I am having some
difficulties.

Trying to run a simple clustal example:
use Bio::Seq;
use Bio::AlignIO;
use Bio::Tools::Run::Alignment::Clustalw;

@params = ('ktuple' => 2, 'matrix' => 'BLOSUM');  
$factory =
Bio::Tools::Run::Alignment::Clustalw->new(@params);
#  Pass the factory a list of sequences to be aligned.
      
$inputfilename = 'c:\\bioinfo\\data\\miniEcoli.fasta';
$aln = $factory->align($inputfilename); # $aln is a
SimpleAlign object.

I get:
   Error Trailing \ in regex m/^\/ at
C:/Perl/site/lib/Bio/Root/IO.pm line 426.

Am I configured incorrectly?  Is there some debug
tips?


Could I also get an example of how to get values out
of a SeqStats and SeqWord objects for the simlpe cases
of:
 $seq_stats  =  Bio::Tools::SeqStats->new($seqobj);
 $weight = $seq_stats->get_mol_wt();
 $monomer_ref = $seq_stats->count_monomers();
 $codon_ref = $seq_stats->count_codons();


Any help would be great.  I am running under windows
and have an ActiveState perl/bioperl install.  

Thanks,
Mo




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