[Bioperl-l] Bio::Align::DNAStatistics.pm

Heikki Lehvaslaiho heikki at sanbi.ac.za
Wed Aug 27 02:23:39 EDT 2008


Dominic,

You are absolutely right. 

I've changed 'print' into '$self->warn' in the SVN. Now it is possible to set 
$object->verbose(-1) to silence the warning or, if deemed necessary, set 
$object->verbose(2) and catch the error with an eval statement.

Thanks for reporting this,

    -Heikki

On Friday 22 August 2008 15:35:21 Dominic Rose wrote:
> Hi,
>
> just a short suggestion to improve the code:
>
> in function
>
> sub _build_nt_matrix()
>
> one finds the following lines:
>
>          my $ti_index = $NucleotideIndexes{$ti};
>          my $tj_index = $NucleotideIndexes{$tj};
>
>          if( ! defined $ti_index ) {
>              print "ti_index not defined for $ti\n";
>              next;
>          }
>
> However, it should be possible to stop/silence the printing of that
> error message. Many alignments contain N's what causes many many
> "ti_index not defined for N" messages. That should be avoidable.
>
> Thanks,
> Dominic

-- 
______ _/      _/_____________________________________________________
      _/      _/
     _/  _/  _/  Heikki Lehvaslaiho    heikki at_sanbi _ac _za
    _/_/_/_/_/  Senior Scientist    skype: heikki_lehvaslaiho
   _/  _/  _/  SANBI, South African National Bioinformatics Institute
  _/  _/  _/  University of Western Cape, South Africa
     _/      Phone: +27 21 959 2096   FAX: +27 21 959 2512
___ _/_/_/_/_/________________________________________________________



More information about the Bioperl-l mailing list