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

Dominic Rose dominic at bioinf.uni-leipzig.de
Mon Aug 25 10:40:42 UTC 2008


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";

However, it should be possible to avoid the printing of that error 
message. Many alignments contain N's what causes many many
"ti_index not defined for N" messages. It should be possible to switch 
that message off.


Dominic Rose
Professur für Bioinformatik
Institut für Informatik
Universität Leipzig
Härtelstr. 16-18
D-04107 Leipzig
WWW    http://www.bioinf.uni-leipzig.de
Phone: +49 341 97-16698
Fax:   +49 341 97-16679

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