[Bioperl-l] DBA_GenericHSP_output???

francois fauteux ffauteux at gmail.com
Fri Aug 18 15:33:24 EDT 2006


Hi;

 DBA with non coding DNA; does something when launched:

Find start end points: [0,1001][0,1002] Score -2990
Recovering alignment: Alignment recoveredplicit read off

I can't find a way to get the output (alignment)...

The code looks like this (see DBA.pm):

  my @params = ('matchA' => 0.75, 'matchB' => '0.55','dymem'=>'linear');
  my  $factory = Bio::Tools::Run::Alignment::DBA->new(@params);
  $inputfilename = 'seqs.fasta';
  #@hsps is an array of GenericHSP objects
  my @hsps = $factory->align($inputfilename);

Missing the howto ouptut pretty alignment...

Many thanks;

François



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