[Bioperl-l] low complexity filter in StandAloneBlastPlus

[Carnë Draug]

On 13 February 2014 22:09, Paul Cantalupo <pcantalupo at gmail.com> wrote:
> Hi Carne,
>
> Take a look at the synopsis of
> Bio::Tools::Run::StandAloneBlastPlus::BlastMethods. I think you need to use
> the method_args parameter:
>
>  $result = $fac->blastn( -query => 'query_seqs.fas',
>                          -outfile => 'query.bls',
>                          -method_args => [ '-dust' => 'no' ] );
>

Hi Paul

thank for your reply but where do you see this documentation? This is
neither in the last release [1], the bioperl-run repository [2], or
the bioperl-live [3] (which doesn't even have ::BlastMethods).

Also, I did what you say but get a "Blast run: parameter 'dust' is not
available for method 'tblastn'" error.

This is my simple code, from the very start (including creation of the
database):

Bio::Tools::Run::StandAloneBlastPlus->new(
  -db_data => $db_data,
  -db_name => $db_name,
  -create => 1,
)->make_db();

my $fac = Bio::Tools::Run::StandAloneBlastPlus->new(
  -db_name => $db_name,
);

foreach my $file (@files) {
  my $result = $fac->tblastn(
    -query   => $file,
    -outfile => $file . '.bls',
    -method_args => ['-dust' => 'no'],
  );
  ## do stuff with $result
}

Thank you
Carnë

[1] https://metacpan.org/pod/Bio::Tools::Run::StandAloneBlastPlus::BlastMethods
[2] https://github.com/bioperl/bioperl-run/blob/master/lib/Bio/Tools/Run/StandAloneBlastPlus/BlastMethods.pm
[3] https://github.com/bioperl/bioperl-live/blob/master/Bio/Tools/Run/StandAloneBlast.pm