[Bioperl-l] RemoteBlast retrieve_blast cannot return Bio::SearchIO::blasttable

[Paul G Cantalupo]

Hello,

When using RemoteBlast with ALIGNMENT_VIEW = 'Tabular' (-m8 output) the 
method 'retrieve_blast' should return a Bio::SearchIO::blasttable object 
to handle the parsing of -m8 output. I think the easiest way to do this is 
by changing 'retrieve_blast'

FROM:

if( $self->readmethod =~ /BPlite/ ) {
    $blastobj = new Bio::Tools::BPlite(-file => $tempfile);
} else {
    $blastobj = new Bio::SearchIO( -file => $tempfile,
                                   -format => 'blast');
}


TO:


if( $self->readmethod =~ /BPlite/ ) {
    $blastobj = new Bio::Tools::BPlite(-file => $tempfile);
} elsif( $self->readmethod =~ /blasttable/ ) {
    $blastobj = new Bio::SearchIO( -file => $tempfile,
                                   -format => 'blasttable');
} else {
    $blastobj = new Bio::SearchIO( -file => $tempfile,
                                   -format => 'blast');
}


Any suggestions/criticisms?

Paul


Paul Cantalupo
Research Specialist/Systems Programmer
559 Crawford Hall
Department of Biological Sciences
University of Pittsburgh
Pittsburgh, PA 15260
Work: 412-624-4687
Fax: 412-624-4759

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