[Bioperl-l] problem with SearchIO and writer

[diriano at uni-potsdam.de]

Dear all,

I have a small problem parsing a BLAST report with SearchIO and using
TextResultWriter.

I have a large file with several BLAST results, I instantiate SearchIO as:

my $searchio = new Bio::SearchIO ('-format' => 'blast', '-file' =>
"$blastFile");

##then I extract each individual report as
while (my $result = $searchio->next_result){
  my $writertxt = Bio::SearchIO::Writer::TextResultWriter->new();
  my $blastresult=$writertxt->to_string($result);
  while (my $hit = $result->next_hit){
    print $hit->name."\n";
  }
}
-- 

Diego Mauricio Riaño-Pachón
Biologist
Institute of Biology and Biochemistry
University of Potsdam
Karl-Liebknecht-Str. 24-25
Haus 20
14476 Golm
Germany
Tel:0331/977-2809
http://www.geocities.com/dmrp.geo/