[Bioperl-l] Is it possible to parse BLAST output using IO:String?

Bernhard Schmalhofer Bernhard.Schmalhofer at biomax.com
Thu Nov 2 03:53:14 EST 2006


Bernd Web wrote:
> Hi Ryan,
> 
> I parse blastn output using IO::String w/o problems:
> 
>  my $stringfh = new IO::String($input);
>  my $in = new Bio::SearchIO(-format => 'blast', -fh => $stringfh);

I do the same with implicitly using IO::String. Works like a charm at 
leaset with Perl 5.8.0.

  # get $blast_report from MySQL
  open my $blast_report_fh, '<', \$blast_report;
  my $in = Bio::SearchIO->new( -format => 'blast',
                               -fh     => $blast_report_fh );

Regards,
   Bernhard


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Dipl.-Physiker Bernhard Schmalhofer
Senior Developer
Biomax Informatics AG
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eMail: Bernhard.Schmalhofer at biomax.com
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