Bioperl: Blast.pm parses a max of 250 hits?

[Phil Xiang]

Dear all,

I am trying to parse the first HSPs of BLAST hits using the following code:

use Bio::Tools::Blast;

        $blast = Bio::Tools::Blast->new( -file   => "$accession.blastn",
                                        -parse  => 1,
                                        -descr  => 1000,
                                        -align  => 1000,
                                        -signif => '1e-10',
                                        );

        foreach $hit ($blast->hits) {
            printf "%d\t%s\t%d\t%s\t%d\t%d\t%.1e\t%d\t%.2f\t%d\t%d\n",
                $phase, $accession, $blast->length, $hit->name,
$hit->length,
                $hit->bits, $hit->expect,
                $hit->hsp->length, $hit->frac_identical,
                $hit->hsp->start('query'), $hit->hsp->end('query');
        }


Why is it that I don't get more than 250 output records even though the
input BLAST result file contains 1000 hits?

I'd appreciate if anybody can tell me how to get around this restriction.


--

      Phil Xiang, Ph. D.                              ~~~~~~~~~~~~~~~~~~~~~
      Manager, Scientific Computing                   ~~~ from wormhole ~~~
      Tularik Inc, South San Francisco                ~~~   to worms    ~~~
      (650) 825-7414 (work), -4318 (fax)              ~~~~~~~~~~~~~~~~~~~~~

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