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

[Phil Xiang]

Steve,

Thank you very much for your response. I find the problem is indeed as you
described: it lies with my BLAST report. I should have been looked at it
more carefully before I ask.


--

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



----------
>From: Steve Chervitz <sac@neomorphic.com>
>To: "Phil Xiang" <xiang@tularik.com>
>Cc: Bioperl Bioperl <vsns-bcd-perl@lists.uni-bielefeld.de>
>Subject: Re: Bioperl: Blast.pm parses a max of 250 hits?
>Date: Sat, Dec 11, 1999, 12:07 PM
>

> Phil,
>
> Is it possible that your BLAST results file contains only 250
> alignment sections but has 1000 description lines? Another possibility
> is that you only have 250 hits that are at or below 1e-10 and you are
> screening out the rest with your -signif parameter, so you can try
> removing the -signif parameter.
>
> Note that the -descr and -align parameters in your example are not
> required when parsing existing reports. These are only used when
> running new BLAST analyses.
>
> Otherwise, there is nothing intrinsic to the Blast module that would
> limit the maximum number of hits that can be parsed.
>
> Steve Chervitz
> sac@neomorphic.com
>
> Phil Xiang writes:
>  >
>  > 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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