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

[Steve Chervitz]

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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