[Bioperl-l] Number of hits

[Jonathan Epstein]

In my experience, this happens with BioPerl when the original query 
parameters were such that there are 365 summaries but only 50 
alignments.  BioPerl only parses the alignments, which is understandable 
but a little frustrating at times.  Naturally, it is not so obvious on 
visual inspection that you only have 50 alignments, but that is probably 
the case here.

You will probably need to redo your BLAST runs (that's what I had to do in 
this situation), judiciously using -v and -b:

   -v  Number of one-line descriptions (V) [Integer]
     default = 500
   -b  Number of alignments to show (B) [Integer]
     default = 250

HTH,

- Jonathan

At 07:42 PM 11/5/01, Ross Gibbs wrote:
>I am parsing a blast report with 365 hits in it but using the following I
>get only 50.
>
>Why?
>
>   $blast = Bio::Tools::Blast->new(-file   =>"$file",
>                                   -signif => 1e-07,
>                                   -parse  => 1,
>                                   -stats  => 1,
>                                   -check_all_hits => 1,
>                                                          );
>  ...
>
>   $num_hits =  $blast->num_hits;
>   print "HITS: $num_hits\n";
>
>
>
>Thanks
>
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