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#!/usr/bin/perl
use strict;
use warnings;
HideShow 39 lines of Pod
=head1 NAME
bp_filter_search - filters searchio results, outputting a tab delimited summary
=head1 SYNOPSIS
  #bp_filter_search -format blast -score 200 < search.bl > search.tab
=head1 DESCRIPTION 
This script filters searchio results allowing a number of different
filters to be applied before outputting to stdout in a tab delimited
format.
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list.  Your participation is much appreciated.
  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via
email or the web:
  https://github.com/bioperl/bioperl-live/issues
=head1 AUTHOR
  Ewan Birney <birney@ebi.ac.uk>
=cut
use Bio::SearchIO;
use Getopt::Long;
my ($format,$score);
$format  = 'blast';
$score   = 150;
GetOptions(
           'format:s'  => \$format,
           'score:s'  => \$score,
        );
my $searchin = Bio::SearchIO->new( -format => $format);
while( (my $result = $searchin->next_result()) ) { 
  while( (my $hit = $result->next_hit())) {
      if( $score ) {
        if( $hit->raw_score < $score ) {
           next;
        }
       }
      foreach my $hsp ( $hit->hsps() ) {
         print $result->query_name,"\t",$hit->score,"\t",$hsp->start,"\t",$hsp->end,"\t",$hsp->strand,"\t",$hsp->hseq_id,"\t",$hsp->hstart,"\t",$hsp->hend,"\t",$hsp->strand,"\n";
      }
    }
}