bin/bp_filter_search

   1 #!/usr/bin/perl
   2 use strict;
   3 use warnings;
   4
   5
   6 =head1 NAME
   7
   8 bp_filter_search - filters searchio results, outputting a tab delimited summary
   9
  10 =head1 SYNOPSIS
  11
  12   #bp_filter_search -format blast -score 200 < search.bl > search.tab
  13
  14 =head1 DESCRIPTION
  15
  16 This script filters searchio results allowing a number of different
  17 filters to be applied before outputting to stdout in a tab delimited
  18 format.
  19
  20 =head1 FEEDBACK
  21
  22 =head2 Mailing Lists
  23
  24 User feedback is an integral part of the evolution of this and other
  25 Bioperl modules. Send your comments and suggestions preferably to
  26 the Bioperl mailing list.  Your participation is much appreciated.
  27
  28   bioperl-l@bioperl.org                  - General discussion
  29   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  30
  31 =head2 Reporting Bugs
  32
  33 Report bugs to the Bioperl bug tracking system to help us keep track
  34 of the bugs and their resolution. Bug reports can be submitted via
  35 email or the web:
  36
  37   https://github.com/bioperl/bioperl-live/issues
  38
  39 =head1 AUTHOR
  40
  41   Ewan Birney <birney@ebi.ac.uk>
  42
  43 =cut
  44
  45 use Bio::SearchIO;
  46 use Getopt::Long;
  47
  48 my ($format,$score);
  49
  50 $format  = 'blast';
  51 $score   = 150;
  52
  53 GetOptions(
  54            'format:s'  => \$format,
  55            'score:s'  => \$score,
  56         );
  57
  58
  59 my $searchin = Bio::SearchIO->new( -format => $format);
  60
  61
  62 while( (my $result = $searchin->next_result()) ) {
  63   while( (my $hit = $result->next_hit())) {
  64
  65       if( $score ) {
  66         if( $hit->raw_score < $score ) {
  67            next;
  68         }
  69        }
  70
  71
  72       foreach my $hsp ( $hit->hsps() ) {
  73          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";
  74       }
  75     }
  76 }
  77
  78