#!/usr/bin/perl use strict; use Bio::SearchIO; use Getopt::Long; use Benchmark; my ($infile,$outfile,$verbose); GetOptions( 'i|input:s' => \$infile, 'o|output:s' => \$outfile, 'v|verbose' => \$verbose, ); $infile = shift unless $infile; my $in = new Bio::SearchIO(-format => 'waba', -file => $infile, #comment out to read from STDIN #-fh => \*ARGV, # uncomment to read from STDIN -verbose => $verbose); my $out; if( defined $outfile) { $out = new Bio::Tools::GFF(-file => ">$outfile"); } else { $out = new Bio::Tools::GFF(-verbose => $verbose); } while( my $r = $in->next_result ) { while( my $hit = $r->next_hit ) { while( my $hsp = $hit->next_hsp ) { $out->write_feature($hsp); } } }