examples/searchio/waba2gff.pl

   1 #!/usr/bin/perl
   2 use strict;
   3 use Bio::SearchIO;
   4 use Getopt::Long;
   5 use Benchmark;
   6
   7 my ($infile,$outfile,$verbose);
   8
   9 GetOptions(
  10             'i|input:s'  => \$infile,
  11             'o|output:s' => \$outfile,
  12             'v|verbose'  => \$verbose,
  13             );
  14 $infile = shift unless $infile;
  15
  16 my $in = new Bio::SearchIO(-format => 'waba',
  17                            -file   => $infile, #comment out to read from STDIN
  18                            #-fh => \*ARGV,  # uncomment to read from STDIN
  19                            -verbose => $verbose);
  20
  21 my $out;
  22 if( defined $outfile) {
  23     $out = new Bio::Tools::GFF(-file => ">$outfile");
  24 } else {
  25     $out = new Bio::Tools::GFF(-verbose => $verbose);
  26 }
  27
  28 while( my $r = $in->next_result ) {
  29     while( my $hit = $r->next_hit ) {
  30         while( my $hsp = $hit->next_hsp ) {
  31             $out->write_feature($hsp);
  32         }
  33     }
  34 }