examples/tools/gb_to_gff.pl

   1 #!/usr/local/bin/perl
   2 use strict;
   3
   4 use Bio::Tools::GFF;
   5 use Bio::SeqIO;
   6
   7 my ($seqfile) = @ARGV;
   8 die("must define a valid seqfile to read") unless ( defined $seqfile && -r $seqfile);
   9
  10 my $seqio = new Bio::SeqIO(-format => 'genbank',
  11                            -file   => $seqfile);
  12 my $count = 0;
  13 while( my $seq = $seqio->next_seq ) {
  14     $count++;
  15     # defined a default name
  16     my $fname = sprintf("%s.gff", $seq->display_id || "seq-$count");
  17     my $gffout = new Bio::Tools::GFF(-file => ">$fname" ,
  18                                      -gff_version => 1);
  19
  20     foreach my $feature ( $seq->top_SeqFeatures() ) {
  21         $gffout->write_feature($feature);
  22     }
  23 }