Given a Fasta file, print out GFF3-compatible '##sequence-region' pragmas. Often when GFF3 files are produced, the sequence-region pragmas indicate the coordinates directly bounding and sequence annotations rather than the entire sequence length. In some cases, having the entire sequence length is useful, and this script facilitates this.

seq-regions.pl

#!/usr/bin/env perl
use strict;
use Bio::SeqIO;
my $instream = Bio::SeqIO->new( -fh => \*STDIN, -format => "Fasta" );
while(my $seq = $instream->next_seq)
{
  printf("##sequence-region   %s %lu %lu\n", $seq->id, 1, $seq->length);
}