bin/gff3-fetch in bio-gff3-0.8.3 vs bin/gff3-fetch in bio-gff3-0.8.4

@@ -24,11 +24,11 @@
   type is any valid type in the GFF3 definition. For example:
 
     mRNA            : assemble mRNA
     CDS             : assemble CDS 
     exon            : list all exons
-    gene/ORF        : list gene ORFs -- NYI
+    gene|ORF        : list gene ORFs 
     other           : use any type from GFF3 definition, e.g. 'Terminate' -- NYI
 
   and the following performance options:
 
     --cache full    : load all in RAM (fast)
@@ -165,12 +165,10 @@
 }
 opts.parse!(ARGV)
 
 gfftype = ARGV.shift
 
-raise "Unknown GFF type '#{gfftype}'" if gfftype !~ /mrna|cds|exon/i
-
 fastafn = nil
 
 ARGV.each do | fn |
   if File.extname(fn) =~ /fa|fas|fasta$/i
     raise "Only one fasta file allowed per GFF3" if fastafn != nil
@@ -187,11 +185,19 @@
   opts[:fix] = options.fix
   gffdb = Bio::GFFbrowser::GFFdb.new(fn,opts)
   gff = gffdb.assembler
   writer = Bio::GFFbrowser::FastaWriter.new(options.translate, options.validate)
   case gfftype.downcase
-    when 'mrna' 
+    when 'gene'
+          gff.each_gene_seq do | id, seq |
+            writer.put(id,seq)
+          end
+    when 'orf'
+          gff.each_gene_seq do | id, seq |
+            writer.put(id,seq)
+          end
+    when 'mrna'
           gff.each_mRNA_seq do | id, seq |
             writer.put(id,seq)
           end
     when 'exon'
           gff.each_exon_seq do | id, seq |
@@ -200,10 +206,10 @@
     when 'cds'
           gff.each_CDS_seq do | id, seq |
             writer.put(id,seq)
           end
     else
-      raise "Unknown action <#{gfftype}>"
+      raise "Unknown action on type <#{gfftype}>"
   end
   fastafn = nil
 end