bin/gff3-fetch in bio-gff3-0.8.7 vs bin/gff3-fetch in bio-gff3-0.9.0

@@ -1,16 +1,15 @@
-#! /usr/bin/ruby
+#! /usr/bin/env ruby
 #
 # Author:: Pjotr Prins
-# Copyright:: August 2010
 # License:: Ruby License
-#
-# Copyright (C) 2010,2011 Pjotr Prins <[e-mail]>
 
+COPYRIGHT = "Copyright (C) 2010-2012 Pjotr Prins <[e-mail]>"
+
 USAGE = <<EOM
 
-  Fetch and assemble GFF3 types (e.g. ORF, mRNA, CDS) + print in FASTA format. 
+  Fetch and assemble GFF3 types (ORF, mRNA, CDS) + print in FASTA format. 
 
     gff3-fetch [options] type [filename.fa] filename.gff3
 
     --translate      : output as amino acid sequence 
     --validate       : validate GFF3 file by translating
@@ -39,14 +38,14 @@
     --emboss         : use EMBOSS translation (fast) -- NYI
 
   Where (NYI == Not Yet Implemented):
 
   Multiple GFF3 files can be used. With external FASTA files, always the last
-  one before the GFF3 filename is matched.
+  one before the GFF3 filename is matched. Make sure the FASTA file
+  comes before the GFF3 file on the command line.
 
-  Note that above switches are only partially implemented at this stage. Full
-  feature support is projected Feb. 2011.
+  Note that above switches are only partially implemented at this stage.
 
   Examples:
 
     Assemble mRNA and CDS information from test.gff3 (which includes sequence information)
 
@@ -124,15 +123,19 @@
 
 == Cite
 
   If you use this software, please cite 
   
+    http://dx.doi.org/10.1093/bioinformatics/bts080
+
+  or
+
     http://dx.doi.org/10.1093/bioinformatics/btq475
 
 == Copyright
 
-Copyright (C) 2010,2011 Pjotr Prins <[e-mail]> 
+#{COPYRIGHT}
 
 EOM
 
 rootpath = File.dirname(File.dirname(__FILE__))
 $: << File.join(rootpath,'lib')
@@ -142,11 +145,11 @@
 require 'bio-gff3'
 require 'optparse'
 require 'ostruct'
 require 'bio/output/gfffastawriter'
 
-$stderr.print "BioRuby GFF3 Plugin "+GFF3_VERSION+" Copyright (C) 2010,2011 Pjotr Prins <[e-mail]>\n\n"
+$stderr.print "gff3-fetch (biogem Ruby #{RUBY_VERSION}) "+GFF3_VERSION+" "+COPYRIGHT+"\n\n"
 
 if ARGV.size == 0
   print USAGE
 end
 
@@ -156,11 +159,11 @@
 options = OpenStruct.new()
 
 # ---- Default options
 options.parser = :line
 
-opts = OptionParser.new() { |opts|
+opts2 = OptionParser.new() { |opts|
   opts.on_tail("-h", "--help", "Show help and examples") {
     print(opts)
     print USAGE
     exit()
   }
@@ -237,9 +240,10 @@
     Bio::Log::CLI.trace('debug')
     options.debug = true
   end
 
  }
+opts = opts2
 opts.parse!(ARGV)
 
 Bio::Log::CLI.configure('bio-gff3')
 
 gfftype = ARGV.shift