# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-require 'biopieces'
-require 'fasta'
-require 'prodigal'
+require 'maasha/biopieces'
+require 'maasha/fasta'
+require 'maasha/prodigal'
casts = []
-casts << {:long=>'full', :short=>'f', :type=>'flag', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'full', :short=>'f', :type=>'flag', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'procedure', :short=>'p', :type=>'string', :mandatory=>true, :default=>'single', :allowed=>'single,meta', :disallowed=>nil}
bp = Biopieces.new
prodigal.run
prodigal.each do |record|
+ record[:DEFINITION].match /seqhdr="([^"]+)/ do |m|
+ record[:S_ID] = $1
+ end
+
bp.puts record
end