# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-require 'biopieces'
-require 'seq'
-require 'pp'
+require 'maasha/biopieces'
+require 'maasha/seq'
casts = []
casts << {:long=>'min', :short=>'m', :type=>'uint', :mandatory=>false, :default=>1, :allowed=>nil, :disallowed=>"0"}
-bp = Biopieces.new
+options = Biopieces.options_parse(ARGV, casts)
-options = bp.parse(ARGV, casts)
+Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
+ input.each_record do |record|
+ if record[:SEQ]
+ seq = Seq.new(nil, record[:SEQ])
-bp.each_record do |record|
- if record.has_key? :SEQ
- seq = Seq.new(nil, record[:SEQ])
+ record[:HOMOPOL_MAX] = seq.homopol_max(options[:min])
+ end
- record[:HOMOPOL_MAX] = seq.homopol_max(options[:min])
+ output.puts record
end
-
- bp.puts record
end