fixed nasty bug in classify_taxonomy

[biopieces.git] / bp_bin / find_homopolymers

diff --git a/bp_bin/find_homopolymers b/bp_bin/find_homopolymers
index 097d651b6dcd2866c4ed749bb10898ddd4dfa267..3cad86f505fd60a28a251dbe7967561347ed4098 100755 (executable)
--- a/bp_bin/find_homopolymers
+++ b/bp_bin/find_homopolymers
@@ -29,24 +29,24 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-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.has_key? :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
+    output.puts record
   end
-
-  bp.puts record
 end