X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bp_bin%2Ffind_homopolymers;h=c0885e3d3bb010a1363af0ff57dd24e8acf819cc;hb=2f0fd91b461033529a4a72e161bd133252a22eb6;hp=5c9cd245dbcef4ba3373a512783b7b0756502510;hpb=494dc53ebd515b1e3e9b91bbebf43059899ca4ce;p=biopieces.git

diff --git a/bp_bin/find_homopolymers b/bp_bin/find_homopolymers
index 5c9cd24..c0885e3 100755
--- a/bp_bin/find_homopolymers
+++ b/bp_bin/find_homopolymers
@@ -1,6 +1,6 @@
 #!/usr/bin/env ruby
 
-# Copyright (C) 2007-2010 Martin A. Hansen.
+# Copyright (C) 2007-2013 Martin A. Hansen.
 
 # This program is free software; you can redistribute it and/or
 # modify it under the terms of the GNU General Public License
@@ -33,21 +33,57 @@ require 'maasha/biopieces'
 require 'maasha/seq'
 require 'pp'
 
-casts = []
-casts << {:long=>'min', :short=>'m', :type=>'uint', :mandatory=>false, :default=>1, :allowed=>nil, :disallowed=>"0"}
-
-bp = Biopieces.new
-
-options = bp.parse(ARGV, casts)
+class Seq; include Homopolymer; end
 
-bp.each_record do |record|
-  if record.has_key? :SEQ
-    seq = Seq.new(nil, record[:SEQ])
-
-    record[:HOMOPOL_MAX] = seq.homopol_max(options[:min])
+casts = []
+casts << {:long=>'min',     :short=>'m', :type=>'uint', :mandatory=>false, :default=>1,   :allowed=>nil, :disallowed=>"0"}
+casts << {:long=>'limit',   :short=>'l', :type=>'uint', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>"0"}
+casts << {:long=>'longest', :short=>'L', :type=>'flag', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
+
+options = Biopieces.options_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])
+
+      longest = Seq::Homopolymer.new("", 0, 0)
+      got_one = false
+      count   = 0
+
+      seq.each_homopolymer(options[:min]) do |h|
+        got_one = true
+
+        record[:HOMOPOL_PAT] = h.pattern
+        record[:HOMOPOL_LEN] = h.length
+        record[:HOMOPOL_POS] = h.pos
+
+        if options[:longest]
+          longest = h.length > longest.length ? h : longest
+        else
+          output.puts record
+
+          count += 1
+
+          break if options[:limit] and options[:limit] == count
+        end
+      end
+
+      if options[:longest]
+        if longest.length > options[:min]
+          record[:HOMOPOL_PAT] = longest.pattern
+          record[:HOMOPOL_LEN] = longest.length
+          record[:HOMOPOL_POS] = longest.pos
+        end
+
+        output.puts record
+      elsif not got_one
+        output.puts record
+      end
+    else
+      output.puts record
+    end
   end
-
-  bp.puts record
 end