revamped find_homopolymers

[biopieces.git] / bp_bin / find_homopolymers

diff --git a/bp_bin/find_homopolymers b/bp_bin/find_homopolymers
index 89b8e8c1d03c3360fe1463855c437b31ee9318c8..c0885e3d3bb010a1363af0ff57dd24e8acf819cc 100755 (executable)
--- 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
@@ -31,9 +31,14 @@
 
 require 'maasha/biopieces'
 require 'maasha/seq'
+require 'pp'
+
+class Seq; include Homopolymer; end
 
 casts = []
-casts << {:long=>'min', :short=>'m', :type=>'uint', :mandatory=>false, :default=>1, :allowed=>nil, :disallowed=>"0"}
+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)
 
@@ -42,10 +47,42 @@ Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
     if record[:SEQ]
       seq = Seq.new(nil, record[:SEQ])
 
-      record[:HOMOPOL_MAX] = seq.homopol_max(options[:min])
+      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
-
-    output.puts record
   end
 end