added classify_taxonomy (unfinished biopiece)

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1841 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/bp_bin/classify_taxonomy b/bp_bin/classify_taxonomy
new file mode 100755 (executable)
index 0000000..12aabb8
--- /dev/null
+++ b/bp_bin/classify_taxonomy
@@ -0,0 +1,180 @@
+#!/usr/bin/env ruby
+
+# Copyright (C) 2007-2012 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
+# as published by the Free Software Foundation; either version 2
+# of the License, or (at your option) any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+
+# http://www.gnu.org/copyleft/gpl.html
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# This program is part of the Biopieces framework (www.biopieces.org).
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# Classify records with taxonomy information.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+require 'pp'
+require 'maasha/biopieces'
+
+class TaxTable
+  def initialize
+    @q_hash = Hash.new { |h, k| h[k] = [] }
+  end
+
+  # Method to add to the TaxTree a GreenGenes entry.
+  def add_gg(q_id, s_id, score)
+    hash = {}
+
+    s_id.scan(/ ([\w])__([^;]+)/) do
+      level = $1
+      name  = $2
+
+      hash[expand_level(level).to_sym] = name
+    end
+
+    @q_hash[q_id.to_sym] << hash
+  end
+
+  def lowest_common_ancestor
+    @q_hash.each do |q_id, list|
+      count_hash = Hash.new { |h, k| h[k] = Hash.new(0) }
+
+      list.each do |elem|
+        elem.each do |level, name|
+          count_hash[level][name] += 1
+        end
+      end
+
+      list.each do |elem|
+        elem.each do |level, name|
+          elem.delete(level) if count_hash[level].size > 1
+        end
+      end
+    end
+  end
+
+  def uniq
+    lookup_hash = Hash.new
+    new_hash    = Hash.new { |h, k| h[k] = [] }
+
+    @q_hash.each do |q_id, list|
+      list.each do |elem|
+        unless lookup_hash[elem.to_s]
+          new_hash[q_id] << elem
+          lookup_hash[elem.to_s] = true
+        end
+      end
+    end
+
+    @q_hash = new_hash
+  end
+
+  def count
+    count_hash = Hash.new { |h, k| h[k] = Hash.new(0) }
+    new_hash   = Hash.new { |h, k| h[k] = [] }
+
+    @q_hash.each do |q_id, list|
+      list.each do |elem|
+        elem.each do |level, name|
+          count_hash[level][name] += 1
+        end
+      end
+    end
+
+    @q_hash.each do |q_id, list|
+      new_list = []
+
+      list.each do |elem|
+        new_elem = {}
+        
+        elem.each do |level, name|
+          new_elem[level] = name
+          new_elem["#{level}_count".to_sym] = count_hash[level][name]
+        end
+
+        new_list << new_elem
+      end
+
+      new_hash[q_id] = new_list
+    end
+
+    @q_hash = new_hash
+  end
+
+  def each
+    @q_hash.each do |q_id, list|
+      list.each do |elem|
+        yield elem
+      end
+    end
+  end
+
+  private
+
+  def expand_level(level)
+    case level
+    when 'd' then level = "domain"
+    when 'k' then level = "kingdom"
+    when 'p' then level = "phylum"
+    when 'c' then level = "class"
+    when 'o' then level = "order"
+    when 'f' then level = "family"
+    when 'g' then level = "genus"
+    when 's' then level = "species"
+    else
+      raise "unknown level: #{level}"
+    end
+
+    level
+  end
+end
+
+casts = []
+casts << {:long=>'LCA',  :short=>'l', :type=>'flag', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'uniq', :short=>'u', :type=>'flag', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
+
+options = Biopieces.options_parse(ARGV, casts)
+
+taxtab = TaxTable.new
+
+Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
+  input.each_record do |record|
+    if record[:Q_ID] and record[:S_ID] and record[:SCORE]
+      taxtab.add_gg(record[:Q_ID], record[:S_ID], record[:SCORE])
+    end
+  end
+
+  taxtab.lowest_common_ancestor if options[:LCA]
+  taxtab.uniq                   if options[:uniq]
+  taxtab.count
+
+  taxtab.each do |tax|
+    record = {}
+
+    tax.each { |k, v| record[k.upcase] = v }
+
+    output.puts record
+  end
+end
+
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+__END__