scbi_blast 0.0.31 → 0.0.32

data/History.txt

@@ -1,3 +1,7 @@
+=== 0.0.32 2011-06-01
+
+Added merge support to hits
+
 === 0.0.31 2011-04-28
 
 * First release at rubygem:

data/Rakefile

@@ -12,7 +12,7 @@ Hoe.plugin :newgem
 # Run 'rake -T' to see list of generated tasks (from gem root directory)
 $hoe = Hoe.spec 'scbi_blast' do
   self.developer 'Dario Guerrero & Almudena Bocinos', 'dariogf@gmail.com, alkoke@gmail.com'
-  self.post_install_message = 'PostInstall.txt' # TODO remove if post-install message not required
+  # self.post_install_message = 'PostInstall.txt' # TODO remove if post-install message not required
   self.rubyforge_name       = self.name # TODO this is default value
   # self.extra_deps         = [['activesupport','>= 2.0.2']]
 
@@ -23,4 +23,4 @@ Dir['tasks/**/*.rake'].each { |t| load t }
 
 # TODO - want other tests/tasks run by default? Add them to the list
 # remove_task :default
-# task :default => [:spec, :features]
+task :default => [:spec, :features, :redocs]

data/lib/scbi_blast/blast_hit.rb

@@ -117,6 +117,14 @@ class BlastHit
   def get_subject
     return @subject_id
   end
+  
+  def query_overlaps?(hit,threshold=0)
+    return ((@q_beg<=(hit.q_end+threshold)) and ((@q_end+threshold)>=hit.q_beg))
+  end
+  
+  def size
+    return (@q_end-@q_beg+1)
+  end
 
   # readers and accessor for properties
   attr_accessor :q_beg, :q_end, :s_beg, :s_end

data/lib/scbi_blast/blast_query.rb

@@ -1,5 +1,5 @@
 # Copyright (c) 2010 Dario Guerrero & Almudena Bocinos
-# 
+#
 # Permission is hereby granted, free of charge, to any person obtaining
 # a copy of this software and associated documentation files (the
 # 'Software'), to deal in the Software without restriction, including
@@ -7,10 +7,10 @@
 # distribute, sublicense, and/or sell copies of the Software, and to
 # permit persons to whom the Software is furnished to do so, subject to
 # the following conditions:
-# 
+#
 # The above copyright notice and this permission notice shall be
 # included in all copies or substantial portions of the Software.
-# 
+#
 # THE SOFTWARE IS PROVIDED 'AS IS', WITHOUT WARRANTY OF ANY KIND,
 # EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
 # MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
@@ -34,7 +34,7 @@ class BlastQuery
     @hits = []
     # inspect
   end
-  
+
   # add a hit to query
   def add_hit(h)
     @hits.push h
@@ -59,6 +59,49 @@ class BlastQuery
     return @hits.sort(comand)
   end
 
-end
+  # merge overlapping hits
+  def merged_hits!(overlap_threshold=0, merged_ids=nil)
+    res = []
+
+    merge_hits(@hits,res,merged_ids)
+
+    begin
+      res2=res # iterate until no more overlaps
+      res = []
+      merge_hits(res2,res,merged_ids)
+    end until (res2.count == res.count)
+
+
+    return res
+  end
+
+private
 
+  # do only one iteration of merge hits 
+  def merge_hits(hits,merged_hits,merged_ids=nil)
+    # puts " merging ============"
+    hits.each do |hit|
 
+      # save definitions
+      merged_ids.push hit.definition if !merged_ids.nil? && (!merged_ids.include?(hit.definition))
+
+      # find overlapping hits
+      c=merged_hits.find{|c| hit.query_overlaps?(c)}
+
+      if (c.nil?)
+        # add new hit
+        merged_hits.push(hit.dup)
+      else
+
+        # merge with old hit
+        c.q_beg=[c.q_beg,hit.q_beg].min
+        c.q_end=[c.q_end,hit.q_end].max
+
+        c.subject_id += ' ' + hit.subject_id if (not c.subject_id.include?(hit.subject_id))
+
+      end
+
+    end
+  end
+
+end

data/lib/scbi_blast.rb

@@ -31,7 +31,7 @@ require 'blast_hit'
 require 'blast_table_result'
 
 module ScbiBlast
-  VERSION = '0.0.31'
+   VERSION = '0.0.32'
 end
 
 

metadata

@@ -2,7 +2,7 @@
 name: scbi_blast
 version: !ruby/object:Gem::Version 
   prerelease: 
-  version: 0.0.31
+  version: 0.0.32
 platform: ruby
 authors: 
 - Dario Guerrero & Almudena Bocinos
@@ -10,7 +10,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2011-04-28 00:00:00 Z
+date: 2011-06-01 00:00:00 Z
 dependencies: 
 - !ruby/object:Gem::Dependency 
   name: hoe
@@ -61,7 +61,7 @@ files:
 homepage: http://www.scbi.uma.es/downloads
 licenses: []
 
-post_install_message: PostInstall.txt
+post_install_message: 
 rdoc_options: 
 - --main
 - README.rdoc