rbfam 0.0.2 → 0.0.5

data/README.md

@@ -0,0 +1,4 @@
+rbfam
+=====
+
+Light wrapper for RFam data in Ruby.

data/lib/rbfam.rb

@@ -1,14 +1,13 @@
 require "bio"
 require "vienna_rna"
+require "entrez"
 require "httparty"
 require "active_support/inflector"
 
+Dir[File.join(File.dirname(__FILE__), "rbfam", "modules", "*.rb")].each { |name| require "rbfam/modules/#{File.basename(name, '.rb')}" }
+
 module Rbfam
-  Dir[File.join(File.dirname(__FILE__), "/modules/*")].each do |file|
-    autoload File.basename(file, ".rb").camelize.to_sym, file
-  end
-  
   def self.script(name)
-    require File.dirname(__FILE__) + "/scripts/#{File.basename(name, '.rb')}.rb"
+    require "rbfam/scripts/#{File.basename(name, '.rb')}"
   end
 end

data/lib/{modules → rbfam/modules}/alignment.rb

@@ -54,7 +54,7 @@ module Rbfam
     def parse_line(line)
       line_match = line.match(LINE_REGEXP)
       
-      Rbfam::Sequence.new(family, line_match[1], line_match[2].to_i, line_match[3].to_i, autoload: { length: 300, extend: 3 })
+      Rbfam::Sequence.new(family, line_match[1], line_match[2].to_i, line_match[3].to_i, autoload: true)
     end
   end
 end

data/lib/{modules → rbfam/modules}/family.rb

@@ -54,7 +54,7 @@ module Rbfam
     def parse_line(line)
       split_line = line.split(/\t/)
       
-      Rbfam::Sequence.new(self, split_line[0], split_line[2].to_i, split_line[3].to_i, autoload: { length: 300, extend: 3 })
+      Rbfam::Sequence.new(self, split_line[0], split_line[2].to_i, split_line[3].to_i, autoload: true)
     end
   end
 end

data/lib/{modules → rbfam/modules}/sequence.rb

@@ -6,7 +6,7 @@ module Rbfam
       @family, @accession, @from, @to = family, accession, from, to
       
       if options[:sequence]
-        @raw_sequence = options[:sequence]
+        @raw_sequence = (options[:sequence].is_a?(String) ? Bio::Sequence::NA.new(options[:sequence]) : options[:sequence])
       end
       
       if options[:autoload]
@@ -24,8 +24,8 @@ module Rbfam
         sequence_length: sequence.length, 
         from:            from, 
         to:              to, 
-        seq_from:        up_coord + coord_window({ length: 300, extend: 3 }).min, 
-        seq_to:          up_coord + coord_window({ length: 300, extend: 3 }).max,
+        seq_from:        up_coord + coord_window(options[:coord_window] || {}).min, 
+        seq_to:          up_coord + coord_window(options[:coord_window] || {}).max,
         seed:            options[:seed]
       })
     end
@@ -66,6 +66,8 @@ module Rbfam
     end
     
     def coord_window(options = {})
+      # Ex: { length: 300, extend: 3 }
+      
       range = 0..(down_coord - up_coord)
       
       if options[:length] && options[:extend]

data/lib/{modules → rbfam/modules}/utils.rb

@@ -1,8 +1,12 @@
-require "entrez"
-
 module Rbfam
   module Utils
     class << self
+      def simple_rna_sequence(id, from, to)
+        sequence = rna_sequence_from_entrez(id, [from, to].min, 0..((to - from).abs))
+          
+        to < from ? sequence.complement : sequence
+      end
+      
       def rna_sequence_from_entrez(id, position, window, buffer_size = 0)
         na_sequence_from_entrez(id, position, window, buffer_size).rna
       end

data/lib/{scripts → rbfam/scripts}/sequences_in_mysql.rb

@@ -6,7 +6,7 @@ class Object; def this; self; end; end
 class SequenceTable < ActiveRecord::Base
   self.table_name = "sequences"
   
-  validates_uniqueness_of :accession, scope: [:seq_from, :seq_to]
+  validates_uniqueness_of :accession, scope: [:sequence, :structure]
   
   def self.connect
     ActiveRecord::Base.establish_connection(config = { adapter: "mysql2", username: "root", reconnect: true })
@@ -20,8 +20,12 @@ class SequenceTable < ActiveRecord::Base
     inline_rails if defined?(inline_rails)
   end
   
-  def to_rbfam_sequence(family)
-    Rbfam::Sequence.new(family, accession, from, to, sequence: sequence)
+  def clean_description
+    ("%s %s %s" % [accession, seq_from, seq_to]).gsub(/[^A-Za-z0-9]/, "_")
+  end
+  
+  def to_rbfam_sequence(family = nil)
+    Rbfam::Sequence.new(family || Rbfam::Family.new(family), accession, from, to, sequence: sequence)
   end
 end
 

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: rbfam
 version: !ruby/object:Gem::Version
-  version: 0.0.2
+  version: 0.0.5
   prerelease: 
 platform: ruby
 authors:
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-07-06 00:00:00.000000000 Z
+date: 2012-07-25 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio
@@ -81,12 +81,13 @@ executables: []
 extensions: []
 extra_rdoc_files: []
 files:
-- ./lib/modules/alignment.rb
-- ./lib/modules/family.rb
-- ./lib/modules/sequence.rb
-- ./lib/modules/utils.rb
-- ./lib/rbfam.rb
-- ./lib/scripts/sequences_in_mysql.rb
+- lib/rbfam/modules/alignment.rb
+- lib/rbfam/modules/family.rb
+- lib/rbfam/modules/sequence.rb
+- lib/rbfam/modules/utils.rb
+- lib/rbfam/scripts/sequences_in_mysql.rb
+- lib/rbfam.rb
+- README.md
 homepage: http://rubygems.org/gems/rbfam
 licenses: []
 post_install_message: