bio 1.5.1 → 2.0.2

data/lib/bio/io/biosql/biosql.rb

@@ -1,39 +0,0 @@
-#require 'dm-ar-finders'
-#require 'dm-core'
-require 'erb'
-require 'composite_primary_keys'
-
-module Bio
- class SQL
-    class DummyBase < ActiveRecord::Base
-      #NOTE: Using postgresql, not setting sequence name, system will discover the name by default.
-      #NOTE: this class will not establish the connection automatically
-      self.abstract_class = true
-      self.pluralize_table_names = false
-      #prepend table name to the usual id, avoid to specify primary id for every table
-      self.primary_key_prefix_type = :table_name_with_underscore
-      #biosql_configurations=YAML::load(ERB.new(IO.read(File.join(File.dirname(__FILE__),'./config', 'database.yml'))).result)
-      #self.configurations=biosql_configurations
-      #self.establish_connection "development"
-    end #DummyBase
-
-    require 'bio/io/biosql/ar-biosql'
-    
-  #  #no check is made
-  def self.establish_connection(configurations, env)
-    #  #configurations is an hash similar what YAML returns.
-
-     #configurations.assert_valid_keys('development', 'production','test')
-     #configurations[env].assert_valid_keys('hostname','database','adapter','username','password')
-     DummyBase.configurations = configurations
-    connection = DummyBase.establish_connection "#{env}"
-    #Init of basis terms and ontologies
-    Ontology.first(:conditions => ["name = ?", 'Annotation Tags']) || Ontology.create({:name => 'Annotation Tags'})
-    Ontology.first(:conditions => ["name = ?", 'SeqFeature Keys']) || Ontology.create({:name => 'SeqFeature Keys'})
-    Ontology.first(:conditions => ["name = ?", 'SeqFeature Sources']) ||Ontology.create({:name => 'SeqFeature Sources'})
-    Term.first(:conditions => ["name = ?", 'EMBLGenBankSwit']) || Term.create({:name => 'EMBLGenBankSwit', :ontology => Ontology.first(:conditions => ["name = ?", 'SeqFeature Sources'])})
-    connection 
-  end #establish_connection
-  
-  end #SQL
-end #Bio

data/lib/bio/io/biosql/config/database.yml

@@ -1,21 +0,0 @@
-#This is the database configuration specific for BioSQL
-#User can configure it's db here
-
-development:
-  adapter: jdbcmysql
-  database: bioseq
-  username: febo
-  password:
-  hostname: localhost
-
-test:
-  adapter: postgresql
-  database: biorails_test
-  username: rails
-  password: 
-  
-production:
-  adapter: postgresql
-  database: biorails_production
-  username: rails
-  password: 

data/lib/bio/io/sql.rb

@@ -1,79 +0,0 @@
-#module Bio
- # class SQL
-  #  #no check is made
-   # def self.establish_connection(configurations, env)
-    #  #configurations is an hash similar what YAML returns.
-     # #{:database=>"biorails_development", :adapter=>"postgresql", :username=>"rails", :password=>nil}
-     # configurations.assert_valid_keys('development', 'production','test')
-     # configurations[env].assert_valid_keys('hostname','database','adapter','username','password')
-     # DummyBase.configurations = configurations
-     # DummyBase.establish_connection "#{env}"
-    #end
-
-
-#require 'rubygems'
-#require 'composite_primary_keys'
-#require 'erb'
-# BiosqlPlug
-
-=begin
-Ok Hilmar gives to me some clarification
-1) "EMBL/GenBank/SwissProt" name in term table, is only a convention assuming data loaded by genbank embl ans swissprot formats.
-   If your features come from others ways for example blast or alignment ... whatever.. the user as to take care about the source.
-
-
-=end
-=begin
-TODO:
-1) source_term_id => surce_term and check before if the source term is present or not and the level, the root should always be something "EMBL/GenBank/SwissProt" or contestualized.
-2) Into DummyBase class delete connection there and use Bio::ArSQL.establish_connection which reads info from a yml file.
-3) Chk Locations in Biofeatures ArSQL
-=end
-module Bio
-  class SQL
-
-    require 'bio/io/biosql/biosql'
-    autoload :Sequence, 'bio/db/biosql/sequence'
-
-    def self.fetch_id(id)
-      Bio::SQL::Bioentry.find(id)
-    end
-
-    def self.fetch_accession(accession)
-#     Bio::SQL::Bioentry.exists?(:accession => accession) ? Bio::SQL::Sequence.new(:entry=>Bio::SQL::Bioentry.find_by_accession(accession)) : nil
-      Bio::SQL::Sequence.new(:entry=>Bio::SQL::Bioentry.find_by_accession(accession.upcase))
-    end
-
-    def self.exists_accession(accession)
-#      Bio::SQL::Bioentry.find_by_accession(accession.upcase).nil? ? false : true
-      !Bio::SQL::Bioentry.find_by_accession(accession.upcase).nil?
-    end
-
-    def self.exists_database(name)
-#      Bio::SQL::Biodatabase.find_by_name(name).nil? ? false : true
-      !Bio::SQL::Biodatabase.first(:name=>name).nil?
-    end
-
-    def self.list_entries
-      Bio::SQL::Bioentry.all.collect do|entry|
-        {:id=>entry.bioentry_id, :accession=>entry.accession}
-      end
-    end
-
-    def self.list_databases
-      Bio::SQL::Biodatabase.all.collect do|entry|
-        {:id=>entry.biodatabase_id, :name => entry.name}
-      end
-    end
-
-    def self.delete_entry_id(id)
-      Bio::SQL::Bioentry.delete(id)
-    end
-
-    def self.delete_entry_accession(accession)
-      Bio::SQL::Bioentry.find_by_accession(accession.upcase).destroy!
-    end
-
-  end #biosql
-
-end #Bio

data/lib/bio/shell.rb

@@ -1,44 +0,0 @@
-#
-# = bio/shell.rb - Loading all BioRuby shell features
-#
-# Copyright::   Copyright (C) 2005, 2006
-#               Toshiaki Katayama <k@bioruby.org>
-# License::     The Ruby License
-#
-# $Id:$
-#
-
-require 'bio'
-require 'yaml'
-require 'open-uri'
-require 'fileutils'
-require 'pp'
-
-module Bio::Shell
-
-  require 'bio/shell/setup'
-  require 'bio/shell/irb'
-  require 'bio/shell/web'
-  require 'bio/shell/script'
-  require 'bio/shell/core'
-  require 'bio/shell/interface'
-  require 'bio/shell/object'
-  require 'bio/shell/demo'
-  require 'bio/shell/plugin/entry'
-  require 'bio/shell/plugin/seq'
-  require 'bio/shell/plugin/midi'
-  require 'bio/shell/plugin/codon'
-  require 'bio/shell/plugin/flatfile'
-  require 'bio/shell/plugin/obda'
-  require 'bio/shell/plugin/das'
-  require 'bio/shell/plugin/emboss'
-  require 'bio/shell/plugin/blast'
-  require 'bio/shell/plugin/psort'
-  require 'bio/shell/plugin/ncbirest'
-  require 'bio/shell/plugin/togows'
-
-  extend Ghost
-
-end
-
-

data/lib/bio/shell/core.rb

@@ -1,578 +0,0 @@
-#
-# = bio/shell/core.rb - internal methods for the BioRuby shell
-#
-# Copyright::   Copyright (C) 2005, 2006
-#               Toshiaki Katayama <k@bioruby.org>
-# License::     The Ruby License
-#
-#
-
-module Bio::Shell::Core
-
-  SHELLDIR = "shell"
-  DATADIR  = "data"
-  SESSION  = File.join(SHELLDIR, "session")
-  PLUGIN   = File.join(SHELLDIR, "plugin")
-  SCRIPT   = File.join(SHELLDIR, "script.rb")
-  CONFIG   = File.join(SESSION, "config")
-  OBJECT   = File.join(SESSION, "object")
-  HISTORY  = File.join(SESSION, "history")
-  BIOFLAT  = File.join(DATADIR, "bioflat")
-
-  MARSHAL = [ Marshal::MAJOR_VERSION, Marshal::MINOR_VERSION ]
-
-  MESSAGE = "...BioRuby in the shell..."
-
-  ESC_SEQ = {
-    :k => "\e[30m",  :black   => "\e[30m",
-    :r => "\e[31m",  :red     => "\e[31m",  :ruby  => "\e[31m",
-    :g => "\e[32m",  :green   => "\e[32m",
-    :y => "\e[33m",  :yellow  => "\e[33m",
-    :b => "\e[34m",  :blue    => "\e[34m",
-    :m => "\e[35m",  :magenta => "\e[35m",
-    :c => "\e[36m",  :cyan    => "\e[36m",
-    :w => "\e[37m",  :white   => "\e[37m",
-    :n => "\e[00m",  :none    => "\e[00m",  :reset => "\e[00m",
-  }
-
-  def colors
-    ESC_SEQ
-  end
-
-  def shell_dir
-    File.join(@cache[:savedir], SHELLDIR)
-  end
-
-  def data_dir
-    File.join(@cache[:savedir], DATADIR)
-  end
-
-  def session_dir
-    File.join(@cache[:savedir], SESSION)
-  end
-
-  def plugin_dir
-    File.join(@cache[:savedir], PLUGIN)
-  end
-
-  def script_file
-    File.join(@cache[:savedir], SCRIPT)
-  end
-
-  def script_dir
-    File.dirname(script_file)
-  end
-
-  def config_file
-    File.join(@cache[:savedir], CONFIG)
-  end
-
-  def object_file
-    File.join(@cache[:savedir], OBJECT)
-  end
-
-  def history_file
-    File.join(@cache[:savedir], HISTORY)
-  end
-
-  def bioflat_dir
-    File.join(@cache[:savedir], BIOFLAT)
-  end
-
-  def ask_yes_or_no(message)
-    loop do
-      STDERR.print "#{message}"
-      answer = gets
-      if answer.nil?
-        # readline support might be broken
-        return false
-      elsif /^\s*[Nn]/.match(answer)
-        return false
-      elsif /^\s*[Yy]/.match(answer)
-        return true
-      else
-        # loop
-      end
-    end
-  end
-
-end
-
-
-module Bio::Shell::Ghost
-
-  include Bio::Shell::Core
-
-  # A hash to store persistent configurations
-  attr_accessor :config
-
-  # A hash to store temporal (per session) configurations
-  attr_accessor :cache
-
-  ### save/restore the environment
-
-  def configure(savedir)
-    @config = {}
-    @cache  = {
-      :savedir => savedir,
-      :workdir => Dir.pwd,
-    }
-    create_save_dir
-    load_config
-    load_plugin
-  end
- 
-  def load_session
-    load_object
-    unless @cache[:mode] == :script
-      load_history
-      opening_splash
-      open_history
-    end
-  end
-
-  def save_session
-    unless @cache[:mode] == :script
-      closing_splash
-    end
-    if create_save_dir_ask
-      #save_history	# changed to use our own...
-      close_history
-      save_object
-      save_config
-    end
-    #STDERR.puts "Leaving directory '#{@cache[:workdir]}'"
-  end
-
-  ### directories
-
-  def create_save_dir
-    create_real_dir(session_dir)
-    create_real_dir(plugin_dir)
-    create_real_dir(data_dir)
-  end
-
-  def create_save_dir_ask
-    if File.directory?(session_dir)
-      @cache[:save] = true
-    end
-    unless @cache[:save]
-      if ask_yes_or_no("Save session in '#{@cache[:workdir]}' directory? [y/n] ")
-        create_real_dir(session_dir)
-        create_real_dir(plugin_dir)
-        create_real_dir(data_dir)
-        create_real_dir(bioflat_dir)
-        @cache[:save] = true
-      else
-        @cache[:save] = false
-      end
-    end
-    return @cache[:save]
-  end
-
-  def create_real_dir(dir)
-    unless File.directory?(dir)
-      begin
-        STDERR.print "Creating directory (#{dir}) ... "
-        FileUtils.makedirs(dir)
-        STDERR.puts "done"
-      rescue
-        warn "Error: Failed to create directory (#{dir}) : #{$!}"
-      end
-    end
-  end
-
-  ### bioflat
-
-  def create_flat_dir(dbname)
-    dir = File.join(bioflat_dir, dbname.to_s.strip)
-    unless File.directory?(dir)
-      FileUtils.makedirs(dir)
-    end
-    return dir
-  end
-
-  def find_flat_dir(dbname)
-    dir = File.join(bioflat_dir, dbname.to_s.strip)
-    if File.exist?(dir)
-      return dir
-    else
-      return nil
-    end
-  end
-
-  ### config
-
-  def load_config
-    load_config_file(config_file)
-  end
-
-  def load_config_file(file)
-    if File.exist?(file)
-      STDERR.print "Loading config (#{file}) ... "
-      if hash = YAML.load(File.read(file))
-        @config.update(hash)
-      end
-      STDERR.puts "done"
-    end
-  end
-
-  def save_config
-    save_config_file(config_file)
-  end
-
-  def save_config_file(file)
-    begin
-      STDERR.print "Saving config (#{file}) ... "
-      File.open(file, "w") do |f|
-        f.puts @config.to_yaml
-      end
-      STDERR.puts "done"
-    rescue
-      warn "Error: Failed to save (#{file}) : #{$!}"
-    end
-  end
-
-  def config_show
-    @config.each do |k, v|
-      STDERR.puts "#{k}\t= #{v.inspect}"
-    end
-  end
-
-  def config_echo
-    bind = Bio::Shell.cache[:binding]
-    flag = ! @config[:echo]
-    @config[:echo] = IRB.conf[:ECHO] = flag
-    eval("conf.echo = #{flag}", bind)
-    STDERR.puts "Echo #{flag ? 'on' : 'off'}"
-  end
-
-  def config_color
-    bind = Bio::Shell.cache[:binding]
-    flag = ! @config[:color]
-    @config[:color] = flag
-    if flag
-      IRB.conf[:PROMPT_MODE] = :BIORUBY_COLOR
-      eval("conf.prompt_mode = :BIORUBY_COLOR", bind)
-    else
-      IRB.conf[:PROMPT_MODE] = :BIORUBY
-      eval("conf.prompt_mode = :BIORUBY", bind)
-    end
-  end
-
-  def config_pager(cmd = nil)
-    @config[:pager] = cmd
-  end
-
-  def config_splash
-    flag = ! @config[:splash]
-    @config[:splash] = flag
-    STDERR.puts "Splash #{flag ? 'on' : 'off'}"
-    opening_splash
-  end
-
-  def config_message(str = nil)
-    str ||= MESSAGE
-    @config[:message] = str
-    opening_splash
-  end
-
-  ### plugin
-
-  def load_plugin
-    load_plugin_dir(plugin_dir)
-  end
-
-  def load_plugin_dir(dir)
-    if File.directory?(dir)
-      Dir.glob("#{dir}/*.rb").sort.each do |file|
-        STDERR.print "Loading plugin (#{file}) ... "
-        load file
-        STDERR.puts "done"
-      end
-    end
-  end
-
-  ### object
-
-  def check_marshal
-    if @config[:marshal] and @config[:marshal] != MARSHAL
-      raise "Marshal version mismatch"
-    end
-  end
-
-  def load_object
-    begin
-      check_marshal
-      load_object_file(object_file)
-    rescue
-      warn "Error: Load aborted : #{$!}"
-    end
-  end
-
-  def load_object_file(file)
-    if File.exist?(file)
-      STDERR.print "Loading object (#{file}) ... "
-      begin
-        bind = Bio::Shell.cache[:binding]
-        hash = Marshal.load(File.read(file))
-        hash.each do |k, v|
-          begin
-            Thread.current[:restore_value] = v
-            eval("#{k} = Thread.current[:restore_value]", bind)
-          rescue
-            STDERR.puts "Warning: object '#{k}' couldn't be loaded : #{$!}"
-          end
-        end
-      rescue
-        warn "Error: Failed to load (#{file}) : #{$!}"
-      end
-      STDERR.puts "done"
-    end
-  end
-
-  def save_object
-    save_object_file(object_file)
-  end
-
-  def save_object_file(file)
-    begin
-      STDERR.print "Saving object (#{file}) ... "
-      File.rename(file, "#{file}.old") if File.exist?(file)
-      File.open(file, "w") do |f|
-        bind = Bio::Shell.cache[:binding]
-        list = eval("local_variables", bind)
-        list.collect! { |x| x.to_s }
-        list -= ["_"]
-        hash = {}
-        list.each do |elem|
-          value = eval(elem, bind)
-          if value
-            begin
-              Marshal.dump(value)
-              hash[elem] = value
-            rescue
-              # value could not be dumped.
-            end
-          end
-        end
-        Marshal.dump(hash, f)
-        @config[:marshal] = MARSHAL
-      end
-      STDERR.puts "done"
-    rescue
-      File.rename("#{file}.old", file) if File.exist?("#{file}.old")
-      warn "Error: Failed to save (#{file}) : #{$!}"
-    end
-  end
-
-  ### history
-
-  def open_history
-    @cache[:histfile] = File.open(history_file, "a")
-    @cache[:histfile].sync = true
-  end
-
-  def store_history(line)
-    Bio::Shell.cache[:histfile].puts "# #{Time.now}"
-    Bio::Shell.cache[:histfile].puts line
-  end
-
-  def close_history
-    if @cache[:histfile]
-      STDERR.print "Saving history (#{history_file}) ... "
-      @cache[:histfile].close
-      STDERR.puts "done"
-    end
-  end
-
-  def load_history
-    if @cache[:readline]
-      load_history_file(history_file)
-    end
-  end
-
-  def load_history_file(file)
-    if File.exist?(file)
-      STDERR.print "Loading history (#{file}) ... "
-      File.open(file).each do |line|
-        unless line[/^# /]
-          Readline::HISTORY.push line.chomp
-        end
-      end
-      STDERR.puts "done"
-    end
-  end
-  
-  # not used (use open_history/close_history instead)
-  def save_history
-    if @cache[:readline]
-      save_history_file(history_file)
-    end
-  end
-
-  def save_history_file(file)
-    begin
-      STDERR.print "Saving history (#{file}) ... "
-      File.open(file, "w") do |f|
-        f.puts Readline::HISTORY.to_a
-      end
-      STDERR.puts "done"
-    rescue
-      warn "Error: Failed to save (#{file}) : #{$!}"
-    end
-  end
-
-  ### script
-
-  def script(mode = nil)
-    case mode
-    when :begin, "begin", :start, "start"
-      @cache[:script] = true
-      script_begin
-    when :end, "end", :stop, "stop"
-      @cache[:script] = false
-      script_end
-      save_script
-    else
-      if @cache[:script]
-        @cache[:script] = false
-        script_end
-        save_script
-      else
-        @cache[:script] = true
-        script_begin
-      end
-    end
-  end
-
-  def script_begin
-    STDERR.puts "-- 8< -- 8< -- 8< --  Script  -- 8< -- 8< -- 8< --"
-    @script_begin = Readline::HISTORY.size
-  end
-
-  def script_end
-    STDERR.puts "-- >8 -- >8 -- >8 --  Script  -- >8 -- >8 -- >8 --"
-    @script_end = Readline::HISTORY.size - 2
-  end
-
-  def save_script
-    if @script_begin and @script_end and @script_begin <= @script_end
-      if File.exist?(script_file)
-        message = "Overwrite script file (#{script_file})? [y/n] "
-      else
-        message = "Save script file (#{script_file})? [y/n] "
-      end
-      if ask_yes_or_no(message)
-        save_script_file(script_file)
-      else
-        STDERR.puts " ... save aborted."
-      end
-    elsif @script_begin and @script_end and @script_begin - @script_end == 1
-      STDERR.puts " ... script aborted."
-    else
-      STDERR.puts "Error: Script range #{@script_begin}..#{@script_end} is invalid"
-    end
-  end
-
-  def save_script_file(file)
-    begin
-      STDERR.print "Saving script (#{file}) ... "
-      File.open(file, "w") do |f|
-        f.puts "#!/usr/bin/env bioruby"
-        f.puts
-        f.puts Readline::HISTORY.to_a[@script_begin..@script_end]
-        f.puts
-      end
-      STDERR.puts "done"
-    rescue
-      @script_begin = nil
-      warn "Error: Failed to save (#{file}) : #{$!}"
-    end
-  end
-
-  ### splash
-
-  def splash_message
-    @config[:message] ||= MESSAGE
-    @config[:message].to_s.split(//).join(" ")
-  end
-
-  def splash_message_color
-    str = splash_message
-    ruby = colors[:ruby]
-    none = colors[:none]
-    return str.sub(/R u b y/) { "#{ruby}R u b y#{none}" }
-  end
-
-  def splash_message_action(message = nil)
-    s = message || splash_message
-    l = s.length
-    x = " "
-    0.step(l,2) do |i|
-      l1 = l-i;  l2 = l1/2;  l4 = l2/2
-      STDERR.print "#{s[0,i]}#{x*l1}#{s[i,1]}\r"
-      sleep(0.001)
-      STDERR.print "#{s[0,i]}#{x*l2}#{s[i,1]}#{x*(l1-l2)}\r"
-      sleep(0.002)
-      STDERR.print "#{s[0,i]}#{x*l4}#{s[i,1]}#{x*(l2-l4)}\r"
-      sleep(0.004)
-      STDERR.print "#{s[0,i+1]}#{x*l4}\r"
-      sleep(0.008)
-    end
-  end
-
-  def splash_message_action_color(message = nil)
-    s = message || splash_message
-    l = s.length
-    c = colors
-    x = " "
-    0.step(l,2) do |i|
-      l1 = l-i;  l2 = l1/2;  l4 = l2/2
-      STDERR.print "#{c[:n]}#{s[0,i]}#{x*l1}#{c[:y]}#{s[i,1]}\r"
-      sleep(0.001)
-      STDERR.print "#{c[:n]}#{s[0,i]}#{x*l2}#{c[:g]}#{s[i,1]}#{x*(l1-l2)}\r"
-      sleep(0.002)
-      STDERR.print "#{c[:n]}#{s[0,i]}#{x*l4}#{c[:r]}#{s[i,1]}#{x*(l2-l4)}\r"
-      sleep(0.004)
-      STDERR.print "#{c[:n]}#{s[0,i+1]}#{x*l4}\r"
-      sleep(0.008)
-    end
-  end
-
-  def opening_splash
-    STDERR.puts
-    if @config[:splash]
-      if @config[:color]
-        splash_message_action_color
-      else
-        splash_message_action
-      end
-    end
-    if @config[:color]
-      STDERR.print splash_message_color
-    else
-      STDERR.print splash_message
-    end
-    STDERR.puts
-    STDERR.puts
-    STDERR.print "  Version : BioRuby #{Bio::BIORUBY_VERSION_ID}"
-    STDERR.print " / Ruby #{RUBY_VERSION}"
-    STDERR.puts
-    STDERR.puts
-  end
-
-  def closing_splash
-    STDERR.puts
-    STDERR.puts
-    if @config[:color]
-      STDERR.print splash_message_color
-    else
-      STDERR.print splash_message
-    end
-    STDERR.puts
-    STDERR.puts
-  end
-
-end
-