bio 1.3.1 → 1.4.0

data/lib/bio/appl/psort/report.rb

@@ -5,7 +5,7 @@
 #               Mitsuteru C. Nakao <n@bioruby.org>
 # License::     The Ruby License
 #
-#  $Id: report.rb,v 1.15 2007/04/05 23:35:40 trevor Exp $
+#  $Id:$
 #
 # == A Report classes for PSORT Systems
 # 
@@ -411,47 +411,3 @@ module Bio
 
 end # module Bio
 
-
-
-
-
-# testing code
-
-if __FILE__ == $0
-
-
-  while entry = $<.gets(Bio::PSORT::PSORT2::Report::DELIMITER)
-
-    puts "\n ==> a = Bio::PSORT::PSORT2::Report.parser(entry)"
-    a = Bio::PSORT::PSORT2::Report.parser(entry)
-
-    puts "\n ==> a.entry_id "
-    p a.entry_id
-    puts "\n ==> a.scl "
-    p a.scl
-    puts "\n ==> a.pred "
-    p a.pred
-    puts "\n ==> a.prob "
-    p a.prob
-    p a.prob.keys.sort.map {|k| k.rjust(4)}.inspect.gsub('"','')
-    p a.prob.keys.sort.map {|k| a.prob[k].to_s.rjust(4) }.inspect.gsub('"','')
-
-    puts "\n ==> a.k "
-    p a.k
-    puts "\n ==> a.definition"
-    p a.definition
-    puts "\n ==> a.seq"
-    p a.seq
-
-    puts "\n ==> a.features.keys.sort "
-    p a.features.keys.sort
-
-    a.features.keys.sort.each do |key|
-      puts "\n ==> a.features['#{key}'] "
-      puts a.features[key]
-    end
-
-    
-  end
-
-end

data/lib/bio/appl/pts1.rb

@@ -41,7 +41,7 @@ require 'bio/command'
 # == References
 #
 # * The PTS1 predictor
-#   http://mendel.imp.ac.at/mendeljsp/sat/pts1/PTS1predictor.jsp
+#   http://mendel.imp.ac.at/pts1/
 #
 # * Neuberger G, Maurer-Stroh S, Eisenhaber B, Hartig A, Eisenhaber F. 
 #   Motif refinement of the peroxisomal targeting signal 1 and evaluation 
@@ -90,8 +90,7 @@ class PTS1
   #   serv_fungi_specific = Bio::PTS1.new(2)    # See Bio::PTS1::FUNCTION.
   #
   def initialize(func = 'METAZOA-specific')
-    @host = "mendel.imp.ac.at"
-    @cgi_path = "/sat/pts1/cgi-bin/pts1.cgi"
+    @uri = "http://mendel.imp.ac.at/jspcgi/cgi-bin/pts1/pts1.cgi"
     @output = nil
     @function = function(func)
   end
@@ -145,7 +144,6 @@ class PTS1
     @form_data = {'function' => @function.values.join(''),
                   'sequence' => seq.seq,
                   'name'     => seq.definition }
-    @uri = URI.parse(["http:/", @host, @cgi_path].join('/'))
 
     result = Bio::Command.post_form(@uri, @form_data)
     @output = Report.new(result.body)

data/lib/bio/appl/sosui/report.rb

@@ -5,13 +5,14 @@
 #               Mitsuteru C. Nakao <n@bioruby.org>
 # License::     The Ruby License
 #
-#  $Id: report.rb,v 1.11 2007/04/05 23:35:40 trevor Exp $
+#  $Id:$
 #
 # == Example
 #
 # == References
 #
-# * http://sosui.proteome.bio.tuat.ac.jp/sosui_submit.html
+# * http://bp.nuap.nagoya-u.ac.jp/sosui/
+# * http://bp.nuap.nagoya-u.ac.jp/sosui/sosui_submit.html
 #
 
 
@@ -22,7 +23,8 @@ module Bio
     # = SOSUI output report parsing class
     #
     # == References
-    # * http://sosui.proteome.bio.tuat.ac.jp/sosui_submit.html
+    # * http://bp.nuap.nagoya-u.ac.jp/sosui/
+    # * http://bp.nuap.nagoya-u.ac.jp/sosui/sosui_submit.html
     class Report
 
       # Delimiter
@@ -98,54 +100,3 @@ module Bio
 end # module Bio
 
 
-
-if __FILE__ == $0
-
-  begin
-    require 'pp'
-    alias p pp 
-  rescue LoadError
-  end
-
-
-  sample = <<HOGE
->HOGE1
- MEMBRANE PROTEIN
- NUMBER OF TM HELIX = 6
- TM 1   12-  34 SECONDARY   LLVPILLPEKCYDQLFVQWDLLH
- TM 2   36-  58 PRIMARY     PCLKILLSKGLGLGIVAGSLLVK
- TM 3  102- 124 SECONDARY   SWGEALFLMLQTITICFLVMHYR
- TM 4  126- 148 PRIMARY     QTVKGVAFLACYGLVLLVLLSPL
- TM 5  152- 174 SECONDARY   TVVTLLQASNVPAVVVGRLLQAA
- TM 6  214- 236 SECONDARY   AGTFVVSSLCNGLIAAQLLFYWN
-
->HOGE2
- SOLUBLE PROTEIN
-
-HOGE
-
-  def hoge(ent)
-    puts '==='
-    puts ent
-    puts '==='
-    sosui = Bio::SOSUI::Report.new(ent)
-    p [:entry_id, sosui.entry_id]
-    p [:prediction, sosui.prediction]
-    p [:tmhs.size, sosui.tmhs]
-    pp [:tmhs, sosui.tmh]
-  end
-
-  sample.split(/#{Bio::SOSUI::Report::DELIMITER}/).each {|ent|
-    hoge(ent)
-  }
-
-  exit if ARGV.size == 0
-
-  while ent = $<.gets(Bio::SOSUI::Report::DELIMITER)
-    hoge(ent)
-  end
-
-end
-
-
-

data/lib/bio/appl/targetp/report.rb

@@ -5,7 +5,7 @@
 #              Mitsuteru C. Nakao <n@bioruby.org>
 # License::    The Ruby License
 #
-#  $Id: report.rb,v 1.9 2007/04/05 23:35:40 trevor Exp $
+#  $Id:$
 #
 # == Description
 #
@@ -162,106 +162,3 @@ module Bio
 
 end # moudel Bio
 
-
-
-if __FILE__ == $0
-
-  begin
-    require 'pp'
-    alias p pp 
-  rescue LoadError
-  end
-
-
-  plant = <<HOGE
- 
-### ### ###  T A R G E T P  1.0  prediction results  ### ### ### 
- 
-# Number of input sequences:  1
-# Cleavage site predictions not included.
-# Using PLANT networks.
- 
-#                        Name   Length	  cTP   mTP    SP other  Loc.  RC
-#----------------------------------------------------------------------------------
-                   MGI_2141503	  640	0.031 0.161 0.271 0.844   _     3
-#----------------------------------------------------------------------------------
-# cutoff                                 0.00  0.00  0.00  0.00
-
-
-HOGE
-
-plant_c = <<HOGE
- 
-### ### ###  T A R G E T P  1.0  prediction results  ### ### ### 
- 
-# Number of input sequences:  1
-# Cleavage site predictions included.
-# Using PLANT networks.
- 
-#                        Name   Length	  cTP   mTP    SP other  Loc.  RC     TPlen
-#----------------------------------------------------------------------------------
-                   MGI_2141503	  640	0.031 0.161 0.271 0.844   _     3	  -
-#----------------------------------------------------------------------------------
-# cutoff                                 0.00  0.00  0.00  0.00
-
-
-
-HOGE
-
-non_plant_c = <<HOGE
- 
-### ### ###  T A R G E T P  1.0  prediction results  ### ### ### 
- 
-# Number of input sequences:  1
-# Cleavage site predictions included.
-# Using NON-PLANT networks.
- 
-#                        Name   Length    mTP   SP  other  Loc.  RC   TPlen
-#--------------------------------------------------------------------------
-                     MGI_96083	 2187	0.292 0.053 0.746   _     3	  -
-#--------------------------------------------------------------------------
-# cutoff                                 0.00  0.00  0.00
-
-
-
-HOGE
-
-
-  def hoge(e)
-    puts e
-    ent = Bio::TargetP::Report.new(e)
-    pp ent
-
-    p [:entry_id, ent.entry_id]
-    p [:name, ent.name]
-    p [:version, ent.version]
-    p [:query_sequnces, ent.query_sequences]
-    p [:cleavage_site_prediction, ent.cleavage_site_prediction]
-    p [:networks, ent.networks]
-    p [:query_len, ent.query_len]
-    p [:prediction, ent.prediction]
-    p [:pred_Name, ent.pred['Name']]
-    p [:pred_SP, ent.pred['SP']]
-    p [:pred_mTP, ent.pred['mTP']]
-    p [:cutoff, ent.cutoff]
-    p [:loc, ent.loc]
-    p [:rc, ent.rc]
-
-    puts '=='
-  end
-
-
-  [plant, plant_c, non_plant_c].each {|e|
-    hoge(e)
-  }
-
-  exit  if ARGV.size == 0
-
-  while ent = $<.gets(Bio::TargetP::Report::DELIMITER)
-    hoge(ent)
-  end
-
-end
-
-
-

data/lib/bio/appl/tmhmm/report.rb

@@ -193,39 +193,3 @@ module Bio
 
 end # module Bio
 
-
-if __FILE__ == $0
-
-  begin
-    require 'pp'
-    alias p pp
-  rescue LoadError
-  end
-
-  Bio::TMHMM.reports(ARGF.read) do |ent|
-    puts '==>'
-    puts ent.to_s
-    pp ent
-
-    p [:entry_id, ent.entry_id]
-    p [:query_len, ent.query_len]
-    p [:predicted_tmhs, ent.predicted_tmhs]
-    p [:tmhs_size, ent.tmhs.size]
-    p [:exp_aas_in_tmhs, ent.exp_aas_in_tmhs]
-    p [:exp_first_60aa, ent.exp_first_60aa]
-    p [:total_prob_of_N_in, ent.total_prob_of_N_in]
-
-    ent.tmhs.each do |t|
-      p t
-      p [:entry_id, t.entry_id]
-      p [:version, t.version]
-      p [:status, t.status]
-      p [:range, t.range]
-      p [:pos, t.pos]
-    end
-
-    p [:helix, ent.helix]
-    p ent.tmhs.map {|t| t if t.status == 'TMhelix' }.compact
-  end
-
-end

data/lib/bio/command.rb

@@ -357,22 +357,33 @@ module Command
 
   # Backport of Dir.mktmpdir in Ruby 1.9.
   #
-  # Same as Dir.mktmpdir(prefix_suffix) in Ruby 1.9 except that
-  # prefix must be a String, nil, or omitted.
+  # Same as Dir.mktmpdir(prefix_suffix) in Ruby 1.9.
   #
   # ---
   # *Arguments*:
-  # * (optional) _prefix_: String
+  # * (optional) <em>prefix_suffix</em>: String (or Array, etc.)
+  # * (optional) <em>tmpdir</em>: String: temporary directory's path
   # 
-  def mktmpdir(prefix = 'd', tmpdir = nil, &block)
-    prefix = prefix.to_str
+  def mktmpdir(prefix_suffix = nil, tmpdir = nil, &block)
     begin
-      Dir.mktmpdir(prefix, tmpdir, &block)
+      Dir.mktmpdir(prefix_suffix, tmpdir, &block)
     rescue NoMethodError
-      suffix = ''
-      # backported from Ruby 1.9.0.
-      # ***** Below is excerpted from Ruby 1.9.0's lib/tmpdir.rb ****
+      # backported from Ruby 1.9.2-preview1.
+      # ***** Below is excerpted from Ruby 1.9.2-preview1's lib/tmpdir.rb ****
       # ***** Be careful about copyright. ****
+      case prefix_suffix
+      when nil
+        prefix = "d"
+        suffix = ""
+      when String
+        prefix = prefix_suffix
+        suffix = ""
+      when Array
+        prefix = prefix_suffix[0]
+        suffix = prefix_suffix[1]
+      else
+        raise ArgumentError, "unexpected prefix_suffix: #{prefix_suffix.inspect}"
+      end
       tmpdir ||= Dir.tmpdir
       t = Time.now.strftime("%Y%m%d")
       n = nil
@@ -396,10 +407,83 @@ module Command
       else
         path
       end
-      # ***** Above is excerpted from Ruby 1.9.0's lib/tmpdir.rb ****
+      # ***** Above is excerpted from Ruby 1.9.2-preview1's lib/tmpdir.rb ****
     end
   end
 
+  # Bio::Command::Tmpdir is a wrapper class to handle temporary directory
+  # like Tempfile class. A temporary directory is created when the object
+  # of the class is created, and automatically removed when the object
+  # is destroyed by GC.
+  #
+  # BioRuby library internal use only.
+  class Tmpdir
+
+    # Returns finalizer object for Tmpdir class.
+    # Internal use only. Users should not call this method directly.
+    # 
+    # Acknowledgement: The essense of the code is taken from tempfile.rb
+    # in Ruby 1.8.7.
+    #
+    # ---
+    # *Arguments*:
+    # * (required) _data_: Array containing internal data
+    # *Returns*:: Proc object
+    def self.callback(data)
+      pid = $$
+      lambda {
+        path, = *data
+        if pid == $$
+          $stderr.print "removing ", path, " ..." if $DEBUG
+          if path and !path.empty? and
+              File.directory?(path) and
+              !File.symlink?(path) then
+            Bio::Command.remove_entry_secure(path)
+            $stderr.print "done\n" if $DEBUG
+          else
+            $stderr.print "skipped\n" if $DEBUG
+          end
+        end
+      }
+    end
+
+    # Creates a new Tmpdir object.
+    # The arguments are the same as Bio::Command.mktmpdir.
+    #
+    # ---
+    # *Arguments*:
+    # * (optional) <em>prefix_suffix</em>: String (or Array)
+    # * (optional) <em>tmpdir</em>: String: temporary directory's path
+    # *Returns*:: Tmpdir object
+    def initialize(prefix_suffix = nil, tmpdir = nil)
+      @data = []
+      @clean_proc = self.class.callback(@data)
+      ObjectSpace.define_finalizer(self, @clean_proc)
+      @data.push(@path = Bio::Command.mktmpdir(prefix_suffix, tmpdir).freeze)
+    end
+
+    # Path to the temporay directory
+    #
+    # *Returns*:: String
+    def path
+      @path || raise(IOError, 'removed temporary directory')
+    end
+
+    # Removes the temporary directory.
+    #
+    # *Returns*:: nil
+    def close!
+      # raise error if path is nil
+      self.path
+      # finilizer object is called to remove the directory
+      @clean_proc.call
+      # unregister finalizer
+      ObjectSpace.undefine_finalizer(self)
+      # @data and @path is removed
+      @data = @path = nil
+    end
+  end #class Tmpdir
+
   # Same as OpenURI.open_uri(uri).read
   # and 
   # it uses proxy if an environment variable (same as OpenURI.open_uri)

data/lib/bio/data/aa.rb

@@ -5,7 +5,7 @@
 #		Toshiaki Katayama <k@bioruby.org>
 # License::	The Ruby License
 #
-# $Id: aa.rb,v 0.22 2007/04/06 04:44:51 k Exp $
+# $Id:$
 #
 
 module Bio
@@ -271,79 +271,3 @@ end
 end # module Bio
 
 
-if __FILE__ == $0
-
-  puts "### aa = Bio::AminoAcid.new"
-  aa = Bio::AminoAcid.new
-
-  puts "# Bio::AminoAcid['A']"
-  p Bio::AminoAcid['A']
-  puts "# aa['A']"
-  p aa['A']
-
-  puts "# Bio::AminoAcid.name('A'), Bio::AminoAcid.name('Ala')"
-  p Bio::AminoAcid.name('A'), Bio::AminoAcid.name('Ala')
-  puts "# aa.name('A'), aa.name('Ala')"
-  p aa.name('A'), aa.name('Ala')
-
-  puts "# Bio::AminoAcid.to_1('alanine'), Bio::AminoAcid.one('alanine')"
-  p Bio::AminoAcid.to_1('alanine'), Bio::AminoAcid.one('alanine')
-  puts "# aa.to_1('alanine'), aa.one('alanine')"
-  p aa.to_1('alanine'), aa.one('alanine')
-  puts "# Bio::AminoAcid.to_1('Ala'), Bio::AminoAcid.one('Ala')"
-  p Bio::AminoAcid.to_1('Ala'), Bio::AminoAcid.one('Ala')
-  puts "# aa.to_1('Ala'), aa.one('Ala')"
-  p aa.to_1('Ala'), aa.one('Ala')
-  puts "# Bio::AminoAcid.to_1('A'), Bio::AminoAcid.one('A')"
-  p Bio::AminoAcid.to_1('A'), Bio::AminoAcid.one('A')
-  puts "# aa.to_1('A'), aa.one('A')"
-  p aa.to_1('A'), aa.one('A')
-
-  puts "# Bio::AminoAcid.to_3('alanine'), Bio::AminoAcid.three('alanine')"
-  p Bio::AminoAcid.to_3('alanine'), Bio::AminoAcid.three('alanine')
-  puts "# aa.to_3('alanine'), aa.three('alanine')"
-  p aa.to_3('alanine'), aa.three('alanine')
-  puts "# Bio::AminoAcid.to_3('Ala'), Bio::AminoAcid.three('Ala')"
-  p Bio::AminoAcid.to_3('Ala'), Bio::AminoAcid.three('Ala')
-  puts "# aa.to_3('Ala'), aa.three('Ala')"
-  p aa.to_3('Ala'), aa.three('Ala')
-  puts "# Bio::AminoAcid.to_3('A'), Bio::AminoAcid.three('A')"
-  p Bio::AminoAcid.to_3('A'), Bio::AminoAcid.three('A')
-  puts "# aa.to_3('A'), aa.three('A')"
-  p aa.to_3('A'), aa.three('A')
-
-  puts "# Bio::AminoAcid.one2three('A')"
-  p Bio::AminoAcid.one2three('A')
-  puts "# aa.one2three('A')"
-  p aa.one2three('A')
-
-  puts "# Bio::AminoAcid.three2one('Ala')"
-  p Bio::AminoAcid.three2one('Ala')
-  puts "# aa.three2one('Ala')"
-  p aa.three2one('Ala')
-
-  puts "# Bio::AminoAcid.one2name('A')"
-  p Bio::AminoAcid.one2name('A')
-  puts "# aa.one2name('A')"
-  p aa.one2name('A')
-
-  puts "# Bio::AminoAcid.name2one('alanine')"
-  p Bio::AminoAcid.name2one('alanine')
-  puts "# aa.name2one('alanine')"
-  p aa.name2one('alanine')
-
-  puts "# Bio::AminoAcid.three2name('Ala')"
-  p Bio::AminoAcid.three2name('Ala')
-  puts "# aa.three2name('Ala')"
-  p aa.three2name('Ala')
-
-  puts "# Bio::AminoAcid.name2three('alanine')"
-  p Bio::AminoAcid.name2three('alanine')
-  puts "# aa.name2three('alanine')"
-  p aa.name2three('alanine')
-
-  puts "# Bio::AminoAcid.to_re('BZACDEFGHIKLMNPQRSTVWYU')"
-  p Bio::AminoAcid.to_re('BZACDEFGHIKLMNPQRSTVWYU')
-
-end
-