bio 1.4.3.0001 → 1.5.0

data/gemfiles/Gemfile.travis-jruby1.8

@@ -1,6 +1,7 @@
-source :rubygems
+source "https://rubygems.org"
 
 gem "rake"
+gem "rdoc"
 
 ## disabled because of build error on Travis
 #gem "libxml-ruby"

data/gemfiles/Gemfile.travis-jruby1.9

@@ -1,10 +1,8 @@
-source :rubygems
+source "https://rubygems.org"
 
 gem "rake"
+gem "rdoc"
 
 ## disabled because of build error on Travis
 #gem "libxml-ruby"
 
-## disabled because of "uninitialized constant XML::SaxParser" error
-#gem "soap4r-ruby1.9"
-

data/gemfiles/Gemfile.travis-rbx

@@ -0,0 +1,13 @@
+source "https://rubygems.org"
+
+gem "rake"
+gem "rdoc"
+
+gem "xmlparser"
+gem "libxml-ruby"
+
+platforms :rbx do
+  gem 'racc'
+  gem 'rubysl', '~> 2.0'
+  gem 'psych'
+end

data/gemfiles/Gemfile.travis-ruby1.8

@@ -1,6 +1,7 @@
-source :rubygems
+source "https://rubygems.org"
 
 gem "rake"
+gem "rdoc"
 
 gem "xmlparser"
 gem "libxml-ruby"

data/gemfiles/Gemfile.travis-ruby1.9

@@ -1,10 +1,8 @@
-source :rubygems
+source "https://rubygems.org"
 
 gem "rake"
+gem "rdoc"
 
 gem "xmlparser"
 gem "libxml-ruby"
 
-## disabled because of "uninitialized constant XML::SaxParser" error
-#gem "soap4r-ruby1.9"
-

data/gemfiles/Gemfile.travis-ruby2.2

@@ -0,0 +1,9 @@
+source "https://rubygems.org"
+
+gem "rake"
+gem "rdoc"
+gem "test-unit"
+
+gem "xmlparser"
+gem "libxml-ruby"
+

data/lib/bio.rb

@@ -73,24 +73,26 @@ module Bio
   autoload :KEGGDB,         'bio/db'
   autoload :EMBLDB,         'bio/db'
 
-  ## GenBank/RefSeq/DDBJ
+  ## GenBank, GenPept
 
   autoload :GenBank,        'bio/db/genbank/genbank'
   autoload :GenPept,        'bio/db/genbank/genpept'
+
+  ## (deprecated) Bio::RefSeq, Bio::DDBJ
   autoload :RefSeq,         'bio/db/genbank/refseq'
   autoload :DDBJ,           'bio/db/genbank/ddbj'
-  ## below are described in bio/db/genbank/ddbj.rb
-  #class DDBJ
-  #  autoload :XML,          'bio/io/ddbjxml'
-  #  autoload :REST,         'bio/io/ddbjrest'
-  #end
 
-  ## EMBL/TrEMBL/Swiss-Prot/SPTR
+  ## EMBL, UniProtKB
 
   autoload :EMBL,           'bio/db/embl/embl'
+  autoload :UniProtKB,      'bio/db/embl/uniprotkb'
+
+  ## aliases of Bio::UniProtKB
   autoload :SPTR,           'bio/db/embl/sptr'
-  autoload :TrEMBL,         'bio/db/embl/trembl'
   autoload :UniProt,        'bio/db/embl/uniprot'
+
+  ## (deprecated) Bio::TrEMBL, Bio::SwissProt
+  autoload :TrEMBL,         'bio/db/embl/trembl'
   autoload :SwissProt,      'bio/db/embl/swissprot'
 
   ## KEGG
@@ -110,7 +112,6 @@ module Bio
     autoload :KGML,         'bio/db/kegg/kgml'
     autoload :PATHWAY,      'bio/db/kegg/pathway'
     autoload :MODULE,       'bio/db/kegg/module'
-    autoload :Taxonomy,     'bio/db/kegg/taxonomy'
   end
 
   ## other formats
@@ -155,7 +156,6 @@ module Bio
   autoload :Registry,       'bio/io/registry'
   autoload :Fetch,          'bio/io/fetch'
   autoload :SQL,            'bio/io/sql'
-  autoload :SOAPWSDL,       'bio/io/soapwsdl'
   autoload :FlatFile,       'bio/io/flatfile'
   autoload :FlatFileIndex,  'bio/io/flatfile/index' # chage to FlatFile::Index ?
   ## below are described in bio/io/flatfile/index.rb
@@ -168,9 +168,7 @@ module Bio
 
   autoload :PubMed,         'bio/io/pubmed'
   autoload :DAS,            'bio/io/das'
-  autoload :DBGET,          'bio/io/dbget'
 
-  autoload :Ensembl,        'bio/io/ensembl'
   autoload :Hinv,           'bio/io/hinv'
 
   ## below are described in bio/appl/blast.rb
@@ -178,27 +176,9 @@ module Bio
   #  autoload :Fastacmd,     'bio/io/fastacmd'
   #end
 
-  class KEGG
-    autoload :API,          'bio/io/keggapi'
-  end
-
-  ## below are described in bio/db/genbank/ddbj.rb
-  #class DDBJ
-  #  autoload :XML,          'bio/io/ddbjxml'
-  #end
-
-  class HGC
-    autoload :HiGet,        'bio/io/higet'
-  end
-
-  class EBI
-    autoload :SOAP,         'bio/io/ebisoap'
-  end
-
   autoload :NCBI,         'bio/io/ncbirest'
   ## below are described in bio/io/ncbirest.rb
   #class NCBI
-  #  autoload :SOAP,       'bio/io/ncbisoap'
   #  autoload :REST,       'bio/io/ncbirest'
   #end
 
@@ -304,18 +284,5 @@ module Bio
   ### Service libraries
   autoload :Command,        'bio/command'
 
-  ### Provide BioRuby shell 'command' also as 'Bio.command' (like ChemRuby)
-
-  def self.method_missing(*args)
-    require 'bio/shell'
-    extend Bio::Shell
-    public_class_method(*Bio::Shell.private_instance_methods)
-    if Bio.respond_to?(args.first)
-      Bio.send(*args)
-    else
-      raise NameError
-    end
-  end
-
 end
 

data/lib/bio/alignment.rb

@@ -1091,7 +1091,7 @@ module Bio
 
       # generates Phylip3.2 (old) non-interleaved format as a string
       def output_phylipnon(options = {})
-        aln, aseqs, lines = __output_phylip_common(options)
+        aln, aseqs, _ = __output_phylip_common(options)
         aln.first + aseqs.join('')
       end
 
@@ -1476,21 +1476,16 @@ module Bio
 
       # Gets the sequence from given object.
       def extract_seq(obj)
-        seq = nil
         if obj.is_a?(Bio::Sequence::NA) or obj.is_a?(Bio::Sequence::AA) then
-          seq = obj
+          obj
         else
-          for m in [ :seq, :naseq, :aaseq ]
-            begin
-              seq = obj.send(m)
-            rescue NameError, ArgumentError
-              seq = nil
-            end
-            break if seq
-          end
-          seq = obj unless seq
+          meth = [ :seq, :naseq, :aaseq ].find {|m|
+            obj.respond_to? m
+          }
+          meth ?
+            obj.__send__(meth) :
+            obj
         end
-        seq
       end
       module_function :extract_seq
 
@@ -1650,7 +1645,6 @@ module Bio
       # (Like Hash#rehash)
       def rehash
         @seqs.rehash
-        oldkeys = @keys
         tmpkeys = @seqs.keys
         @keys.collect! do |k|
           tmpkeys.delete(k)

data/lib/bio/appl/blast.rb

@@ -7,7 +7,6 @@
 # Copyright::  Copyright (C) 2008       Naohisa Goto <ng@bioruby.org>
 # License::    The Ruby License
 #
-# $Id:$
 #
 
 require 'bio/command'
@@ -399,7 +398,7 @@ module Bio
       if fmt = ncbiopt.get('-m') then
         @format = fmt.to_i
       else
-        dummy = Bio::Blast::Report #dummy to load XMLParser or REXML
+        _ = Bio::Blast::Report #dummy to load XMLParser or REXML
         if defined?(XMLParser) or defined?(REXML)
           @format ||= 7
         else

data/lib/bio/appl/blast/format0.rb

@@ -256,7 +256,7 @@ module Bio
         # Parses the first line of the BLAST result.
         def format0_parse_header
           unless defined?(@program)
-            if /([\-\w]+) +([\w\-\.\d]+) *\[ *([\-\.\w]+) *\] *(\[.+\])?/ =~ @f0header.to_s
+            if /([\-\w]+) +([\w\-\.]+) *\[ *([\-\.\w]+) *\] *(\[.+\])?/ =~ @f0header.to_s
               @program = $1
               @version = "#{$1} #{$2} [#{$3}]"
               @version_number = $2
@@ -384,10 +384,17 @@ module Bio
 
           # Returns name of the matrix.
           def matrix;      parse_params; @matrix;      end
+
           # Returns the match score of the matrix.
-          def sc_match;    parse_params; @sc_match;    end
+          def sc_match
+            parse_params
+            (defined? @sc_match) ? @sc_match : nil
+          end
           # Returns the mismatch score of the matrix.
-          def sc_mismatch; parse_params; @sc_mismatch; end
+          def sc_mismatch
+            parse_params
+            (defined? @sc_mismatch) ? @sc_mismatch : nil
+          end
 
           # Returns gap open penalty value.
           def gap_open;    parse_params; @gap_open;    end
@@ -571,7 +578,9 @@ module Bio
           # Returns nil if it is not a PHI-BLAST result.
           def pattern
             #PHI-BLAST
-            if !defined?(@pattern) and defined?(@pattern_in_database) then
+            if defined? @pattern
+              @pattern
+            elsif defined? @pattern_in_database then
               @pattern = nil
               @pattern_positions = []
               @f0message.each do |r|
@@ -582,8 +591,10 @@ module Bio
                   @pattern_positions << sc[1].to_i
                 end
               end
+              @pattern
+            else
+              nil
             end
-            @pattern
           end
 
           # (PHI-BLAST) Returns pattern positions.
@@ -662,7 +673,7 @@ module Bio
                     y = b[j]; y.strip!
                     y.reverse!
                     z = y.split(/\s+/, 3)
-                    z.each { |y| y.reverse! }
+                    z.each { |yy| yy.reverse! }
                     h = Hit.new([ z.pop.to_s.sub(/\.+\z/, '') ])
                     bs = z.pop.to_s
                     bs = '1' + bs if bs[0] == ?e
@@ -1043,7 +1054,7 @@ module Bio
           # Defines attributes which call parse_score before accessing.
           def self.method_after_parse_score(*names)
             names.each do |x|
-              module_eval("def #{x}; parse_score; @#{x}; end")
+              module_eval("def #{x}; parse_score; (defined? @#{x}) ? @#{x} : nil; end")
             end
           end
           private_class_method :method_after_parse_score

data/lib/bio/appl/blast/remote.rb

@@ -17,21 +17,12 @@ class Blast
     autoload :GenomeNet, 'bio/appl/blast/genomenet'
     autoload :Genomenet, 'bio/appl/blast/genomenet'
 
-    autoload :DDBJ, 'bio/appl/blast/ddbj'
-    autoload :Ddbj, 'bio/appl/blast/ddbj'
-
     # creates a remote BLAST factory using GenomeNet
     def self.genomenet(program, db, options = [])
       GenomeNet.new(program, db, options)
       #Bio::Blast.new(program, db, options, 'genomenet')
     end
 
-    # creates a remote BLAST factory using DDBJ Web service
-    def self.ddbj(program, db, options = [])
-      DDBJ.new(program, db, options)
-      #Bio::Blast.new(program, db, options, 'ddbj')
-    end
-
     # Common methods for meta-information processing
     # (e.g. list of databases).
     module Information

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

@@ -518,7 +518,7 @@ class Report
     # get an entry as a Bio::Blast::Report object
     def get_parsed_entry
       if @parsed_entries.empty? then
-        ent = get_entry
+        get_entry
       else
         self.parsed_entry = @parsed_entries.shift
         self.entry = nil

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

@@ -143,7 +143,9 @@ module Bio
           a[0].gsub!(/\A(\r?\n)+/, '')
           a.collect! { |x| x.split(/\r?\n/) }
           a.each { |x|
-            x.each { |y| y.sub!(/ +\d+\s*$/, '') }} #for -SEQNOS=on option
+            x.each { |y| y.sub!(/ +\d+\s*\z/, '') if /\d\s*\z/ =~ y }
+            # The above "if /\d\s*\z/ =~ y" is for optimization only.
+          } #for -SEQNOS=on option
           @tagsize = ( a[0][0].rindex(/\s/) or -1 ) + 1
           a.each do |x|
             @match_line << x.pop.to_s[@tagsize..-1]

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

@@ -5,7 +5,6 @@
 #              Mitsuteru C. Nakao <n@bioruby.org>
 # License::    The Ruby License
 #
-#  $Id:$
 #
 # == Description
 #
@@ -96,7 +95,7 @@ class Genscan
       genes_region = report[i...j]
       genes_region.each_line("\n") do |line|
         if /Init|Intr|Term|PlyA|Prom|Sngl/ =~ line
-          gn, en = line.strip.split(" +")[0].split(/\./).map {|i| i.to_i }
+          gn, en = line.strip.split(" +")[0].split(/\./).map {|ii| ii.to_i }
           add_exon(gn, en, line)
         end
       end

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

@@ -5,7 +5,6 @@
 #               Mitsuteru C. Nakao <mn@kazusa.or.jp>
 # License::     The Ruby License
 #
-#  $Id: report.rb,v 1.9 2007/07/18 11:11:57 nakao Exp $
 #
 # == Report classes for the iprscan program.
 # 
@@ -296,7 +295,7 @@ module Bio
       #   end
       #
       def to_hash
-        unless @ipr_ids
+        unless (defined? @ipr_ids) && @ipr_ids
           @ipr_ids = {} 
           @matches.each_with_index do |match, i|
             @ipr_ids[match.ipr_id] ||= []

data/lib/bio/appl/meme/mast.rb

@@ -94,7 +94,7 @@ module Meme
     # *Returns*:: a Bio::Meme::Mast object
     
     def initialize(mast_location, options = {})
-      unless File.exists?(mast_location)
+      unless File.exist?(mast_location)
         raise ArgumentError.new("mast: command not found : #{mast_location}")
       end
       @binary = mast_location
@@ -137,8 +137,8 @@ module Meme
       @options.each_key do |k|
         raise ArgumentError.new("Invalid option: #{k}") unless DEFAULT_OPTIONS.has_key?(k)
       end
-      raise ArgumentError.new("Motif file not found: #{@options[:mfile]}") if @options[:mfile].nil? or !File.exists?(@options[:mfile])
-      raise ArgumentError.new("Database not found: #{@options[:d]}") if @options[:d].nil? or !File.exists?(@options[:d])
+      raise ArgumentError.new("Motif file not found: #{@options[:mfile]}") if @options[:mfile].nil? or !File.exist?(@options[:mfile])
+      raise ArgumentError.new("Database not found: #{@options[:d]}") if @options[:d].nil? or !File.exist?(@options[:d])
     end
 
     # Run the mast program
@@ -153,4 +153,4 @@ module Meme
     
   end # End class Mast
 end # End module Meme
-end # End module Bio
+end # End module Bio

data/lib/bio/appl/meme/mast/report.rb

@@ -74,7 +74,7 @@ module Bio
             fields = line.split(/\s/)
             
             if fields.size == 5
-              motifs << Motif.new(fields[0], strand = nil, fields[1], fields[2], fields[3], fields[4])
+              motifs << Motif.new(fields[0], nil, fields[1], fields[2], fields[3], fields[4])
             elsif fields.size == 6
               motifs << Motif.new(fields[0], fields[1], fields[2], fields[3], fields[4], fields[5])
             else

data/lib/bio/appl/paml/codeml.rb

@@ -37,9 +37,9 @@ module PAML
   #   require 'bio'
   #   # Reads multi-fasta formatted file and gets a Bio::Alignment object.
   #   alignment = Bio::FlatFile.open(Bio::Alignment::MultiFastaFormat,
-  #                                  'example.fst').alignment
+  #                                  'example.fst').next_entry.alignment
   #   # Reads newick tree from a file
-  #   tree = Bio::FlatFile.open(Bio::Newick, 'example.tree').tree
+  #   tree = Bio::FlatFile.open(Bio::Newick, 'example.tree').next_entry.tree
   #   # Creates a Codeml object
   #   codeml = Bio::PAML::Codeml.new
   #   # Sets parameters

data/lib/bio/appl/paml/codeml/report.rb

@@ -589,6 +589,7 @@ module Bio::PAML
       def graph_seq
         graph_to_s(lambda { |site |
           symbol = site.aaref
+          symbol
         })
       end
       

data/lib/bio/appl/paml/common.rb

@@ -195,7 +195,7 @@ module PAML
             raise RuntimeError, msg.join("; ")
           end
           # exec command
-          stdout = exec_local([ ctlfn ], { :chdir => path })
+          exec_local([ ctlfn ], { :chdir => path })
           # get main output
           outfile.open
           @output = outfile.read