ngoto-bio 1.2.9.9001 → 1.2.9.9501

data/KNOWN_ISSUES.rdoc

@@ -0,0 +1,66 @@
+= KNOWN_ISSUES.rdoc - Known issues and bugs in BioRuby
+Copyright:: Copyright (C) 2009 Naohisa Goto <ng@bioruby.org>
+License::   The Ruby License
+
+= Known issues and bugs in BioRuby
+
+Below are known issues and bugs in BioRuby. They will be fixed in the future,
+except items with (WONT_FIX) tags.
+
+== 1. Ruby version specific issues
+
+=== Ruby 1.9.1 or later
+
+Some classes/modules/methods still may not work or may return incorrect
+results in Ruby 1.9.1, especially those not covered by the unit tests.
+
+==== String encodings
+
+Currently, BioRuby do not care string encodings. In some cases,
+Encoding::CompatibilityError may be raised.
+
+=== Ruby 1.9.0
+
+(WONT_FIX) Ruby 1.9.0 is NOT supported because it isn't a stable release.
+Use Ruby 1.9.1 or later.
+
+=== Ruby 1.8.2 or earlier
+
+(WONT_FIX) In some cases, temporary files and directories may not be
+removed because of the lack of FileUtils.remove_entry_secure.
+
+(WONT_FIX) We will soon end support for Ruby 1.8.2. Note that Ruby
+1.8.1 or earlier is no longer supported, as described in README.rdoc.
+
+=== Issues about SOAP/WSDL
+
+SOAP4R (SOAP and WSDL implementation) is no longer bundled with Ruby 1.9.
+In addition, because of the API changes in recent SOAP4R, some
+classes/modules using SOAP4R may not work.
+
+== 2. OS and/or architecture-dependent issues
+
+=== Microsoft Windows
+
+Following 4 tests failed because of the processing of file contents in the
+text mode.
+
+* test_ended_pos and test_start_pos in test/unit/bio/io/test_flatfile.rb
+* test_pos in test/unit/bio/io/flatfile/test_buffer.rb
+* test_entry_pos in test/unit/bio/appl/blast/test_rpsblast.rb
+
+(WONT_FIX) Some methods that call external programs may not work in
+Windows 95/98/98SE/ME because of the limitation of COMMAND.COM.
+
+== 3. Known issues and bugs in BioRuby
+
+=== Bio::Ensembl
+
+Due to the renewal of Ensembl web site, Bio::Ensembl does not work for
+the latest Ensembl. For a workaround, use an archive server. For example,
+"jul2008.archive.ensembl.org" seems to be the last server before the renewal.
+  human = Bio::Ensembl.new("Homo_sapiens", "jul2008.archive.ensembl.org")
+
+Alternatively, consider using Ruby Ensembl API.
+* http://github.com/jandot/ruby-ensembl-api
+

data/Rakefile

@@ -10,6 +10,18 @@ require 'erb'
 require 'rake/testtask'
 require 'rake/packagetask'
 require 'rake/gempackagetask'
+require 'rake/rdoctask'
+load "./lib/bio.rb"
+
+# Version string for tar.gz, tar.bz2, or zip archive.
+# If nil, use the value in lib/bio.rb
+# Note that gem version is always determined from bioruby.gemspec.erb.
+version = ENV['BIORUBY_VERSION'] || Bio::BIORUBY_VERSION.join(".")
+version = nil if version.to_s.empty?
+extraversion = ENV['BIORUBY_EXTRAVERSION']
+extraversion = nil if extraversion.to_s.empty?
+version += extraversion.to_s if version and extraversion
+BIORUBY_VERSION = version
 
 task :default => "test"
 
@@ -44,6 +56,12 @@ end
 desc "Update gem spec file"
 task :gemspec => GEM_SPEC_FILE
 
+desc "Force update gem spec file"
+task :regemspec do
+  #rm GEM_SPEC_FILE, :force => true
+  Rake::Task[GEM_SPEC_FILE].execute
+end
+
 desc "Update #{GEM_SPEC_FILE}"
 file GEM_SPEC_FILE => [ GEM_SPEC_TEMPLATE_FILE, 'Rakefile' ] do |t|
   puts "creates #{GEM_SPEC_FILE}"
@@ -53,7 +71,7 @@ file GEM_SPEC_FILE => [ GEM_SPEC_TEMPLATE_FILE, 'Rakefile' ] do |t|
 end
 
 task :package => [ GEM_SPEC_FILE ] do
-  Rake::Task[GEM_SPEC_FILE].invoke if flag_update_gemspec
+  Rake::Task[:regemspec].invoke if flag_update_gemspec
 end
 
 Rake::PackageTask.new("bioruby") do |pkg|
@@ -61,10 +79,26 @@ Rake::PackageTask.new("bioruby") do |pkg|
   pkg.need_tar_gz = true
   pkg.package_files.import(spec.files)
   pkg.package_files.include(*tar_additional_files)
-  pkg.version = spec.version
+  pkg.version = BIORUBY_VERSION || spec.version
 end
 
 Rake::GemPackageTask.new(spec) do |pkg|
   #pkg.package_dir = "./pkg"
 end
 
+Rake::RDocTask.new do |r|
+  r.rdoc_dir = "rdoc"
+  r.rdoc_files.include(*spec.extra_rdoc_files)
+  r.rdoc_files.import(spec.files.find_all {|x| /\Alib\/.+\.rb\z/ =~ x})
+  #r.rdoc_files.exclude /\.yaml\z"
+  opts = spec.rdoc_options.to_a.dup
+  if i = opts.index('--main') then
+    main = opts[i + 1]
+    opts.delete_at(i)
+    opts.delete_at(i)
+  else
+    main = 'README.rdoc'
+  end
+  r.main = main
+  r.options = opts
+end

data/bioruby.gemspec

@@ -3,7 +3,7 @@
 # 
 Gem::Specification.new do |s|
   s.name = 'bio'
-  s.version = "1.2.9.9001"
+  s.version = "1.2.9.9501"
 
   s.author = "BioRuby project"
   s.email = "staff@bioruby.org"
@@ -15,6 +15,7 @@ Gem::Specification.new do |s|
   s.platform = Gem::Platform::RUBY
   s.files = [
     "ChangeLog",
+    "KNOWN_ISSUES.rdoc",
     "README.rdoc",
     "README_DEV.rdoc",
     "Rakefile",
@@ -229,6 +230,7 @@ Gem::Specification.new do |s|
     "lib/bio/shell/plugin/flatfile.rb",
     "lib/bio/shell/plugin/keggapi.rb",
     "lib/bio/shell/plugin/midi.rb",
+    "lib/bio/shell/plugin/ncbirest.rb",
     "lib/bio/shell/plugin/obda.rb",
     "lib/bio/shell/plugin/psort.rb",
     "lib/bio/shell/plugin/seq.rb",
@@ -441,12 +443,16 @@ Gem::Specification.new do |s|
 
   s.has_rdoc = true
   s.extra_rdoc_files = [ 
+    "KNOWN_ISSUES.rdoc",
     "README.rdoc",
     "README_DEV.rdoc",
-    "doc/Changes-1.3.rdoc"
+    "doc/Changes-1.3.rdoc",
+    "ChangeLog"
   ]
   s.rdoc_options << '--main' << 'README.rdoc'
+  s.rdoc_options << '--title' << 'BioRuby API documentation'
   s.rdoc_options << '--exclude' << '\.yaml\z'
+  s.rdoc_options << '--line-numbers' << '--inline-source'
 
   s.require_path = 'lib'
   s.autorequire = 'bio'

data/bioruby.gemspec.erb

@@ -1,6 +1,6 @@
 Gem::Specification.new do |s|
   s.name = 'bio'
-  s.version = "1.2.9.9001"
+  s.version = "1.2.9.9501"
 
   s.author = "BioRuby project"
   s.email = "staff@bioruby.org"
@@ -12,13 +12,14 @@ Gem::Specification.new do |s|
   s.platform = Gem::Platform::RUBY
   s.files = [
     <% ###### Below is executed in ERB environment ######
-    # Gets file list from the "git-ls-files" command.
-    files = `git-ls-files 2>/dev/null`.to_s.split(/\r?\n/)
+    # Gets file list from the "git ls-files" command.
+    files = (`git ls-files` rescue nil).to_s.split(/\r?\n/)
     files.delete_if { |x| x.empty? }
     # When git-ls-files isn't available, creates a list from current files.
     unless $?.success? or files.size <= 0 then
       files =
-        [ "README.rdoc", "README_DEV.rdoc", "ChangeLog",
+        [ "README.rdoc", "README_DEV.rdoc", 
+          "ChangeLog", "KNOWN_ISSUES.rdoc",
           "Rakefile", "bioruby.gemspec.erb",
           "bioruby.gemspec", "setup.rb",
           "extconf.rb", "rdoc.zsh"
@@ -31,7 +32,6 @@ Gem::Specification.new do |s|
               end
             end
     end
-    files.push "bioruby.gemspec" unless files.include?("bioruby.gemspec")
     %><%= 
     files.collect { |x| x.dump }.join(",\n    ")
        ###### Above is executed in ERB environment ######
@@ -48,12 +48,15 @@ Gem::Specification.new do |s|
           rdoc_files = [ 'README.rdoc', 'README_DEV.rdoc',
                          'doc/Changes-1.3.rdoc' ]
         end
+        rdoc_files.push "ChangeLog" unless rdoc_files.include?("ChangeLog")
         rdoc_files.collect { |x| x.dump }.join(",\n    ")
         ###### Above is executed in ERB environment ######
     %>
   ]
   s.rdoc_options << '--main' << 'README.rdoc'
+  s.rdoc_options << '--title' << 'BioRuby API documentation'
   s.rdoc_options << '--exclude' << '\.yaml\z'
+  s.rdoc_options << '--line-numbers' << '--inline-source'
 
   s.require_path = 'lib'
   s.autorequire = 'bio'

data/doc/Changes-1.3.rdoc

@@ -94,6 +94,23 @@ Bio::Locations#operator is used.  When "order(...)" or "group(...)",
 the attribute is set to :order or :group, respectively.  Note that
 "group(...)" is already deprecated in EMBL/GenBank/DDBJ.
 
+=== Bio::Blast
+
+Return value of Bio::Blast#exec_* is changed to String instead of Report
+object. Parsing the string is now processed in Bio::Blast#query method.
+
+Bio::Blast#exec_genomenet_tab and Bio::Blast#server="genomenet_tab" is
+deprecated.
+
+Bio::Blast#options=() can now change the following attributes: program, db,
+format, matrix, and filter.
+
+Bio::Blast.reports now supports default (-m 0) and tabular (-m 8) formats.
+Old implementation (only supports XML) is renamed to Bio::Blast.reports_xml,
+to keep compatibility for older BLAST XML documents which might not be parsed
+by the new Bio::Blast.reports nor Bio::FlatFile, although we are not sure
+whether such documents really exist or not.
+
 === Bio::Blast::Default::Report and Bio::Blast::WU::Report
 
 Iteration#lambda, #kappa, #entropy, #gapped_lambda, #gapped_kappa,
@@ -187,6 +204,16 @@ and "##FASTA" lines.
 * "###" lines are parsed to Bio::GFF::GFF3::RecordBoundary objects.
 * "##FASTA" is regarded as the beginning of bundled sequences.
 
+=== Bio::Pathway
+
+Bio::Pathway#cliquishness is changed to calculate cliquishness (clustering
+coefficient) for not only undirected graphs but also directed graphs.
+
+In Bio::Pathway#to_matrix, dump_matrix, dump_list, and depth_first_search
+methods, to avoid dependency to the order of objects in Hash#each (and
+each_keys etc.), Bio::Pathway#index is used to specify preferences of
+nodes in a graph.
+
 === Bio::SQL and BioSQL related classes
 
 BioSQL support is completely rewritten by using ActiveRecord. See documents

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

@@ -65,7 +65,8 @@ class Bio::Blast
 
       # Returns a list of available databases for given program.
       #
-      # Note: It parses http://blast.genome.jp/ to obtain database information.
+      # Note: It parses remote sites to obtain database information
+      # (e.g. http://blast.genome.jp/ for Bio::Blast::Remote::GenomeNet).
       # Thus, if the site is changed, this method can not return correct data.
       # Please tell BioRuby developers when the site is changed.
       #

data/lib/bio/shell/plugin/entry.rb

@@ -5,7 +5,7 @@
 #               Toshiaki Katayama <k@bioruby.org>
 # License::     The Ruby License
 #
-# $Id: entry.rb,v 1.10 2007/04/05 23:35:41 trevor Exp $
+# $Id:$
 #
 
 module Bio::Shell
@@ -88,8 +88,14 @@ module Bio::Shell
 
       # KEGG API at http://www.genome.jp/kegg/soap/
       else
-        puts "Retrieving entry from KEGG API (#{arg})"
-        entry = bget(arg)
+        case db.to_s.downcase
+        when 'genbank', 'gb', 'embl', 'emb', 'ddbj', 'dbj'
+          puts "Retrieving entry from NCBI eUtils"
+          entry = efetch(entry_id)
+        else
+          puts "Retrieving entry from KEGG API (#{arg})"
+          entry = bget(arg)
+        end
       end
     end
 

data/lib/bio/shell/plugin/ncbirest.rb

@@ -0,0 +1,66 @@
+#
+# = bio/shell/plugin/ncbirest.rb - plugin for NCBI eUtils
+#
+# Copyright::   Copyright (C) 2009
+#               Naohisa Goto <ng@bioruby.org>
+# License::     The Ruby License
+#
+# $Id:$
+#
+
+module Bio::Shell
+
+  private
+
+  # NCBI eUtils EFetch service.
+  # When two or more arguments are given, or multiple accession numbers
+  # are given it acts the same as Bio::NCBI::REST.efetch.
+  # Otherwise, assumes nucleotide or protein accessin is given, and
+  # automatically tries several databases.
+  def efetch(ids, *arg)
+    if !arg.empty? or ids.kind_of?(Array) or /\,/ =~ ids then
+      return Bio::NCBI::REST.efetch(ids, *arg)
+    end
+
+    rettype = 'gb'
+    prot_dbs = [ 'protein' ]
+    nucl_dbs = [ 'nuccore', 'nucleotide', 'nucgss', 'nucest' ]
+
+    case ids
+    when /\A[A-Z][A-Z][A-Z][0-9]+(\.[0-9]+)?\z/i,
+      /\A[OPQ][A-Z0-9]+(\.[0-9]+)?\z/i
+      # protein accession
+      dbs = prot_dbs
+    when /\A[0-9]+\z/, /\A[A-Z0-9]+\_[A-Z0-9]+\z/i
+      # NCBI GI or UniProt accession (with fail-safe)
+      dbs = prot_dbs + nucl_dbs
+    else
+      # nucleotide accession
+      dbs = nucl_dbs
+    end
+    result = nil
+    dbs.each do |db|
+      hash = { 'db' => db, 'rettype' => 'gb' }
+      result = Bio::NCBI::REST.efetch(ids, hash)
+      break if result and !result.empty?
+    end
+    result
+  end
+
+  # NCBI eUtils EInfo
+  def einfo
+    Bio::NCBI::REST.einfo
+  end
+
+  # NCBI eUtils ESearch
+  def esearch(str, *arg)
+    Bio::NCBI::REST.esearch(str, *arg)
+  end
+
+  # Same as Bio::NCBI::REST.esearch_count
+  def esearch_count(str, *arg)
+    Bio::NCBI::REST.esearch_count(str, *arg)
+  end
+
+end
+

data/lib/bio/shell.rb

@@ -5,7 +5,7 @@
 #               Toshiaki Katayama <k@bioruby.org>
 # License::     The Ruby License
 #
-# $Id: shell.rb,v 1.20 2007/07/09 11:17:09 k Exp $
+# $Id:$
 #
 
 require 'bio'
@@ -36,6 +36,7 @@ module Bio::Shell
   require 'bio/shell/plugin/emboss'
   require 'bio/shell/plugin/blast'
   require 'bio/shell/plugin/psort'
+  require 'bio/shell/plugin/ncbirest'
 
   extend Ghost
 

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification 
 name: ngoto-bio
 version: !ruby/object:Gem::Version 
-  version: 1.2.9.9001
+  version: 1.2.9.9501
 platform: ruby
 authors: 
 - BioRuby project
@@ -24,11 +24,14 @@ executables:
 extensions: []
 
 extra_rdoc_files: 
+- KNOWN_ISSUES.rdoc
 - README.rdoc
 - README_DEV.rdoc
 - doc/Changes-1.3.rdoc
+- ChangeLog
 files: 
 - ChangeLog
+- KNOWN_ISSUES.rdoc
 - README.rdoc
 - README_DEV.rdoc
 - Rakefile
@@ -243,6 +246,7 @@ files:
 - lib/bio/shell/plugin/flatfile.rb
 - lib/bio/shell/plugin/keggapi.rb
 - lib/bio/shell/plugin/midi.rb
+- lib/bio/shell/plugin/ncbirest.rb
 - lib/bio/shell/plugin/obda.rb
 - lib/bio/shell/plugin/psort.rb
 - lib/bio/shell/plugin/seq.rb
@@ -457,8 +461,12 @@ post_install_message:
 rdoc_options: 
 - --main
 - README.rdoc
+- --title
+- BioRuby API documentation
 - --exclude
 - \.yaml\z
+- --line-numbers
+- --inline-source
 require_paths: 
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement