bio 1.4.0 → 1.4.1

data/KNOWN_ISSUES.rdoc

@@ -4,7 +4,7 @@ License::   The Ruby License
 
 = Known issues and bugs in BioRuby
 
-Below are known issues and bugs in BioRuby. Pathes to fix them are welcomed.
+Below are known issues and bugs in BioRuby. Patches to fix them are welcome.
 We hope they will be fixed in the future.
 
 Items marked with (WONT_FIX) tags would not be fixed within BioRuby because
@@ -69,6 +69,16 @@ This indicates that br_bioflat.rb and Bio::FlatFileIndex may create
 incorrect indexes on mswin32, mingw32, and bccwin32. In addition,
 Bio::FlatFile may return incorrect data.
 
+==== String escaping of command-line arguments
+
+After BioRuby 1.4.1, in Ruby 1.9.X running on Windows, escaping of
+command-line arguments are processed by the Ruby interpreter. Before BioRuby
+1.4.0, the escaping is executed in Bio::Command#escape_shell_windows, and
+the behavior is different from the Ruby interpreter's one.
+
+Curreltly, due to the change, test/functional/bio/test_command.rb may fail
+on Windows with Ruby 1.9.X.
+
 ==== Windows 95/98/98SE/ME
 
 (WONT_FIX) Some methods that call external programs may not work in

data/README.rdoc

@@ -9,7 +9,7 @@ License::   The Ruby License
 
 = BioRuby
 
-Copyright (C) 2001-2009 Toshiaki Katayama <k@bioruby.org>
+Copyright (C) 2001-2010 Toshiaki Katayama <k@bioruby.org>
 
 BioRuby is an open source Ruby library for developing bioinformatics
 software.  Object oriented scripting language Ruby has many features
@@ -42,6 +42,7 @@ services including KEGG API can be easily utilized by BioRuby.
 README.rdoc:: This file. General information and installation procedure.
 RELEASE_NOTES.rdoc:: News and important changes in this release.
 KNOWN_ISSUES.rdoc:: Known issues and bugs in BioRuby.
+doc/RELEASE_NOTES-1.4.0.rdoc:: News and incompatible changes from 1.3.1 to 1.4.0.
 doc/Changes-1.3.rdoc:: News and incompatible changes from 1.2.1 to 1.3.0.
 doc/Changes-0.7.rd:: News and incompatible changes from 0.6.4 to 1.2.1.
 
@@ -116,7 +117,7 @@ and could be obtained by the following procedure.
 * Ruby 1.8.2 or later (except Ruby 1.9.0) -- http://www.ruby-lang.org/
   * Ruby 1.8.7-p174 or later, or Ruby 1.8.6-p383 or later is recommended.
   * Not yet fully ready with Ruby 1.9, although many components can now work
-    in Ruby 1.9.1.
+    in Ruby 1.9.1 and Ruby 1.9.2.
 
 == OPTIONAL REQUIREMENTS
 

data/RELEASE_NOTES.rdoc

@@ -1,166 +1,104 @@
-= BioRuby 1.4.0 RELEASE NOTES
+= BioRuby 1.4.1 RELEASE NOTES
 
-A lot of changes have been made to the BioRuby 1.4.0 after the version 1.3.1
+A lot of changes have been made to the BioRuby 1.4.1 after the version 1.4.0
 is released. This document describes important and/or incompatible changes
-since the BioRuby 1.3.1 release.
+since the BioRuby 1.4.0 release.
 
-== New features
-
-=== PhyloXML support
-
-Support for reading and writing PhyloXML file format is added. New classes
-Bio::PhyloXML::Parser and Bio::PhyloXML::Writer are used to read and write
-a PhyloXML file, respectively.
-
-The code is developed by Diana Jaunzeikare, mentored by Christian M Zmasek
-and co-mentors, supported by Google Summer of Code 2009 in collaboration
-with the National Evolutionary Synthesis Center (NESCent).
-
-=== FASTQ file format support
+For known problems, see KNOWN_ISSUES.rdoc.
 
-Support for reading and writing FASTQ file format is added. All of the
-three FASTQ format variants are supported.
+== New features
 
-To read a FASTQ file, Bio::FlatFile can be used. File format auto-detection
-of the FASTQ format is supported (although the three format variants should
-be specified later by users if quality scores are needed).
+=== PAML Codeml support is significantly improved
 
-New class Bio::Fastq is the parser class for the FASTQ format. An object
-of the Bio::Fastq class can be converted to a Bio::Sequence object with the
-"to_biosequnece" method. Bio::Sequence#output now supports output of the
-FASTQ format.
+PAML Codeml result parser is completely rewritten and is significantly
+improved. The code is developed by Pjotr Prins.
 
-The code is written by Naohisa Goto, with the help of discussions in the
-open-bio-l mailing list. The prototype of Bio::Fastq class was first
-developed during the BioHackathon 2009 held in Okinawa.
+=== KEGG PATHWAY and KEGG MODULE parser
 
-=== DNA chromatogram support
+Parsers for KEGG PATHWAY and KEGG MODULE data are added. The code is developed
+by Kozo Nishida and Toshiaki Katayama.
 
-Support for reading DNA chromatogram files are added. SCF and and ABIF file
-formats are supported. The code is developed by Anthony Underwood.
+=== Bio::KEGG improvements
 
-=== MEME (motif-based sequence analysis tools) support
+Following new methods are added.
 
-Support for running MAST (Motif Aliginment & Search Tool, part of the MEME
-Suite, motif-based sequence analysis tools) and parsing its results are
-added. The code is developed by Adam Kraut.
+* Bio::KEGG::GENES#keggclass, keggclasses, names_as_array, names,
+  motifs_as_strings, motifs_as_hash, motifs
+* Bio::KEGG::GENOME#original_databases
 
-=== Improvement of KEGG parser classes
+=== Test codes are added and improved.
 
-Some new methods are added to parse new fields added to some KEGG file
-formats. Unit tests for KEGG parsers are also added and improved. In
-addition, return value types of some methods are also changed for unifying
-APIs among KEGG parser classes. See incompatible changes below for details.
+Test codes are added and improved. Tney are developed by Kazuhiro Hayashi,
+Kozo Nishida, John Prince, and Naohisa Goto.
 
-=== Many sample scripts are added
+=== Other new methods
 
-Many sample scripts showing demonstrations of usages of classes are added.
-They are moved from primitive test codes for the classes described in the
-"if __FILE__ == $0" convention in the library files.
+* Bio::Fastq#mask
+* Bio::Sequence#output_fasta
+* Bio::ClustalW::Report#get_sequence
+* Bio::Reference#==
+* Bio::Location#==
+* Bio::Locations#==
+* Bio::FastaNumericFormat#to_biosequence
 
-=== Unit tests can test installed BioRuby
+== Bug fixes
 
-Mechanism to load library and to find test data in the unit tests are changed,
-and the library path and test data path can be specified with environment
-variables. BIORUBY_TEST_LIB is the path to be added to the Ruby's $LOAD_PATH.
-For example, to test BioRuby installed in
-/usr/local/lib/site_ruby/1.8, run
-  env BIORUBY_TEST_LIB=/usr/local/lib/site_ruby/1.8 ruby test/runner.rb
+=== Bio::Tree
 
-BIORUBY_TEST_DATA is the path of the test data, and BIORUBY_TEST_DEBUG is a
-flag to turn on debug of the tests.
+Following methods did not work correctly.
 
-== Deprecated features
+* Bio::Tree#collect_edge!
+* Bio::Tree#remove_edge_if
 
-=== ChangeLog is replaced by git log
+=== Bio::KEGG::GENES and Bio::KEGG::GENOME
 
-ChangeLog is replaced by the output of git-log command, and ChangeLog before
-the 1.3.1 release is moved to doc/ChangeLog-before-1.3.1.
+* Fixed bugs in Bio::KEGG::GENES#pathway.
+* Fixed parser errors due to the format changes of KEGG GENES and KEGG GENOME.
 
-=== "if __FILE__ == $0" convention
+=== Other bug fixes
 
-Primitive test codes in the "if __FILE__ == $0" convention are removed and
-the codes are moved to the sample scripts named sample/demo_*.rb (except
-some older or deprecated files).
+* In Bio::Command, changed not to call fork(2) on platforms that do not
+  support it.
+* Bio::MEDLINE#initialize should handle continuation of lines.
+* Typo and a missing field in Bio::GO::GeneAssociation#to_str.
+* Bug fix of Bio::FastaNumericFormat#to_biosequence.
+* Fixed UniProt GN parsing issue in Bio::SPTR.
 
 == Incompatible changes
 
-=== Bio::NCBI::REST
-
-NCBI announces that all Entrez E-utility requests must contain email and
-tool parameters, and requests without them will return error after June
-2010.
-
-To set default email address and tool name, following methods are added.
-* Bio::NCBI.default_email=(email)
-* Bio::NCBI.default_tool=(tool_name)
-
-For every query, Bio::NCBI::REST checks the email and tool parameters and
-raises error if they are empty.
-
-IMPORTANT NOTE: No default email address is preset in BioRuby. Programmers
-using BioRuby must set their own email address or implement to get user's
-email address in some way (from input form, configuration file, etc).
-
-Default tool name is set as "#{$0} (bioruby/#{Bio::BIORUBY_VERSION_ID})".
-For example, if you run "ruby my_script.rb" with BioRuby 1.4.0, the value is
-"my_script.rb (bioruby/1.4.0)".
-
-=== Bio::KEGG
-
-==== dblinks method
-
-In Bio::KEGG::COMPOUND, DRUG, ENZYME, GLYCAN and ORTHOLOGY, the method
-dblinks is changed to return a Hash. Each key of the hash is a database name
-and its value is an array of entry IDs in the database. If old behavior
-(returns raw entry lines as an array of strings) is needed, use
-dblinks_as_strings.
-
-==== pathways method
-
-In Bio::KEGG::COMPOUND, DRUG, ENZYME, GENES, GLYCAN and REACTION, the
-method pathways is changed to return a Hash. Each key of the hash is a
-pathway ID and its value is the description of the pathway.
-
-In Bio::KEGG::GENES, if old behavior (returns pathway IDs as an Array) is
-needed, use pathways.keys.
-
-In Bio::KEGG::COMPOUND, DRUG, ENZYME, GLYCAN, and REACTION, if old behavior
-(returns raw entry lines as an array of strings) is needed, use
-pathways_as_strings.
-
-Note that Bio::KEGG::ORTHOLOGY#pathways is not changed (returns an array
-containing pathway IDs).
+=== Bio::PAML::Codeml::Report
 
-==== orthologs method
+The code is completely rewritten. See the RDoc for details.
 
-In Bio::KEGG::ENZYME, GENES, GLYCAN and REACTION, the method orthologs is
-changed to return a Hash. Each key of the hash is a ortholog ID and its
-value is the name of the ortholog. If old behavior (returns raw entry lines
-as an array of strings) is needed, use orthologs_as_strings.
+=== Bio::KEGG::ORTHOLOGY
 
-==== genes method
+Bio::KEGG::ORTHOLOGY#pathways is changed to return a hash. The old pathway
+method is renamed to pathways_in_keggclass for compatibility.
 
-In Bio::KEGG::ENZYME#genes and Bio::KEGG::ORTHOLOGY#genes is changed to
-return a Hash that is the same as Bio::KEGG::ORTHOLOGY#genes_as_hash.
-If old behavior (returns raw entry lines as an array of strings) is needed,
-use genes_as_strings.
+=== Bio::AAindex2
 
-==== Bio::KEGG:REACTION#rpairs
+Bio::AAindex2 now copies each symmetric element for lower triangular matrix
+to the upper right part, because the Matrix class in Ruby 1.9.2 no longer
+accepts any dimension mismatches. We think the previous behavior is a bug.
 
-Bio::KEGG::REACTION#rpairs is changed to return a Hash. Each key of the
-hash is a KEGG Rpair ID and its value is an array containing name and type.
-If old behavior (returns as tokens) is needed, use rpairs_as_tokens.
+=== Bio::MEDLINE
 
-==== Bio::KEGG::ORTHOLOGY
+Bio::MEDLINE#reference no longer puts empty values in the returned
+Bio::Reference object. We think the previous behavior is a bug.
+We also think the effect is very small.
 
-Bio::KEGG:ORTHOLOGY#dblinks_as_hash does not lower-case database names.
+== Known issues
 
-=== Bio::RestrictionEnzyme
+The following issues are added or updated. See KNOWN_ISSUES.rdoc for other
+already known issues.
 
-Format validation when creating an object is turned off because of efficiency.
+=== String escaping of command-line arguments in Ruby 1.9.X on Windows
 
-== Known problems
+After BioRuby 1.4.1, in Ruby 1.9.X running on Windows, escaping of
+command-line arguments are processed by the Ruby interpreter. Before BioRuby
+1.4.0, the escaping is executed in Bio::Command#escape_shell_windows, and
+the behavior is different from the Ruby interpreter's one.
 
-See KNOWN_ISSUES.rdoc for details.
+Curreltly, due to the change, test/functional/bio/test_command.rb may fail
+on Windows with Ruby 1.9.X.
 

data/bioruby.gemspec

@@ -3,7 +3,7 @@
 # 
 Gem::Specification.new do |s|
   s.name = 'bio'
-  s.version = "1.4.0"
+  s.version = "1.4.1"
 
   s.author = "BioRuby project"
   s.email = "staff@bioruby.org"
@@ -37,6 +37,7 @@ Gem::Specification.new do |s|
     "doc/Changes-1.3.rdoc",
     "doc/KEGG_API.rd",
     "doc/KEGG_API.rd.ja",
+    "doc/RELEASE_NOTES-1.4.0.rdoc",
     "doc/Tutorial.rd",
     "doc/Tutorial.rd.html",
     "doc/Tutorial.rd.ja",
@@ -124,6 +125,7 @@ Gem::Specification.new do |s|
     "lib/bio/db/fasta/format_fasta.rb",
     "lib/bio/db/fasta/format_qual.rb",
     "lib/bio/db/fasta/qual.rb",
+    "lib/bio/db/fasta/qual_to_biosequence.rb",
     "lib/bio/db/fastq.rb",
     "lib/bio/db/fastq/fastq_to_biosequence.rb",
     "lib/bio/db/fastq/format_fastq.rb",
@@ -147,7 +149,9 @@ Gem::Specification.new do |s|
     "lib/bio/db/kegg/glycan.rb",
     "lib/bio/db/kegg/keggtab.rb",
     "lib/bio/db/kegg/kgml.rb",
+    "lib/bio/db/kegg/module.rb",
     "lib/bio/db/kegg/orthology.rb",
+    "lib/bio/db/kegg/pathway.rb",
     "lib/bio/db/kegg/reaction.rb",
     "lib/bio/db/kegg/taxonomy.rb",
     "lib/bio/db/lasergene.rb",
@@ -219,6 +223,7 @@ Gem::Specification.new do |s|
     "lib/bio/sequence/generic.rb",
     "lib/bio/sequence/na.rb",
     "lib/bio/sequence/quality_score.rb",
+    "lib/bio/sequence/sequence_masker.rb",
     "lib/bio/shell.rb",
     "lib/bio/shell/core.rb",
     "lib/bio/shell/demo.rb",
@@ -370,7 +375,17 @@ Gem::Specification.new do |s|
     "test/data/KEGG/G00024.glycan",
     "test/data/KEGG/G01366.glycan",
     "test/data/KEGG/K02338.orthology",
+    "test/data/KEGG/M00118.module",
     "test/data/KEGG/R00006.reaction",
+    "test/data/KEGG/T00005.genome",
+    "test/data/KEGG/T00070.genome",
+    "test/data/KEGG/b0529.gene",
+    "test/data/KEGG/ec00072.pathway",
+    "test/data/KEGG/hsa00790.pathway",
+    "test/data/KEGG/ko00312.pathway",
+    "test/data/KEGG/map00030.pathway",
+    "test/data/KEGG/map00052.pathway",
+    "test/data/KEGG/rn00250.pathway",
     "test/data/SOSUI/sample.report",
     "test/data/TMHMM/sample.report",
     "test/data/aaindex/DAYM780301",
@@ -383,6 +398,7 @@ Gem::Specification.new do |s|
     "test/data/blast/b0002.faa.m7",
     "test/data/blast/b0002.faa.m8",
     "test/data/blast/blastp-multi.m7",
+    "test/data/clustalw/example1.aln",
     "test/data/command/echoarg2.bat",
     "test/data/embl/AB090716.embl",
     "test/data/embl/AB090716.embl.rel89",
@@ -441,13 +457,23 @@ Gem::Specification.new do |s|
     "test/data/fastq/wrapping_original_sanger.fastq",
     "test/data/gcg/pileup-aa.msf",
     "test/data/genscan/sample.report",
+    "test/data/go/selected_component.ontology",
+    "test/data/go/selected_gene_association.sgd",
+    "test/data/go/selected_wikipedia2go",
     "test/data/iprscan/merged.raw",
     "test/data/iprscan/merged.txt",
+    "test/data/medline/20146148_modified.medline",
     "test/data/meme/db",
     "test/data/meme/mast",
     "test/data/meme/mast.out",
     "test/data/meme/meme.out",
     "test/data/paml/codeml/control_file.txt",
+    "test/data/paml/codeml/models/aa.aln",
+    "test/data/paml/codeml/models/aa.dnd",
+    "test/data/paml/codeml/models/aa.ph",
+    "test/data/paml/codeml/models/alignment.phy",
+    "test/data/paml/codeml/models/results0-3.txt",
+    "test/data/paml/codeml/models/results7-8.txt",
     "test/data/paml/codeml/output.txt",
     "test/data/paml/codeml/rates",
     "test/data/phyloxml/apaf.xml",
@@ -479,6 +505,7 @@ Gem::Specification.new do |s|
     "test/unit/bio/appl/blast/test_ncbioptions.rb",
     "test/unit/bio/appl/blast/test_report.rb",
     "test/unit/bio/appl/blast/test_rpsblast.rb",
+    "test/unit/bio/appl/clustalw/test_report.rb",
     "test/unit/bio/appl/gcg/test_msf.rb",
     "test/unit/bio/appl/genscan/test_report.rb",
     "test/unit/bio/appl/hmmer/test_report.rb",
@@ -489,6 +516,7 @@ Gem::Specification.new do |s|
     "test/unit/bio/appl/meme/test_motif.rb",
     "test/unit/bio/appl/paml/codeml/test_rates.rb",
     "test/unit/bio/appl/paml/codeml/test_report.rb",
+    "test/unit/bio/appl/paml/codeml/test_report_single.rb",
     "test/unit/bio/appl/paml/test_codeml.rb",
     "test/unit/bio/appl/sim4/test_report.rb",
     "test/unit/bio/appl/sosui/test_report.rb",
@@ -508,13 +536,18 @@ Gem::Specification.new do |s|
     "test/unit/bio/db/embl/test_embl_to_bioseq.rb",
     "test/unit/bio/db/embl/test_sptr.rb",
     "test/unit/bio/db/embl/test_uniprot.rb",
+    "test/unit/bio/db/fasta/test_defline.rb",
+    "test/unit/bio/db/fasta/test_defline_misc.rb",
     "test/unit/bio/db/fasta/test_format_qual.rb",
     "test/unit/bio/db/kegg/test_compound.rb",
     "test/unit/bio/db/kegg/test_drug.rb",
     "test/unit/bio/db/kegg/test_enzyme.rb",
     "test/unit/bio/db/kegg/test_genes.rb",
+    "test/unit/bio/db/kegg/test_genome.rb",
     "test/unit/bio/db/kegg/test_glycan.rb",
+    "test/unit/bio/db/kegg/test_module.rb",
     "test/unit/bio/db/kegg/test_orthology.rb",
+    "test/unit/bio/db/kegg/test_pathway.rb",
     "test/unit/bio/db/kegg/test_reaction.rb",
     "test/unit/bio/db/pdb/test_pdb.rb",
     "test/unit/bio/db/sanger_chromatogram/test_abif.rb",
@@ -523,6 +556,7 @@ Gem::Specification.new do |s|
     "test/unit/bio/db/test_fasta.rb",
     "test/unit/bio/db/test_fastq.rb",
     "test/unit/bio/db/test_gff.rb",
+    "test/unit/bio/db/test_go.rb",
     "test/unit/bio/db/test_lasergene.rb",
     "test/unit/bio/db/test_medline.rb",
     "test/unit/bio/db/test_newick.rb",
@@ -548,6 +582,7 @@ Gem::Specification.new do |s|
     "test/unit/bio/sequence/test_dblink.rb",
     "test/unit/bio/sequence/test_na.rb",
     "test/unit/bio/sequence/test_quality_score.rb",
+    "test/unit/bio/sequence/test_sequence_masker.rb",
     "test/unit/bio/shell/plugin/test_seq.rb",
     "test/unit/bio/test_alignment.rb",
     "test/unit/bio/test_command.rb",
@@ -588,7 +623,8 @@ Gem::Specification.new do |s|
     "README.rdoc",
     "README_DEV.rdoc",
     "RELEASE_NOTES.rdoc",
-    "doc/Changes-1.3.rdoc"
+    "doc/Changes-1.3.rdoc",
+    "doc/RELEASE_NOTES-1.4.0.rdoc"
   ]
   s.rdoc_options << '--main' << 'README.rdoc'
   s.rdoc_options << '--title' << 'BioRuby API documentation'

data/doc/RELEASE_NOTES-1.4.0.rdoc

@@ -0,0 +1,167 @@
+= BioRuby 1.4.0 RELEASE NOTES
+
+A lot of changes have been made to the BioRuby 1.4.0 after the version 1.3.1
+is released. This document describes important and/or incompatible changes
+since the BioRuby 1.3.1 release.
+
+== New features
+
+=== PhyloXML support
+
+Support for reading and writing PhyloXML file format is added. New classes
+Bio::PhyloXML::Parser and Bio::PhyloXML::Writer are used to read and write
+a PhyloXML file, respectively.
+
+The code is developed by Diana Jaunzeikare, mentored by Christian M Zmasek
+and co-mentors, supported by Google Summer of Code 2009 in collaboration
+with the National Evolutionary Synthesis Center (NESCent).
+
+=== FASTQ file format support
+
+Support for reading and writing FASTQ file format is added. All of the
+three FASTQ format variants are supported.
+
+To read a FASTQ file, Bio::FlatFile can be used. File format auto-detection
+of the FASTQ format is supported (although the three format variants should
+be specified later by users if quality scores are needed).
+
+New class Bio::Fastq is the parser class for the FASTQ format. An object
+of the Bio::Fastq class can be converted to a Bio::Sequence object with the
+"to_biosequnece" method. Bio::Sequence#output now supports output of the
+FASTQ format.
+
+The code is written by Naohisa Goto, with the help of discussions in the
+open-bio-l mailing list. The prototype of Bio::Fastq class was first
+developed during the BioHackathon 2009 held in Okinawa.
+
+=== DNA chromatogram support
+
+Support for reading DNA chromatogram files are added. SCF and and ABIF file
+formats are supported. The code is developed by Anthony Underwood.
+
+=== MEME (motif-based sequence analysis tools) support
+
+Support for running MAST (Motif Aliginment & Search Tool, part of the MEME
+Suite, motif-based sequence analysis tools) and parsing its results are
+added. The code is developed by Adam Kraut.
+
+=== Improvement of KEGG parser classes
+
+Some new methods are added to parse new fields added to some KEGG file
+formats. Unit tests for KEGG parsers are also added and improved. In
+addition, return value types of some methods are also changed for unifying
+APIs among KEGG parser classes. See incompatible changes below for details.
+Most of them are contributed by Kozo Nishida.
+
+=== Many sample scripts are added
+
+Many sample scripts showing demonstrations of usages of classes are added.
+They are moved from primitive test codes for the classes described in the
+"if __FILE__ == $0" convention in the library files.
+
+=== Unit tests can test installed BioRuby
+
+Mechanism to load library and to find test data in the unit tests are changed,
+and the library path and test data path can be specified with environment
+variables. BIORUBY_TEST_LIB is the path to be added to the Ruby's $LOAD_PATH.
+For example, to test BioRuby installed in
+/usr/local/lib/site_ruby/1.8, run
+  env BIORUBY_TEST_LIB=/usr/local/lib/site_ruby/1.8 ruby test/runner.rb
+
+BIORUBY_TEST_DATA is the path of the test data, and BIORUBY_TEST_DEBUG is a
+flag to turn on debug of the tests.
+
+== Deprecated features
+
+=== ChangeLog is replaced by git log
+
+ChangeLog is replaced by the output of git-log command, and ChangeLog before
+the 1.3.1 release is moved to doc/ChangeLog-before-1.3.1.
+
+=== "if __FILE__ == $0" convention
+
+Primitive test codes in the "if __FILE__ == $0" convention are removed and
+the codes are moved to the sample scripts named sample/demo_*.rb (except
+some older or deprecated files).
+
+== Incompatible changes
+
+=== Bio::NCBI::REST
+
+NCBI announces that all Entrez E-utility requests must contain email and
+tool parameters, and requests without them will return error after June
+2010.
+
+To set default email address and tool name, following methods are added.
+* Bio::NCBI.default_email=(email)
+* Bio::NCBI.default_tool=(tool_name)
+
+For every query, Bio::NCBI::REST checks the email and tool parameters and
+raises error if they are empty.
+
+IMPORTANT NOTE: No default email address is preset in BioRuby. Programmers
+using BioRuby must set their own email address or implement to get user's
+email address in some way (from input form, configuration file, etc).
+
+Default tool name is set as "#{$0} (bioruby/#{Bio::BIORUBY_VERSION_ID})".
+For example, if you run "ruby my_script.rb" with BioRuby 1.4.0, the value is
+"my_script.rb (bioruby/1.4.0)".
+
+=== Bio::KEGG
+
+==== dblinks method
+
+In Bio::KEGG::COMPOUND, DRUG, ENZYME, GLYCAN and ORTHOLOGY, the method
+dblinks is changed to return a Hash. Each key of the hash is a database name
+and its value is an array of entry IDs in the database. If old behavior
+(returns raw entry lines as an array of strings) is needed, use
+dblinks_as_strings.
+
+==== pathways method
+
+In Bio::KEGG::COMPOUND, DRUG, ENZYME, GENES, GLYCAN and REACTION, the
+method pathways is changed to return a Hash. Each key of the hash is a
+pathway ID and its value is the description of the pathway.
+
+In Bio::KEGG::GENES, if old behavior (returns pathway IDs as an Array) is
+needed, use pathways.keys.
+
+In Bio::KEGG::COMPOUND, DRUG, ENZYME, GLYCAN, and REACTION, if old behavior
+(returns raw entry lines as an array of strings) is needed, use
+pathways_as_strings.
+
+Note that Bio::KEGG::ORTHOLOGY#pathways is not changed (returns an array
+containing pathway IDs).
+
+==== orthologs method
+
+In Bio::KEGG::ENZYME, GENES, GLYCAN and REACTION, the method orthologs is
+changed to return a Hash. Each key of the hash is a ortholog ID and its
+value is the name of the ortholog. If old behavior (returns raw entry lines
+as an array of strings) is needed, use orthologs_as_strings.
+
+==== genes method
+
+In Bio::KEGG::ENZYME#genes and Bio::KEGG::ORTHOLOGY#genes is changed to
+return a Hash that is the same as Bio::KEGG::ORTHOLOGY#genes_as_hash.
+If old behavior (returns raw entry lines as an array of strings) is needed,
+use genes_as_strings.
+
+==== Bio::KEGG:REACTION#rpairs
+
+Bio::KEGG::REACTION#rpairs is changed to return a Hash. Each key of the
+hash is a KEGG Rpair ID and its value is an array containing name and type.
+If old behavior (returns as tokens) is needed, use rpairs_as_tokens.
+
+==== Bio::KEGG::ORTHOLOGY
+
+Bio::KEGG:ORTHOLOGY#dblinks_as_hash does not lower-case database names.
+
+=== Bio::RestrictionEnzyme
+
+Format validation when creating an object is turned off because of efficiency.
+
+== Known problems
+
+See KNOWN_ISSUES.rdoc for details.
+