bio 1.3.1 → 1.4.0

data/KNOWN_ISSUES.rdoc

@@ -4,8 +4,11 @@ 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.
+Below are known issues and bugs in BioRuby. Pathes to fix them are welcomed.
+We hope they will be fixed in the future.
+
+Items marked with (WONT_FIX) tags would not be fixed within BioRuby because
+they are not BioRuby's issues and/or it is very difficult to fix them.
 
 == 1. Ruby version specific issues
 
@@ -17,7 +20,8 @@ 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.
+Encoding::CompatibilityError or "ArgumentError: invalid byte sequence in
+(encoding name)" may be raised.
 
 === Ruby 1.9.0
 
@@ -86,3 +90,31 @@ the latest Ensembl. For a workaround, use an archive server. For example,
 Alternatively, consider using Ruby Ensembl API.
 * http://github.com/jandot/ruby-ensembl-api
 
+=== Bio::DBGET and sample/dbget
+
+(WONT_FIX) Because the DBGET service have not been publically available for
+a long time, we give up support for Bio::DBGET and sample/dbget. Instead,
+using Bio::TogoWS or Bio::KEGG::API is recommended.
+
+=== Bio::NCBI::SOAP
+
+It seems that Bio::NCBI::SOAP (in lib/bio/io/ncbisoap.rb) does not work
+correctly, even running on Ruby 1.8.x. Instead, use Bio::NCBI::REST.
+
+=== Bio::KEGG::Taxonomy and sample/demo_kegg_taxonomy.rb
+
+Bio::KEGG::Taxonomy fails to parse current KEGG taxonomy data file probably
+because of the growth of the data size.
+
+== 4. Compatibility issues with other libraries/extensions
+
+=== ActiveRecord
+
+BioSQL support uses ActiveRecord, but the author of the document does not
+know which version is suitable.
+
+=== Ruby on Rails
+
+BioRuby Shell on Web uses Ruby on Rails, but the author of the document does
+not know which version is suitable.
+

data/README.rdoc

@@ -40,6 +40,7 @@ services including KEGG API can be easily utilized by BioRuby.
 ==== General information
 
 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/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.
@@ -112,8 +113,8 @@ and could be obtained by the following procedure.
 
 == REQUIREMENTS
 
-* Ruby 1.8.2 or later -- http://www.ruby-lang.org/
-  * Ruby 1.8.5 or later is recommended.
+* 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.
 
@@ -145,6 +146,11 @@ Accessing BioSQL database created by other Open Bio* libraries:
   {RubyForge:ruby-oci8}[http://ruby-oci8.rubyforge.org/]
   (note that ruby-oci8 can only work with ruby-dbi 0.2.2).
 
+For parsing PhyloXML format files:
+
+* {RubyForge:libxml-ruby}[http://libxml.rubyforge.org/] (Ruby language
+  bindings for the {GNOME Libxml2 XML toolkit}[http://xmlsoft.org/])
+
 
 == INSTALL
 

data/RELEASE_NOTES.rdoc

@@ -0,0 +1,166 @@
+= 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.
+
+=== 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.
+

data/bin/bioruby

@@ -6,7 +6,7 @@
 #               Toshiaki Katayama <k@bioruby.org>
 # License::     The Ruby License
 #
-# $Id: bioruby,v 1.21 2007/07/26 10:46:46 k Exp $
+# $Id:$
 #
 
 begin
@@ -26,6 +26,9 @@ Bio::Shell::Setup.new
 # loading workspace and command history
 Bio::Shell.load_session
 
+# sets default email address for Entrez eUtils.
+Bio::NCBI.default_email ||= 'staff@bioruby.org'
+
 # main loop
 if Bio::Shell.cache[:rails]
   Bio::Shell.cache[:rails].join

data/bioruby.gemspec

@@ -3,7 +3,7 @@
 # 
 Gem::Specification.new do |s|
   s.name = 'bio'
-  s.version = "1.3.1"
+  s.version = "1.4.0"
 
   s.author = "BioRuby project"
   s.email = "staff@bioruby.org"
@@ -23,6 +23,7 @@ Gem::Specification.new do |s|
     "LGPL",
     "README.rdoc",
     "README_DEV.rdoc",
+    "RELEASE_NOTES.rdoc",
     "Rakefile",
     "bin/bioruby",
     "bin/br_biofetch.rb",
@@ -31,6 +32,7 @@ Gem::Specification.new do |s|
     "bin/br_pmfetch.rb",
     "bioruby.gemspec",
     "bioruby.gemspec.erb",
+    "doc/ChangeLog-before-1.3.1",
     "doc/Changes-0.7.rd",
     "doc/Changes-1.3.rdoc",
     "doc/KEGG_API.rd",
@@ -71,6 +73,9 @@ Gem::Specification.new do |s|
     "lib/bio/appl/iprscan/report.rb",
     "lib/bio/appl/mafft.rb",
     "lib/bio/appl/mafft/report.rb",
+    "lib/bio/appl/meme/mast.rb",
+    "lib/bio/appl/meme/mast/report.rb",
+    "lib/bio/appl/meme/motif.rb",
     "lib/bio/appl/muscle.rb",
     "lib/bio/appl/paml/baseml.rb",
     "lib/bio/appl/paml/baseml/report.rb",
@@ -117,6 +122,11 @@ Gem::Specification.new do |s|
     "lib/bio/db/fasta/defline.rb",
     "lib/bio/db/fasta/fasta_to_biosequence.rb",
     "lib/bio/db/fasta/format_fasta.rb",
+    "lib/bio/db/fasta/format_qual.rb",
+    "lib/bio/db/fasta/qual.rb",
+    "lib/bio/db/fastq.rb",
+    "lib/bio/db/fastq/fastq_to_biosequence.rb",
+    "lib/bio/db/fastq/format_fastq.rb",
     "lib/bio/db/genbank/common.rb",
     "lib/bio/db/genbank/ddbj.rb",
     "lib/bio/db/genbank/format_genbank.rb",
@@ -127,6 +137,7 @@ Gem::Specification.new do |s|
     "lib/bio/db/gff.rb",
     "lib/bio/db/go.rb",
     "lib/bio/db/kegg/brite.rb",
+    "lib/bio/db/kegg/common.rb",
     "lib/bio/db/kegg/compound.rb",
     "lib/bio/db/kegg/drug.rb",
     "lib/bio/db/kegg/enzyme.rb",
@@ -153,8 +164,16 @@ Gem::Specification.new do |s|
     "lib/bio/db/pdb/pdb.rb",
     "lib/bio/db/pdb/residue.rb",
     "lib/bio/db/pdb/utils.rb",
+    "lib/bio/db/phyloxml/phyloxml.xsd",
+    "lib/bio/db/phyloxml/phyloxml_elements.rb",
+    "lib/bio/db/phyloxml/phyloxml_parser.rb",
+    "lib/bio/db/phyloxml/phyloxml_writer.rb",
     "lib/bio/db/prosite.rb",
     "lib/bio/db/rebase.rb",
+    "lib/bio/db/sanger_chromatogram/abif.rb",
+    "lib/bio/db/sanger_chromatogram/chromatogram.rb",
+    "lib/bio/db/sanger_chromatogram/chromatogram_to_biosequence.rb",
+    "lib/bio/db/sanger_chromatogram/scf.rb",
     "lib/bio/db/soft.rb",
     "lib/bio/db/transfac.rb",
     "lib/bio/feature.rb",
@@ -199,6 +218,7 @@ Gem::Specification.new do |s|
     "lib/bio/sequence/format_raw.rb",
     "lib/bio/sequence/generic.rb",
     "lib/bio/sequence/na.rb",
+    "lib/bio/sequence/quality_score.rb",
     "lib/bio/shell.rb",
     "lib/bio/shell/core.rb",
     "lib/bio/shell/demo.rb",
@@ -280,7 +300,42 @@ Gem::Specification.new do |s|
     "sample/biofetch.rb",
     "sample/color_scheme_na.rb",
     "sample/dbget",
+    "sample/demo_aaindex.rb",
+    "sample/demo_aminoacid.rb",
+    "sample/demo_bl2seq_report.rb",
+    "sample/demo_blast_report.rb",
+    "sample/demo_codontable.rb",
+    "sample/demo_das.rb",
+    "sample/demo_ddbjxml.rb",
+    "sample/demo_fasta_remote.rb",
+    "sample/demo_fastaformat.rb",
+    "sample/demo_genbank.rb",
+    "sample/demo_genscan_report.rb",
+    "sample/demo_gff1.rb",
+    "sample/demo_go.rb",
+    "sample/demo_hmmer_report.rb",
+    "sample/demo_kegg_compound.rb",
+    "sample/demo_kegg_drug.rb",
+    "sample/demo_kegg_genome.rb",
+    "sample/demo_kegg_glycan.rb",
+    "sample/demo_kegg_orthology.rb",
+    "sample/demo_kegg_reaction.rb",
+    "sample/demo_kegg_taxonomy.rb",
+    "sample/demo_keggapi.rb",
+    "sample/demo_litdb.rb",
+    "sample/demo_locations.rb",
+    "sample/demo_ncbi_rest.rb",
+    "sample/demo_nucleicacid.rb",
+    "sample/demo_pathway.rb",
+    "sample/demo_prosite.rb",
+    "sample/demo_psort.rb",
+    "sample/demo_psort_report.rb",
+    "sample/demo_pubmed.rb",
     "sample/demo_sequence.rb",
+    "sample/demo_sirna.rb",
+    "sample/demo_sosui_report.rb",
+    "sample/demo_targetp_report.rb",
+    "sample/demo_tmhmm_report.rb",
     "sample/enzymes.rb",
     "sample/fasta2tab.rb",
     "sample/fastagrep.rb",
@@ -302,11 +357,20 @@ Gem::Specification.new do |s|
     "sample/psortplot_html.rb",
     "sample/ssearch2tab.rb",
     "sample/tdiary.rb",
+    "sample/test_phyloxml_big.rb",
     "sample/tfastx2tab.rb",
     "sample/vs-genes.rb",
     "setup.rb",
+    "test/bioruby_test_helper.rb",
     "test/data/HMMER/hmmpfam.out",
     "test/data/HMMER/hmmsearch.out",
+    "test/data/KEGG/1.1.1.1.enzyme",
+    "test/data/KEGG/C00025.compound",
+    "test/data/KEGG/D00063.drug",
+    "test/data/KEGG/G00024.glycan",
+    "test/data/KEGG/G01366.glycan",
+    "test/data/KEGG/K02338.orthology",
+    "test/data/KEGG/R00006.reaction",
     "test/data/SOSUI/sample.report",
     "test/data/TMHMM/sample.report",
     "test/data/aaindex/DAYM780301",
@@ -324,16 +388,79 @@ Gem::Specification.new do |s|
     "test/data/embl/AB090716.embl.rel89",
     "test/data/fasta/example1.txt",
     "test/data/fasta/example2.txt",
+    "test/data/fastq/README.txt",
+    "test/data/fastq/error_diff_ids.fastq",
+    "test/data/fastq/error_double_qual.fastq",
+    "test/data/fastq/error_double_seq.fastq",
+    "test/data/fastq/error_long_qual.fastq",
+    "test/data/fastq/error_no_qual.fastq",
+    "test/data/fastq/error_qual_del.fastq",
+    "test/data/fastq/error_qual_escape.fastq",
+    "test/data/fastq/error_qual_null.fastq",
+    "test/data/fastq/error_qual_space.fastq",
+    "test/data/fastq/error_qual_tab.fastq",
+    "test/data/fastq/error_qual_unit_sep.fastq",
+    "test/data/fastq/error_qual_vtab.fastq",
+    "test/data/fastq/error_short_qual.fastq",
+    "test/data/fastq/error_spaces.fastq",
+    "test/data/fastq/error_tabs.fastq",
+    "test/data/fastq/error_trunc_at_plus.fastq",
+    "test/data/fastq/error_trunc_at_qual.fastq",
+    "test/data/fastq/error_trunc_at_seq.fastq",
+    "test/data/fastq/error_trunc_in_plus.fastq",
+    "test/data/fastq/error_trunc_in_qual.fastq",
+    "test/data/fastq/error_trunc_in_seq.fastq",
+    "test/data/fastq/error_trunc_in_title.fastq",
+    "test/data/fastq/illumina_full_range_as_illumina.fastq",
+    "test/data/fastq/illumina_full_range_as_sanger.fastq",
+    "test/data/fastq/illumina_full_range_as_solexa.fastq",
+    "test/data/fastq/illumina_full_range_original_illumina.fastq",
+    "test/data/fastq/longreads_as_illumina.fastq",
+    "test/data/fastq/longreads_as_sanger.fastq",
+    "test/data/fastq/longreads_as_solexa.fastq",
+    "test/data/fastq/longreads_original_sanger.fastq",
+    "test/data/fastq/misc_dna_as_illumina.fastq",
+    "test/data/fastq/misc_dna_as_sanger.fastq",
+    "test/data/fastq/misc_dna_as_solexa.fastq",
+    "test/data/fastq/misc_dna_original_sanger.fastq",
+    "test/data/fastq/misc_rna_as_illumina.fastq",
+    "test/data/fastq/misc_rna_as_sanger.fastq",
+    "test/data/fastq/misc_rna_as_solexa.fastq",
+    "test/data/fastq/misc_rna_original_sanger.fastq",
+    "test/data/fastq/sanger_full_range_as_illumina.fastq",
+    "test/data/fastq/sanger_full_range_as_sanger.fastq",
+    "test/data/fastq/sanger_full_range_as_solexa.fastq",
+    "test/data/fastq/sanger_full_range_original_sanger.fastq",
+    "test/data/fastq/solexa_full_range_as_illumina.fastq",
+    "test/data/fastq/solexa_full_range_as_sanger.fastq",
+    "test/data/fastq/solexa_full_range_as_solexa.fastq",
+    "test/data/fastq/solexa_full_range_original_solexa.fastq",
+    "test/data/fastq/wrapping_as_illumina.fastq",
+    "test/data/fastq/wrapping_as_sanger.fastq",
+    "test/data/fastq/wrapping_as_solexa.fastq",
+    "test/data/fastq/wrapping_original_sanger.fastq",
     "test/data/gcg/pileup-aa.msf",
     "test/data/genscan/sample.report",
     "test/data/iprscan/merged.raw",
     "test/data/iprscan/merged.txt",
+    "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/output.txt",
     "test/data/paml/codeml/rates",
+    "test/data/phyloxml/apaf.xml",
+    "test/data/phyloxml/bcl_2.xml",
+    "test/data/phyloxml/made_up.xml",
+    "test/data/phyloxml/ncbi_taxonomy_mollusca_short.xml",
+    "test/data/phyloxml/phyloxml_examples.xml",
     "test/data/prosite/prosite.dat",
     "test/data/refseq/nm_126355.entret",
     "test/data/rpsblast/misc.rpsblast",
+    "test/data/sanger_chromatogram/test_chromatogram_abif.ab1",
+    "test/data/sanger_chromatogram/test_chromatogram_scf_v2.scf",
+    "test/data/sanger_chromatogram/test_chromatogram_scf_v3.scf",
     "test/data/sim4/complement-A4.sim4",
     "test/data/sim4/simple-A4.sim4",
     "test/data/sim4/simple2-A4.sim4",
@@ -357,6 +484,9 @@ Gem::Specification.new do |s|
     "test/unit/bio/appl/hmmer/test_report.rb",
     "test/unit/bio/appl/iprscan/test_report.rb",
     "test/unit/bio/appl/mafft/test_report.rb",
+    "test/unit/bio/appl/meme/mast/test_report.rb",
+    "test/unit/bio/appl/meme/test_mast.rb",
+    "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/test_codeml.rb",
@@ -378,16 +508,29 @@ 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_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_glycan.rb",
+    "test/unit/bio/db/kegg/test_orthology.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",
+    "test/unit/bio/db/sanger_chromatogram/test_scf.rb",
     "test/unit/bio/db/test_aaindex.rb",
     "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_lasergene.rb",
     "test/unit/bio/db/test_medline.rb",
     "test/unit/bio/db/test_newick.rb",
     "test/unit/bio/db/test_nexus.rb",
+    "test/unit/bio/db/test_phyloxml.rb",
+    "test/unit/bio/db/test_phyloxml_writer.rb",
     "test/unit/bio/db/test_prosite.rb",
+    "test/unit/bio/db/test_qual.rb",
     "test/unit/bio/db/test_rebase.rb",
     "test/unit/bio/db/test_soft.rb",
     "test/unit/bio/io/flatfile/test_autodetection.rb",
@@ -404,6 +547,7 @@ Gem::Specification.new do |s|
     "test/unit/bio/sequence/test_compat.rb",
     "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/shell/plugin/test_seq.rb",
     "test/unit/bio/test_alignment.rb",
     "test/unit/bio/test_command.rb",
@@ -443,6 +587,7 @@ Gem::Specification.new do |s|
     "KNOWN_ISSUES.rdoc",
     "README.rdoc",
     "README_DEV.rdoc",
+    "RELEASE_NOTES.rdoc",
     "doc/Changes-1.3.rdoc"
   ]
   s.rdoc_options << '--main' << 'README.rdoc'