bio 1.3.1 → 1.4.0

data/test/unit/bio/util/restriction_enzyme/test_single_strand_complement.rb

@@ -8,10 +8,12 @@
 #  $Id:$
 #
 
+# loading helper routine for testing bioruby
 require 'pathname'
-libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5, 'lib')).cleanpath.to_s
-$:.unshift(libpath) unless $:.include?(libpath)
+load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4,
+                            'bioruby_test_helper.rb')).cleanpath.to_s
 
+# libraries needed for the tests
 require 'test/unit'
 require 'bio/util/restriction_enzyme/single_strand_complement'
 
@@ -128,17 +130,19 @@ class TestSingleStrandComplement < Test::Unit::TestCase #:nodoc:
     assert_raise(ArgumentError) { @t.new('a', [1,1,2]) }
     assert_raise(ArgumentError) { @t.new('a', 1,1,2,2) }
 
-    assert_raise(ArgumentError) { @t.new(1, [1,2,3]) }
-    assert_raise(ArgumentError) { @t.new('gaat^aca', [1,2,3]) }
-    assert_raise(ArgumentError) { @t.new('gaat^^aca') }
-    assert_raise(ArgumentError) { @t.new('z', [1,2,3]) }
-
-    assert_raise(ArgumentError) { @t.new('g', [0,1,2]) }
-    assert_raise(ArgumentError) { @t.new('g', 0,1,2,0) }
-    assert_raise(ArgumentError) { @t.new('g', [0,1,1,2]) }
-    assert_raise(ArgumentError) { @t.new('g', 0,1,1,2,2) }
-    assert_raise(ArgumentError) { @t.new(1,2,3) }
-    assert_raise(ArgumentError) { @t.new(1,2,'g') }
+  # NOTE t| 2009-09-19 commented out for library efficiency
+  # re: validate_args(sequence, c) in util/restriction_enzyme/single_strand/single_strand.rb
+    # assert_raise(ArgumentError) { @t.new(1, [1,2,3]) }
+    # assert_raise(ArgumentError) { @t.new('gaat^aca', [1,2,3]) }
+    # assert_raise(ArgumentError) { @t.new('gaat^^aca') }
+    # assert_raise(ArgumentError) { @t.new('z', [1,2,3]) }
+    # 
+    # assert_raise(ArgumentError) { @t.new('g', [0,1,2]) }
+    # assert_raise(ArgumentError) { @t.new('g', 0,1,2,0) }
+    # assert_raise(ArgumentError) { @t.new('g', [0,1,1,2]) }
+    # assert_raise(ArgumentError) { @t.new('g', 0,1,1,2,2) }
+    # assert_raise(ArgumentError) { @t.new(1,2,3) }
+    # assert_raise(ArgumentError) { @t.new(1,2,'g') }
   end
 
 

data/test/unit/bio/util/restriction_enzyme/test_string_formatting.rb

@@ -8,10 +8,12 @@
 #  $Id:$
 #
 
+# loading helper routine for testing bioruby
 require 'pathname'
-libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5, 'lib')).cleanpath.to_s
-$:.unshift(libpath) unless $:.include?(libpath)
+load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4,
+                            'bioruby_test_helper.rb')).cleanpath.to_s
 
+# libraries needed for the tests
 require 'test/unit'
 require 'bio/util/restriction_enzyme/string_formatting'
 

data/test/unit/bio/util/test_color_scheme.rb

@@ -5,13 +5,15 @@
 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
 # License::   The Ruby License
 #
-#  $Id: test_color_scheme.rb,v 1.3 2007/04/05 23:35:44 trevor Exp $
+#  $Id:$
 #
 
+# loading helper routine for testing bioruby
 require 'pathname'
-libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4 , 'lib')).cleanpath.to_s
-$:.unshift(libpath) unless $:.include?(libpath)
+load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 3,
+                            'bioruby_test_helper.rb')).cleanpath.to_s
 
+# libraries needed for the tests
 require 'test/unit'
 require 'bio/util/color_scheme'
 

data/test/unit/bio/util/test_contingency_table.rb

@@ -5,13 +5,15 @@
 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
 # License::   The Ruby License
 #
-#  $Id: test_contingency_table.rb,v 1.4 2007/04/05 23:35:44 trevor Exp $
+#  $Id:$
 #
 
+# loading helper routine for testing bioruby
 require 'pathname'
-libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4 , 'lib')).cleanpath.to_s
-$:.unshift(libpath) unless $:.include?(libpath)
+load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 3,
+                            'bioruby_test_helper.rb')).cleanpath.to_s
 
+# libraries needed for the tests
 require 'test/unit'
 require 'bio/util/contingency_table'
 

data/test/unit/bio/util/test_restriction_enzyme.rb

@@ -8,10 +8,12 @@
 #  $Id:$
 #
 
+# loading helper routine for testing bioruby
 require 'pathname'
-libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4, 'lib')).cleanpath.to_s
-$:.unshift(libpath) unless $:.include?(libpath)
+load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 3,
+                            'bioruby_test_helper.rb')).cleanpath.to_s
 
+# libraries needed for the tests
 require 'test/unit'
 require 'bio/util/restriction_enzyme.rb'
 

data/test/unit/bio/util/test_sirna.rb

@@ -1,16 +1,18 @@
 #
 # test/unit/bio/util/test_sirna.rb - Unit test for Bio::SiRNA.
 #
-# Copyright::  Copyright (C) 2005 Mitsuteru C. Nakap <n@bioruby.org>
+# Copyright::  Copyright (C) 2005 Mitsuteru C. Nakao <n@bioruby.org>
 # License::    The Ruby License
 #
-#  $Id: test_sirna.rb,v 1.4 2007/04/05 23:35:44 trevor Exp $
+#  $Id:$
 #
 
+# loading helper routine for testing bioruby
 require 'pathname'
-libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4 , 'lib')).cleanpath.to_s
-$:.unshift(libpath) unless $:.include?(libpath)
+load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 3,
+                            'bioruby_test_helper.rb')).cleanpath.to_s
 
+# libraries needed for the tests
 require 'test/unit'
 require 'bio/util/sirna'
 

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification 
 name: bio
 version: !ruby/object:Gem::Version 
-  version: 1.3.1
+  version: 1.4.0
 platform: ruby
 authors: 
 - BioRuby project
@@ -9,7 +9,7 @@ autorequire: bio
 bindir: bin
 cert_chain: []
 
-date: 2009-09-02 00:00:00 +09:00
+date: 2009-12-28 00:00:00 +09:00
 default_executable: bioruby
 dependencies: []
 
@@ -28,6 +28,7 @@ extra_rdoc_files:
 - KNOWN_ISSUES.rdoc
 - README.rdoc
 - README_DEV.rdoc
+- RELEASE_NOTES.rdoc
 - doc/Changes-1.3.rdoc
 files: 
 - COPYING
@@ -39,6 +40,7 @@ files:
 - LGPL
 - README.rdoc
 - README_DEV.rdoc
+- RELEASE_NOTES.rdoc
 - Rakefile
 - bin/bioruby
 - bin/br_biofetch.rb
@@ -47,6 +49,7 @@ files:
 - 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
@@ -87,6 +90,9 @@ files:
 - 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
@@ -133,6 +139,11 @@ files:
 - 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
@@ -143,6 +154,7 @@ files:
 - 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
@@ -169,8 +181,16 @@ files:
 - 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
@@ -215,6 +235,7 @@ files:
 - 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
@@ -296,7 +317,42 @@ files:
 - 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
@@ -318,11 +374,20 @@ files:
 - 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
@@ -340,16 +405,79 @@ files:
 - 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
@@ -373,6 +501,9 @@ files:
 - 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
@@ -394,16 +525,29 @@ files:
 - 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
@@ -420,6 +564,7 @@ files:
 - 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