bio 1.5.1 → 2.0.2

data/sample/fastq2html.testdata.yaml

@@ -0,0 +1,5 @@
+fastq:
+  - class: File
+    location: ../test/data/fastq/longreads_as_sanger.fastq
+  - class: File
+    location: ../test/data/fastq/sanger_full_range_original_sanger.fastq

data/sample/na2aa.cwl

@@ -0,0 +1,23 @@
+#!/usr/bin/env cwl-runner
+
+cwlVersion: v1.0
+class: CommandLineTool
+baseCommand: [ruby]
+
+inputs:
+ - id: script
+   type: File
+   default:
+     class: File
+     location: na2aa.rb
+   inputBinding:
+     position: -1
+ - id: seqFile
+   type: File[]
+   inputBinding:
+     position: 1
+
+outputs:
+ - id: out
+   type: stdout
+stdout: $(inputs.script.nameroot)-$(inputs.seqFile[0].nameroot).fst

data/sample/na2aa.rb

@@ -1,34 +1,20 @@
 #!/usr/bin/env ruby
 #
-# translate.rb - translate any NA input into AA FASTA format
+# na2aa.rb - translate any NA input into AA FASTA format
 #
-#   Copyright (C) 2008 KATAYAMA Toshiaki <k@bioruby.org> & Pjotr Prins
-#
-#  This program is free software; you can redistribute it and/or modify
-#  it under the terms of the GNU General Public License as published by
-#  the Free Software Foundation; either version 2 of the License, or
-#  (at your option) any later version.
-#
-#  This program is distributed in the hope that it will be useful,
-#  but WITHOUT ANY WARRANTY; without even the implied warranty of
-#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-#  GNU General Public License for more details.
-#
-#  $Id: na2aa.rb,v 1.1 2008/02/06 16:25:53 pjotr Exp $
+# Copyright::   Copyright (C) 2019 BioRuby Project
+# License::     The Ruby License
 #
 
 require 'bio'
-require 'pp'
 
-include Bio
-
-ARGV.each do | fn |
-  Bio::FlatFile.auto(fn).each do | item |
-    seq = Sequence::NA.new(item.data)
-    aa = seq.translate
-    aa.gsub!(/X/,'-')
-    rec = Bio::FastaFormat.new('> '+item.definition+"\n"+aa)
-    print rec
+ARGV.each do |fn|
+  Bio::FlatFile.open(fn) do |ff|
+    ff.each do |entry|
+      next if /\A\s*\z/ =~ ff.entry_raw.to_s
+      na = entry.naseq
+      aa = na.translate
+      print aa.to_fasta(entry.definition, 70)
+    end
   end
 end
-

data/sample/na2aa.testdata.yaml

@@ -0,0 +1,7 @@
+seqFile:
+  - class: File
+    location: ../test/data/fasta/example1.txt
+  - class: File
+    location: ../test/data/fasta/example2.txt
+  - class: File
+    location: ../test/data/genbank/SCU49845.gb

data/sample/rev_comp.cwl

@@ -0,0 +1,23 @@
+#!/usr/bin/env cwl-runner
+
+cwlVersion: v1.0
+class: CommandLineTool
+baseCommand: [ruby]
+
+inputs:
+ - id: script
+   type: File
+   default:
+     class: File
+     location: rev_comp.rb
+   inputBinding:
+     position: -1
+ - id: seqFile
+   type: File[]
+   inputBinding:
+     position: 1
+
+outputs:
+ - id: out
+   type: stdout
+stdout: $(inputs.script.nameroot)-$(inputs.seqFile[0].nameroot).fst

data/sample/rev_comp.rb

@@ -0,0 +1,20 @@
+#!/usr/bin/env ruby
+#
+# rev_comp.rb - Reverse complement DNA sequences
+#
+# Copyright::   Copyright (C) 2019 BioRuby Project
+# License::     The Ruby License
+#
+
+require 'bio'
+
+ARGV.each do |fn|
+  Bio::FlatFile.open(fn) do |ff|
+    ff.each do |entry|
+      next if /\A\s*\z/ =~ ff.entry_raw.to_s
+      na = entry.naseq
+      revcomp = na.reverse_complement
+      print revcomp.to_fasta("complement(#{entry.entry_id}) " + entry.definition, 70)
+    end
+  end
+end

data/sample/rev_comp.testdata.yaml

@@ -0,0 +1,7 @@
+seqFile:
+  - class: File
+    location: ../test/data/fasta/example2.txt
+  - class: File
+    location: ../test/data/fasta/example1.txt
+  - class: File
+    location: ../test/data/genbank/SCU49845.gb

data/sample/test_restriction_enzyme_long.rb

@@ -14,7 +14,7 @@ require 'test/unit'
 require 'benchmark'
 require 'bio'
 
-entry = Bio::TogoWS::REST.entry('genbank', 'BA000007.2')
+entry = Bio::TogoWS::REST.entry('ncbi-nucleotide', 'BA000007.2')
 EcoliO157H7Seq = Bio::GenBank.new(entry).naseq.freeze
 
 module TestRestrictionEnzymeAnalysisCutLong

data/test/network/bio/db/kegg/test_genes_hsa7422.rb

@@ -0,0 +1,91 @@
+#
+# test/network/bio/db/kegg/test_genes_hsa7422.rb - Unit test for Bio::KEGG::GENES
+#
+# Copyright::  Copyright (C) 2019 BioRuby Project <staff@bioruby.org>
+# License::    The Ruby License
+# Contributor:: kojix2 <2xijok@gmail.com>
+#
+
+# loading helper routine for testing bioruby
+require 'pathname'
+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/db/kegg/genes'
+require 'bio/io/togows'
+
+module Bio
+
+  # This test is moved from test/unit/bio/db/kegg/test_genes.rb
+  # and modified to get sample data from the internet
+  # because of KEGG data license issue.
+  #
+  # Note that this test may fail due to the data entry updates in KEGG.
+  class TestBioKEGGGENES_hsa7422 < Test::Unit::TestCase
+
+    str = Bio::TogoWS::REST.entry("kegg-genes", "hsa:7422")
+    DATA = str.freeze
+
+    def setup
+      #filename = File.join(BioRubyTestDataPath, 'KEGG/hsa7422.gene')
+      @obj = Bio::KEGG::GENES.new(DATA)
+    end
+
+    def test_diseases_as_strings
+      expected = ["H01456  Diabetic nephropathy",
+                  "H01457  Diabetic retinopathy",
+                  "H01459  Diabetic neuropathy",
+                  "H01529  Avascular necrosis of femoral head",
+                  "H01709  Glucocorticoid-induced osteonecrosis"]
+
+      assert_equal(expected, @obj.diseases_as_strings)
+    end
+
+    def test_diseases_as_hash
+      expected = {"H01456"=>"Diabetic nephropathy",
+                  "H01457"=>"Diabetic retinopathy",
+                  "H01459"=>"Diabetic neuropathy",
+                  "H01529"=>"Avascular necrosis of femoral head",
+                  "H01709"=>"Glucocorticoid-induced osteonecrosis"}
+      assert_equal(expected, @obj.diseases_as_hash)
+    end
+
+    def test_drug_targets_as_strings
+      expected = ["Abicipar pegol: D11517",
+                  "Aflibercept: D09574",
+                  "Aflibercept beta: D10819",
+                  "Bevacizumab: D06409",
+                  "Bevasiranib sodium: D08874",
+                  "Brolucizumab: D11083",
+                  "Faricimab: D11516",
+                  "Navicixizumab: D11126",
+                  "Pegaptanib: D05386",
+                  "Ranibizumab: D05697",
+                  "Vanucizumab: D11244"]
+      assert_equal(expected, @obj.drug_targets_as_strings)
+    end
+
+    def test_networks_as_strings
+      expected = ["nt06114  PI3K signaling (virus)",
+                  "nt06124  Chemokine signaling (virus)",
+                  "nt06164  Kaposi sarcoma-associated herpesvirus (KSHV)",
+                  "nt06214  PI3K signaling",
+                  "nt06219  JAK-STAT signaling",
+                  "nt06224  CXCR signaling",
+                  "nt06225  HIF-1 signaling",
+                  "nt06262  Pancreatic cancer",
+                  "nt06264  Renal cell carcinoma",
+                  "N00079  HIF-1 signaling pathway",
+                  "N00080  Loss of VHL to HIF-1 signaling pathway",
+                  "N00081  Mutation-inactivated VHL to HIF-1 signaling pathway",
+                  "N00095  ERBB2-overexpression to EGF-Jak-STAT signaling pathway",
+                  "N00157  KSHV vGPCR to GNB/G-ERK signaling pathway",
+                  "N00179  KSHV K1 to PI3K-NFKB signaling pathway"]
+      assert_equal(expected, @obj.networks_as_strings)
+    end
+
+  end #class TestBioKEGGGENES_hsa7422
+
+end #module Bio

data/test/unit/bio/appl/blast/test_report.rb

@@ -479,7 +479,7 @@ module Bio
     include TemplateTestBlastReportHsp
   end
 
-  if defined? XMLParser then
+  if Bio::Blast::Report.private_method_defined? :xmlparser_parse then
 
   class TestBlastReportXMLParser < Test::Unit::TestCase
     include TemplateTestBlastReport
@@ -497,7 +497,7 @@ module Bio
     include TemplateTestBlastReportHsp
   end
 
-  end #if defined? XMLParser
+  end #if
 
   class TestBlastReportDefault < Test::Unit::TestCase
     include TemplateTestBlastReport
@@ -1294,7 +1294,7 @@ module Bio
   end
 
   # Tests for XMLParser version
-  if defined? XMLParser then
+  if Bio::Blast::Report.private_method_defined? :xmlparser_parse then
 
   class TestBlastReportMultiXMLParser < Test::Unit::TestCase
     include TemplateTestBlastReportMulti
@@ -1312,6 +1312,6 @@ module Bio
     include TemplateTestBlastReportHspMulti
   end
 
-  end #if defined? XMLParser
+  end #if
 
 end # module Bio

data/test/unit/bio/data/test_codontable.rb

@@ -71,6 +71,9 @@ module Bio
 
     def test_accessor #[]
       assert_equal('M', @ct['atg'])
+      assert_equal('*', @ct['tag'])
+      assert_equal('*', @ct['tra'])
+      assert_equal('*', @ct['tar'])
     end
 
     def test_set_accessor #[]=

data/test/unit/bio/db/test_gff.rb

@@ -182,6 +182,11 @@ END_OF_DATA
       assert_equal(str, @obj.to_s)
     end
 
+    def test_self_parse
+      obj2 = Bio::GFF::GFF2::Record.parse(@obj.to_s)
+      assert_equal(@obj, obj2)
+    end
+
     def test_eqeq
       obj2 = Bio::GFF::GFF2::Record.new(@obj.to_s)
       assert_equal(true, @obj == obj2)

data/test/unit/bio/test_alignment.rb

@@ -628,9 +628,9 @@ module Bio
 
     def test_seqclass_when_seqclass_set
       alignment = Alignment.new
-      alignment.seqclass = Fixnum
+      alignment.seqclass = Integer
       alignment << "this doesn't really make sense"
-      assert_equal(Fixnum, alignment.seqclass)
+      assert_equal(Integer, alignment.seqclass)
     end
 
     # Alignment#gap_char

metadata

@@ -1,23 +1,18 @@
 --- !ruby/object:Gem::Specification
 name: bio
 version: !ruby/object:Gem::Version
-  version: 1.5.1
+  version: 2.0.2
 platform: ruby
 authors:
 - BioRuby project
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2016-09-07 00:00:00.000000000 Z
+date: 2020-12-31 00:00:00.000000000 Z
 dependencies: []
 description: BioRuby is a library for bioinformatics (biology + information science).
 email: staff@bioruby.org
-executables:
-- bioruby
-- br_biofetch.rb
-- br_bioflat.rb
-- br_biogetseq.rb
-- br_pmfetch.rb
+executables: []
 extensions: []
 extra_rdoc_files:
 - KNOWN_ISSUES.rdoc
@@ -29,6 +24,7 @@ extra_rdoc_files:
 - doc/RELEASE_NOTES-1.4.1.rdoc
 - doc/RELEASE_NOTES-1.4.2.rdoc
 - doc/RELEASE_NOTES-1.4.3.rdoc
+- doc/RELEASE_NOTES-1.5.0.rdoc
 files:
 - ".travis.yml"
 - BSDL
@@ -36,6 +32,7 @@ files:
 - COPYING.ja
 - ChangeLog
 - GPL
+- Gemfile
 - KNOWN_ISSUES.rdoc
 - LEGAL
 - LGPL
@@ -43,14 +40,11 @@ files:
 - README_DEV.rdoc
 - RELEASE_NOTES.rdoc
 - Rakefile
-- bin/bioruby
-- bin/br_biofetch.rb
-- bin/br_bioflat.rb
-- bin/br_biogetseq.rb
-- bin/br_pmfetch.rb
+- appveyor.yml
 - bioruby.gemspec
 - bioruby.gemspec.erb
 - doc/ChangeLog-1.4.3
+- doc/ChangeLog-1.5.0
 - doc/ChangeLog-before-1.3.1
 - doc/ChangeLog-before-1.4.2
 - doc/Changes-0.7.rd
@@ -59,6 +53,7 @@ files:
 - doc/RELEASE_NOTES-1.4.1.rdoc
 - doc/RELEASE_NOTES-1.4.2.rdoc
 - doc/RELEASE_NOTES-1.4.3.rdoc
+- doc/RELEASE_NOTES-1.5.0.rdoc
 - doc/Tutorial.rd
 - doc/Tutorial.rd.html
 - doc/Tutorial.rd.ja
@@ -70,7 +65,7 @@ files:
 - gemfiles/Gemfile.travis-rbx
 - gemfiles/Gemfile.travis-ruby1.8
 - gemfiles/Gemfile.travis-ruby1.9
-- gemfiles/Gemfile.travis-ruby2.2
+- gemfiles/Gemfile.windows
 - gemfiles/modify-Gemfile.rb
 - gemfiles/prepare-gemspec.rb
 - lib/bio.rb
@@ -86,7 +81,6 @@ files:
 - lib/bio/appl/blast/rexml.rb
 - lib/bio/appl/blast/rpsblast.rb
 - lib/bio/appl/blast/wublast.rb
-- lib/bio/appl/blast/xmlparser.rb
 - lib/bio/appl/blat/report.rb
 - lib/bio/appl/clustalw.rb
 - lib/bio/appl/clustalw/report.rb
@@ -135,8 +129,6 @@ files:
 - lib/bio/data/na.rb
 - lib/bio/db.rb
 - lib/bio/db/aaindex.rb
-- lib/bio/db/biosql/biosql_to_biosequence.rb
-- lib/bio/db/biosql/sequence.rb
 - lib/bio/db/embl/common.rb
 - lib/bio/db/embl/embl.rb
 - lib/bio/db/embl/embl_to_biosequence.rb
@@ -195,10 +187,6 @@ 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
@@ -208,9 +196,6 @@ files:
 - lib/bio/db/soft.rb
 - lib/bio/db/transfac.rb
 - lib/bio/feature.rb
-- lib/bio/io/biosql/ar-biosql.rb
-- lib/bio/io/biosql/biosql.rb
-- lib/bio/io/biosql/config/database.yml
 - lib/bio/io/das.rb
 - lib/bio/io/fastacmd.rb
 - lib/bio/io/fetch.rb
@@ -225,7 +210,6 @@ files:
 - lib/bio/io/ncbirest.rb
 - lib/bio/io/pubmed.rb
 - lib/bio/io/registry.rb
-- lib/bio/io/sql.rb
 - lib/bio/io/togows.rb
 - lib/bio/location.rb
 - lib/bio/map.rb
@@ -243,44 +227,6 @@ files:
 - 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
-- lib/bio/shell/interface.rb
-- lib/bio/shell/irb.rb
-- lib/bio/shell/object.rb
-- lib/bio/shell/plugin/blast.rb
-- lib/bio/shell/plugin/codon.rb
-- lib/bio/shell/plugin/das.rb
-- lib/bio/shell/plugin/emboss.rb
-- lib/bio/shell/plugin/entry.rb
-- lib/bio/shell/plugin/flatfile.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
-- lib/bio/shell/plugin/togows.rb
-- lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/bioruby_generator.rb
-- lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_classes.rhtml
-- lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_log.rhtml
-- lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_methods.rhtml
-- lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_modules.rhtml
-- lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_variables.rhtml
-- lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-bg.gif
-- lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-gem.png
-- lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-link.gif
-- lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.css
-- lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.rhtml
-- lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_controller.rb
-- lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_helper.rb
-- lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/commands.rhtml
-- lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/history.rhtml
-- lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/index.rhtml
-- lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/spinner.gif
-- lib/bio/shell/script.rb
-- lib/bio/shell/setup.rb
-- lib/bio/shell/web.rb
 - lib/bio/tree.rb
 - lib/bio/tree/output.rb
 - lib/bio/util/color_scheme.rb
@@ -323,6 +269,7 @@ files:
 - sample/any2fasta.rb
 - sample/benchmark_clustalw_report.rb
 - sample/biofetch.rb
+- sample/color_scheme_aa.rb
 - sample/color_scheme_na.rb
 - sample/demo_aaindex.rb
 - sample/demo_aminoacid.rb
@@ -361,6 +308,9 @@ files:
 - sample/fasta2tab.rb
 - sample/fastagrep.rb
 - sample/fastasort.rb
+- sample/fastq2html.cwl
+- sample/fastq2html.rb
+- sample/fastq2html.testdata.yaml
 - sample/fsplit.rb
 - sample/gb2fasta.rb
 - sample/gb2tab.rb
@@ -372,17 +322,20 @@ files:
 - sample/genome2tab.rb
 - sample/goslim.rb
 - sample/gt2fasta.rb
+- sample/na2aa.cwl
 - sample/na2aa.rb
+- sample/na2aa.testdata.yaml
 - sample/pmfetch.rb
 - sample/pmsearch.rb
+- sample/rev_comp.cwl
+- sample/rev_comp.rb
+- sample/rev_comp.testdata.yaml
 - sample/seqdatabase.ini
 - sample/ssearch2tab.rb
 - sample/tdiary.rb
-- sample/test_phyloxml_big.rb
 - sample/test_restriction_enzyme_long.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
@@ -500,11 +453,6 @@ files:
 - test/data/paml/codeml/models/results7-8.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/pir/CRAB_ANAPL.pir
 - test/data/prosite/prosite.dat
 - test/data/refseq/nm_126355.entret
@@ -523,6 +471,7 @@ files:
 - test/network/bio/appl/blast/test_remote.rb
 - test/network/bio/appl/test_blast.rb
 - test/network/bio/appl/test_pts1.rb
+- test/network/bio/db/kegg/test_genes_hsa7422.rb
 - test/network/bio/io/test_pubmed.rb
 - test/network/bio/io/test_togows.rb
 - test/network/bio/test_command.rb
@@ -554,8 +503,6 @@ files:
 - test/unit/bio/data/test_aa.rb
 - test/unit/bio/data/test_codontable.rb
 - test/unit/bio/data/test_na.rb
-- test/unit/bio/db/biosql/tc_biosql.rb
-- test/unit/bio/db/biosql/ts_suite_biosql.rb
 - test/unit/bio/db/embl/test_common.rb
 - test/unit/bio/db/embl/test_embl.rb
 - test/unit/bio/db/embl/test_embl_rel89.rb
@@ -594,8 +541,6 @@ files:
 - test/unit/bio/db/test_nbrf.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
@@ -613,7 +558,6 @@ files:
 - 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
 - test/unit/bio/test_db.rb
@@ -623,7 +567,6 @@ files:
 - test/unit/bio/test_pathway.rb
 - test/unit/bio/test_reference.rb
 - test/unit/bio/test_sequence.rb
-- test/unit/bio/test_shell.rb
 - test/unit/bio/test_tree.rb
 - test/unit/bio/util/restriction_enzyme/analysis/test_calculated_cuts.rb
 - test/unit/bio/util/restriction_enzyme/analysis/test_cut_ranges.rb
@@ -674,7 +617,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.2.2
+rubygems_version: 2.7.6.2
 signing_key: 
 specification_version: 4
 summary: Bioinformatics library