bio 1.6.0.pre.20181210 → 2.0.3

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/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/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)