bio 2.0.0 → 2.0.1

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 4962e411aae8be8955dbf62675371e1828caad0e9c465e5935c4198bffd96639
-  data.tar.gz: 9aa98b72bdb24f80bf2b209f3ddd2abc47aced3b54764c44b27a0dc65eef00ce
+  metadata.gz: ee0226eebc0265a4cab075c2aaba3de55d82eff2767d1e00f6889d385c0037bd
+  data.tar.gz: ea4940449ac518b918ad0ddefa512b1ba51cb5ff22d9cbfff2ad1c2eca7433ab
 SHA512:
-  metadata.gz: 6b93a323e2c9c605987b98602a174b80023de62e2b27d5449866fc9101cfc574e5538f8e13c54cc9cf6f8fdcab10c6714373e1d02d0475f0378525c907c8e558
-  data.tar.gz: d07903f10960791dc7b73d4b4eca54e83d0b45911604547a7e39e35b4238b1710daf4ffc79cd4f69f76fba35a6fc40c7c73b3fc0bca2e3b44b574e40bc16f30a
+  metadata.gz: be1ed472712c090d5de731e801b644356d3d155a7dd3db1c75cb91c2a9580ecdf50b4f58dd972810900dd9cbb1c907c000fdb968e2b18585901396fef3d01dcb
+  data.tar.gz: 53fd895fb65c582f1e2ed9abd21e3c8598056db4f408bbf84b527561cafe17976ece11a9b6a29d3fc89d3eb790a0de1611aa4d08a3d4856ff7344efdd718cde6

data/ChangeLog

@@ -1,3 +1,188 @@
+commit 21bf51a1ec8c18c9cdf8528ffc3c59c503cef042
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Fri Sep 6 15:45:47 2019 +0900
+
+    RELEASE_NOTES.rdoc: describe notable changes since 2.0.0
+
+ RELEASE_NOTES.rdoc | 40 ++++++++++++++++++++++++++++++++++++++++
+ 1 file changed, 40 insertions(+)
+
+commit 9092a629e0e28b416ee7288d349fb9d73dd2b961
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Fri Sep 6 15:06:11 2019 +0900
+
+    regenerate bioruby.gemspec with rake regemspec
+
+ bioruby.gemspec | 11 ++++++++++-
+ 1 file changed, 10 insertions(+), 1 deletion(-)
+
+commit 59e24b6e55d2c9a8887e8e01a91999d33a008042
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Fri Sep 6 15:04:33 2019 +0900
+
+    prepare for BioRuby 2.0.1 release
+
+ lib/bio/version.rb | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+commit 9635a38a158db434fd2b6aff7a2ee75622ddecef
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Fri Sep 6 14:51:23 2019 +0900
+
+    sample/fastq2html.rb: A html visualization of FASTQ sequences
+    
+     * sample/fastq2html: A html visualization of FASTQ sequences.
+       Each sequence is colored with the quality score.
+     * sample/fastq2html.cwl: CWL workflow for the above sample script
+     * sample/fastq2html.testdata.yaml: Test data for the above workflow
+
+ sample/fastq2html.cwl           | 23 ++++++++++
+ sample/fastq2html.rb            | 94 +++++++++++++++++++++++++++++++++++++++++
+ sample/fastq2html.testdata.yaml |  5 +++
+ 3 files changed, 122 insertions(+)
+ create mode 100644 sample/fastq2html.cwl
+ create mode 100644 sample/fastq2html.rb
+ create mode 100644 sample/fastq2html.testdata.yaml
+
+commit 6bbcf8b66310c225d686f2c59359680a0bc0b4b6
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Fri Sep 6 14:42:19 2019 +0900
+
+    sample/rev_comp.rb: Generates reverse-complement sequences
+    
+     * sample/rev_comp.rb: Generates reverse-complement sequences of
+       the given nucleotide sequences.
+     * sample/rev_comp.cwl: CWL cowkflow for the sample script
+     * sample/rev_comp.testdata.yaml: Test data for the above CWL workflow
+
+ sample/rev_comp.cwl           | 23 +++++++++++++++++++++++
+ sample/rev_comp.rb            | 20 ++++++++++++++++++++
+ sample/rev_comp.testdata.yaml |  7 +++++++
+ 3 files changed, 50 insertions(+)
+ create mode 100644 sample/rev_comp.cwl
+ create mode 100644 sample/rev_comp.rb
+ create mode 100644 sample/rev_comp.testdata.yaml
+
+commit ff0e6c3c6b6f1b56d81b5a4b579a6d0984bfc607
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Fri Sep 6 14:40:45 2019 +0900
+
+    sample/color_scheme_(na|aa).rb: use String#each_char instead of each_byte
+
+ sample/color_scheme_aa.rb | 6 +++---
+ sample/color_scheme_na.rb | 6 +++---
+ 2 files changed, 6 insertions(+), 6 deletions(-)
+
+commit 6f7c1be09aa3d6cdb76fd029fc0f84efda31c907
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Thu Sep 5 17:32:07 2019 +0900
+
+    sample/color_scheme_aa.rb: new sample based on color_scheme_na.rb
+
+ sample/color_scheme_aa.rb | 82 +++++++++++++++++++++++++++++++++++++++++++++++
+ 1 file changed, 82 insertions(+)
+ create mode 100644 sample/color_scheme_aa.rb
+
+commit 51864c3857178f58133b759f7608b8d6d8991c44
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Thu Sep 5 17:13:20 2019 +0900
+
+    sample/color_scheme_na.rb: use const_get instead of eval
+
+ sample/color_scheme_na.rb | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+commit ba0b554971a9a387a54fc04c5002853d91357347
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Thu Sep 5 17:02:20 2019 +0900
+
+    sample/na2aa.cwl: inputBinding position -1 for the script
+    
+     * sample/na2aa.cwl: inputBinding position -1 is used for the script
+       to emphasize that the argument is the first one.
+
+ sample/na2aa.cwl | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+commit 26a27ec261e2251f3ff3a85007147d33682778d0
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Thu Sep 5 16:56:08 2019 +0900
+
+    sample/color_scheme_na.rb: Supports more file formats
+    
+     * sample/color_scheme_na.rb: Supports more file formats other than
+       fasta format, by using Bio::Flatfile.
+
+ sample/color_scheme_na.rb | 3 +--
+ 1 file changed, 1 insertion(+), 2 deletions(-)
+
+commit 5c053a606382bb578a2b6884ee639805154433e5
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Thu Sep 5 12:32:00 2019 +0900
+
+    sample/na2aa.cwl: use inputBinding
+
+ sample/na2aa.cwl | 5 ++++-
+ 1 file changed, 4 insertions(+), 1 deletion(-)
+
+commit 6a3c3e02f08549d47dda00dca92d55bbadfc468f
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Wed Sep 4 22:59:21 2019 +0900
+
+    Sample CWL workflow to run sample/na2aa.rb
+    
+     * na2aa.cwl: A sample CWL workflow to run na2aa.rb in sample/ dir
+     * na2aa.testdata.yaml: Test data for the workflow
+
+ sample/na2aa.cwl           | 20 ++++++++++++++++++++
+ sample/na2aa.testdata.yaml |  7 +++++++
+ 2 files changed, 27 insertions(+)
+ create mode 100644 sample/na2aa.cwl
+ create mode 100644 sample/na2aa.testdata.yaml
+
+commit 960b885036f549863e3cfe9c693c90f9bef27d3d
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Wed Sep 4 21:00:50 2019 +0900
+
+    LEGAL: na2aa.rb is now Ruby's License
+
+ LEGAL | 1 -
+ 1 file changed, 1 deletion(-)
+
+commit 7af9e81988939007eb36dab6b102a7422e8196d8
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Wed Sep 4 14:34:05 2019 +0900
+
+    sample/na2aa.rb: Completely rewritten
+    
+     * sample/na2aa.rb: Completely rewritten. License is changed because
+       old code is completely wiped out. Note that the old code always
+       raises error due to a bug in the code.
+     * The old code was trying to replace 'X' (any) to '-' (gap) but
+       the new code does not modify translated sequences anymore.
+
+ sample/na2aa.rb | 36 +++++++++++-------------------------
+ 1 file changed, 11 insertions(+), 25 deletions(-)
+
+commit cf8cac5e32db42b6683c1a837adc9e1c04994062
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Mon Sep 2 17:11:08 2019 +0900
+
+    Bug fix: Bio::GFF::GFF2::Record.parse did not return correct object
+
+ lib/bio/db/gff.rb            | 4 +++-
+ test/unit/bio/db/test_gff.rb | 5 +++++
+ 2 files changed, 8 insertions(+), 1 deletion(-)
+
+commit 80b387e7e2bb8570d9204e389b6c5d90c6ea31de
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Fri Jun 14 14:33:19 2019 +0900
+
+    BioRuby 2.0.0 is released
+
+ ChangeLog | 1051 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-
+ 1 file changed, 1043 insertions(+), 8 deletions(-)
+
 commit 2e4046517fd8ee1c105ef53131e69f787d790099
 Author: Naohisa Goto <ng@bioruby.org>
 Date:   Fri Jun 14 14:23:19 2019 +0900

data/LEGAL

@@ -59,7 +59,6 @@ sample/vs-genes.rb:
 
 sample/fastagrep.rb:
 sample/fastasort.rb:
-sample/na2aa.rb:
 
    Copyright (C) 2008 KATAYAMA Toshiaki <k@bioruby.org> & Pjotr Prins
 

data/RELEASE_NOTES.rdoc

@@ -1,3 +1,43 @@
+= BioRuby 2.0.1 RELEASE NOTES
+
+Some bug fixes and improvements have been made to the BioRuby 2.0.1 after
+the version 2.0.0 is released.
+
+== Bug fixes
+
+* Bio::GFF::GFF2::Record.parse did not return correct object.
+
+== Improvement of sample scripts
+
+The following scripts in the sample/ directiry are newly added.
+
+* color_scheme_aa.rb: Example of Bio::ColorScheme for an amino acid sequence.
+* fastq2html.rb: Visualization of FASTQ sequences, colored by quality scores.
+* rev_comp.rb: Shows reverse-complement sequences of the given sequences.
+
+The floowing scripts are modified to fix bug and/or to improve features.
+
+* na2aa.rb: Completely rewritten to fix bug. Shows translated sequences.
+* color_scheme_na.rb: Added support for various sequence formats.
+
+=== CWL (Common Workflow Language) workflow files are added
+
+CWL (Common Workflow Language) workflow files are added for some sample
+scripts. The usage of each sample script will be clarified with the CWL
+workflow files.
+
+Two type of files are prepared for CWL workflow engine. *.cwl is a workflow
+definition file for each sample script. *.testdata.yaml describes sample
+input data for each CWL workflow.
+
+In this version, cwl files for the 3 sample scripts are added.
+
+* fastq2html.rb: fastq2html.cwl with fastq2html.testdata.yaml
+* na2aa.rb: na2aa.cwl with na2aa.testdata.yaml
+* rev_comp.rb: rev_comp.cwl with rev_comp.testdata.yaml
+
+
+
 = BioRuby 2.0.0 RELEASE NOTES
 
 A lot of changes have been made to the BioRuby 2.0.0 after the version 1.5.x

data/bioruby.gemspec

@@ -3,7 +3,7 @@
 # 
 Gem::Specification.new do |s|
   s.name = 'bio'
-  s.version = "2.0.0"
+  s.version = "2.0.1"
 
   s.author = "BioRuby project"
   s.email = "staff@bioruby.org"
@@ -258,6 +258,7 @@ Gem::Specification.new do |s|
     "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",
@@ -296,6 +297,9 @@ Gem::Specification.new do |s|
     "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",
@@ -307,9 +311,14 @@ Gem::Specification.new do |s|
     "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",

data/lib/bio/db/gff.rb

@@ -359,7 +359,9 @@ module Bio
         # Parses a GFF2-formatted line and returns a new
         # Bio::GFF::GFF2::Record object.
         def self.parse(str)
-          self.new.parse(str)
+          ret = self.new
+          ret.parse(str)
+          ret
         end
        
         # Creates a Bio::GFF::GFF2::Record object.

data/lib/bio/version.rb

@@ -10,7 +10,7 @@
 module Bio
 
   # BioRuby version (Array containing Integer)
-  BIORUBY_VERSION = [2, 0, 0].extend(Comparable).freeze
+  BIORUBY_VERSION = [2, 0, 1].extend(Comparable).freeze
 
   # Extra version specifier (String or nil).
   # Existance of the value indicates development version.

data/sample/color_scheme_aa.rb

@@ -0,0 +1,82 @@
+#!/usr/bin/env ruby
+#
+# color_scheme_aa.rb - A Bio::ColorScheme demo script for Amino Acid sequences.
+#
+#  Usage:
+#
+#   % ruby color_scheme_aa.rb > cs-seq-faa.html
+#
+#   % cat seq.faa
+#   >AA_sequence
+#   MKRISTTITTTITITTGNGAG
+#   % ruby color_scheme_aa.rb seq.faa > colored-seq-faa.html
+#
+#
+# Copyright::  Copyright (C) 2005
+#              Mitsuteru C. Nakao <n@bioruby.org>
+# License::    The Ruby License
+#
+
+require 'bio'
+
+
+# returns folded sequence with <br>.
+def br(i, width = 80)
+  return "<br\n>"  if i % width == 0
+  ""
+end
+
+
+# returns sequence html doc
+def display(seq, cs)
+  html = '<p style="font-family: monospace">'
+  postfix = '</span>'
+  i = 0
+  seq.each_char do |c|
+    color = cs[c]
+    prefix = %Q(<span style="background:\##{color};">)
+    html += prefix + c + postfix
+    html += br(i += 1)
+  end
+  html + '</p>'
+end
+
+
+# returns scheme wise html doc
+def display_scheme(scheme, aaseq)
+  html = ''
+  cs = Bio::ColorScheme.const_get(scheme.intern)
+  [aaseq].each do |seq|
+    html += display(seq, cs)
+  end
+  return  ['<div>', "<h3>#{cs}</h3>", html, '</div>']
+end
+
+
+
+if fna = ARGV.shift
+  aaseq = Bio::FlatFile.open(fna) { |ff| ff.next_entry.aaseq }
+else
+  aaseq = Bio::Sequence::AA.new('ARNDCQEGHILKMFPSTWYV' * 20).randomize
+end
+
+title =  'Bio::ColorScheme for amino acid sequences'
+doc = ['<html>',
+       '<header>', '<title>', title, '</title>', '</header>',
+       '<body>',  '<h1>', title, '</h1>']
+
+doc << ['<div>', '<h2>', 'Simple colors', '</h2>']
+
+['Zappo', 'Taylor' ].each do |scheme|
+  doc << display_scheme(scheme, aaseq)
+end
+doc << ['</div>']
+
+
+doc << ['<div>', '<h2>', 'Score colors', '</h2>']
+['Buried', 'Helix', 'Hydropathy', 'Strand', 'Turn'].each do |score|
+  doc << display_scheme(score, aaseq)
+end
+doc << ['</div>']
+
+puts doc + ['</body>','</html>']

data/sample/color_scheme_na.rb

@@ -17,7 +17,6 @@
 #              Mitsuteru C. Nakao <n@bioruby.org>
 # License::    The Ruby License
 #
-#  $Id: color_scheme_na.rb,v 1.3 2007/04/05 23:35:42 trevor Exp $
 #
 
 require 'bio'
@@ -35,10 +34,10 @@ def display(seq, cs)
   html = '<p style="font-family: monospace">'
   postfix = '</span>'
   i = 0
-  seq.each_byte do |c|
-    color = cs[c.chr]
+  seq.each_char do |c|
+    color = cs[c]
     prefix = %Q(<span style="background:\##{color};">)
-    html += prefix + c.chr + postfix
+    html += prefix + c + postfix
     html += br(i += 1)
   end
   html + '</p>'
@@ -48,7 +47,7 @@ end
 # returns scheme wise html doc
 def display_scheme(scheme, naseq, aaseq)
   html = ''
-  cs = eval("Bio::ColorScheme::#{scheme}")
+  cs = Bio::ColorScheme.const_get(scheme.intern)
   [naseq, aaseq].each do |seq|
     html += display(seq, cs)
   end
@@ -58,7 +57,7 @@ end
 
 
 if fna = ARGV.shift
-  naseq = Bio::FastaFormat.new(File.open(fna, 'r').read).naseq
+  naseq = Bio::FlatFile.open(fna) { |ff| ff.next_entry.naseq }
   aaseq = naseq.translate
 else
   naseq = Bio::Sequence::NA.new('acgtu' * 20).randomize

data/sample/fastq2html.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: fastq2html.rb
+   inputBinding:
+     position: -1
+ - id: fastq
+   type: File[]
+   inputBinding:
+     position: 1
+
+outputs:
+ - id: out
+   type: stdout
+stdout: $(inputs.script.nameroot)-$(inputs.fastq[0].nameroot).html

data/sample/fastq2html.rb

@@ -0,0 +1,94 @@
+#!/usr/bin/env ruby
+#
+# fastq2html.rb - HTML visualization of FASTQ sequences
+#
+#  Usage:
+#
+#   % ruby fastq2html.rb seq00.fastq > seq00.html
+#
+#
+# Copyright::  Copyright (C) 2019 BioRuby Project
+#              Copyright (C) 2005 Mitsuteru C. Nakao <n@bioruby.org>
+# License::    The Ruby License
+#
+#
+
+require 'bio'
+
+# thickness to color
+def thickness2color(t)
+  c = "%02X" % ((t * 255.0).to_i)
+  c * 3
+end
+
+# Creates 
+def create_score2color_hashes
+  h_bg = {}
+  h_char = {}
+  cutoff_low = 0
+  cutoff_high = 50
+  range = cutoff_high - cutoff_low
+  sc_min = -5
+  sc_max = 100
+  (sc_min..sc_max).each do |i|
+    t = if i <= cutoff_low then
+          0.0
+        elsif i >= cutoff_high then
+          1.0
+        else
+          (i - cutoff_low).to_f / range
+        end
+    h_bg[i] = thickness2color(t)
+    h_char[i] = thickness2color((t > 0.3) ? 0.0 : 0.55)
+  end
+  h_bg.default = h_bg[cutoff_low]
+  h_char.default = h_char[cutoff_low]
+  [h_bg, h_char]
+end
+
+# Color code from quality score
+SCORE2COLOR_BG, SCORE2COLOR_CHAR = create_score2color_hashes
+
+# returns folded sequence with <br>.
+def br(i, width = 80)
+  return "<br\n>"  if i % width == 0
+  ""
+end
+
+# returns sequence html doc
+def display(naseq, scores)
+  html = '<p style="font-family: monospace">'
+  postfix = '</span>'
+  i = 0
+  naseq.each_char.with_index do |c, i|
+    sc = scores[i]
+    bgcol = SCORE2COLOR_BG[sc]
+    col = SCORE2COLOR_CHAR[sc]
+    prefix = %Q(<span style="color:\##{col}; background:\##{bgcol};">)
+    html += prefix + c + postfix
+    html += br(i += 1)
+  end
+  html + '</p>'
+end
+
+# returns colorized html doc
+def fastq2html(definition, naseq, scores)
+  html = display(naseq, scores)
+  return  ['<div>', "<div>&gt;#{CGI.escapeHTML(definition)}</div>", html, '</div>']
+end
+
+title =  'Sequences with quality scores'
+puts ['<html>',
+       '<header>', '<title>', title, '</title>', '</header>',
+       '<body>',  '<h1>', title, '</h1>']
+
+#main loop
+ARGV.each do |filename|
+  Bio::FlatFile.open(filename) do |ff|
+    ff.each do |e|
+      puts fastq2html(e.definition, e.naseq, e.quality_scores)
+    end
+  end
+end
+
+puts ['</body>','</html>']

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/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)

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bio
 version: !ruby/object:Gem::Version
-  version: 2.0.0
+  version: 2.0.1
 platform: ruby
 authors:
 - BioRuby project
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2019-06-14 00:00:00.000000000 Z
+date: 2019-09-06 00:00:00.000000000 Z
 dependencies: []
 description: BioRuby is a library for bioinformatics (biology + information science).
 email: staff@bioruby.org
@@ -269,6 +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
@@ -307,6 +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
@@ -318,9 +322,14 @@ 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