viral_seq 1.6.1 → 1.7.0

checksums.yaml

@@ -1,7 +1,7 @@
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data/Gemfile.lock

@@ -1,10 +1,10 @@
 PATH
   remote: .
   specs:
-    viral_seq (1.6.0)
+    viral_seq (1.6.5)
       colorize (~> 0.1)
       combine_pdf (~> 1.0, >= 1.0.0)
-      muscle_bio (~> 0.4)
+      muscle_bio (~> 0.5)
       prawn (~> 2.3, >= 2.3.0)
       prawn-table (~> 0.2, >= 0.2.0)
 
@@ -15,7 +15,7 @@ GEM
     combine_pdf (1.0.21)
       ruby-rc4 (>= 0.1.5)
     diff-lcs (1.3)
-    muscle_bio (0.4.0)
+    muscle_bio (0.5.0)
     pdf-core (0.9.0)
     prawn (2.4.0)
       pdf-core (~> 0.9.0)

data/README.md

@@ -10,6 +10,8 @@ A Ruby Gem containing bioinformatics tools for processing viral NGS data.
 
 Specifically for Primer ID sequencing and HIV drug resistance analysis.
 
+CLI tools `tcs`, `tcs_sdrm`, `tcs_log` and `locator` included in the gem. 
+
 #### tcs web app - https://primer-id.org/
 
 ## Illustration for the Primer ID Sequencing
@@ -22,6 +24,12 @@ Specifically for Primer ID sequencing and HIV drug resistance analysis.
 [Primer ID MiSeq protocol](https://doi.org/10.1128/JVI.00522-15)  
 [Application of Primer ID sequencing in COVID-19 research](https://doi.org/10.1126/scitranslmed.abb5883)
 
+## Requirements
+
+Required Ruby Version: >= 2.5
+
+Required RubyGems version: >= 1.3.6
+
 ## Install
 
 ```bash
@@ -179,10 +187,27 @@ qc_seqhash.sdrm_hiv_pr(cut_off)
 
 ## Updates
 
+### Version-1.7.0-08242022
+
+  1. Add warnings if `tcs` pipeline is excecuting through source instead of installing from `gem`. 
+  2. Optimized `ViralSeq:SeqHash#a3g` hypermut algorithm. Allowing a external reference other than the sample reference. 
+
+### Version-1.6.4-07182022
+
+  1. Included region "P17" in the default `tcs -d` pipeline setting. `tcs` pipeline updated to version 2.5.1. 
+  2. Loosen the locator params for the "V1V3" end region for rare alignment issues. Now the default "V1V3" region end with position 7205 to 7210 instead of 7208.
+  3. `tcs_sdrm` now analyse "P17" region for pairwise diversity.
+
+### Version-1.6.3-02052022
+
+  1. Updated on `ViralSeq::Muscle` module along with the update of `muscle` from version 3.8.1 to 5.1.
+  2. Optimized the `locator` algorithm based on `muscle` v5.1.
+  3. Optimized the `tcs_sdrm` pipeline based on `muscle` v5.1.
+
 ### Version-1.6.1-02022022
 
   1. Fixed the `nav bar` in tcs_log html file.
-  2. Fixed a typo in `tcs`. 
+  2. Fixed a typo in `tcs`.
 
 ### Version 1.6.0-01042022
 

data/bin/tcs

@@ -22,20 +22,38 @@
 # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
 # THE SOFTWARE.
 
+# Install using `gem install viral_seq`
 # Use JSON file as the run param
 # run `tcs -j` to generate param json file.
 
-require 'viral_seq'
+def gem_installed?(gem_name)
+  found_gem = false
+  begin
+    found_gem = Gem::Specification.find_by_name(gem_name)
+  rescue Gem::LoadError
+    return false   
+  else
+    return true 
+  end
+end
+
+if gem_installed?('viral_seq')
+  require 'viral_seq'
+else 
+  printf "\n****************************************************\n"
+  printf "**** THIS PACKAGE CANNOT BE RAN FROM SOURCE ********\n"
+  printf "**** PLEASE INSTALL USING `gem install viral_seq` **\n"
+  printf "****************************************************\n\n"
+  exit 1
+end
+
+
 require 'json'
 require 'colorize'
 require 'optparse'
 
 options = {}
 
-# banner = '-'*50 + "\n" +
-#         '| The TCS Pipeline ' + "Version #{ViralSeq::TCS_VERSION}".red.bold + " by " + "Shuntai Zhou".blue.bold + ' |' + "\n" +
-#         '-'*50 + "\n"
-
 banner = "\n" +
 "████████  ██████ ███████     ██████  ██ ██████  ███████ ██      ██ ███    ██ ███████\n".light_red +
 "   ██    ██      ██          ██   ██ ██ ██   ██ ██      ██      ██ ████   ██ ██\n".light_yellow +

data/bin/tcs_sdrm

@@ -172,6 +172,25 @@ libs.each do |lib|
       linkage_list += sdrm[1]
       aa_report_list += sdrm[2]
 
+    elsif seq_basename =~/P17/i
+      a3g_check = seqs.a3g
+      a3g_seqs = a3g_check[:a3g_seq]
+      a3g_filtered_seqs = a3g_check[:filtered_seq]
+      stop_codon_check = a3g_filtered_seqs.stop_codon(2)
+      stop_codon_seqs = stop_codon_check[:with_stop_codon]
+      filtered_seqs = stop_codon_check[:without_stop_codon]
+      poisson_minority_cutoff = filtered_seqs.pm
+      fdr_hash = filtered_seqs.fdr
+      summary_hash[:P17] = [
+                            seqs.size.to_s,
+                            a3g_seqs.size.to_s,
+                            stop_codon_seqs.size.to_s,
+                            filtered_seqs.size.to_s,
+                            poisson_minority_cutoff.to_s
+                          ].join(',')
+      next if filtered_seqs.size < 3
+      filtered_seqs.write_nt_fa(File.join(filtered_seq_dir,seq_basename))
+
     elsif seq_basename =~/RT/i
       rt_seq1 = {}
       rt_seq2 = {}
@@ -229,7 +248,7 @@ libs.each do |lib|
     filtered_seq_files.each do |seq_file|
       filtered_sh = ViralSeq::SeqHash.fa(seq_file)
       next if filtered_sh.size < 3
-      aligned_sh = filtered_sh.random_select(1000).align
+      aligned_sh = filtered_sh.random_select(1000).align(:Super5)
       aligned_sh.write_nt_fa(File.join(aln_seq_dir, File.basename(seq_file)))
     end
 
@@ -249,7 +268,7 @@ libs.each do |lib|
         tag = data[0].split("_")[-1].gsub(/\W/,"").to_sym
         summary_hash[tag] += "," + data[1].to_f.round(4).to_s + "," + data[2].to_f.round(4).to_s
       end
-      [:PR, :RT, :IN, :V1V3].each do |regions|
+      [:PR, :RT, :IN, :V1V3, :P17].each do |regions|
         next unless summary_hash[regions]
         seq_summary_out.puts regions.to_s + "," + summary_hash[regions]
       end
@@ -270,10 +289,13 @@ libs.each do |lib|
   tcs_RT = 0
   tcs_IN = 0
   tcs_V1V3 = 0
+  tcs_P17 = 0
   pi_RT = 0.0
   pi_V1V3 = 0.0
+  pi_P17 = 0.0
   dist20_RT = 0.0
   dist20_V1V3 = 0.0
+  dist20_P17 = 0.0
   summary_lines.each do |line|
       data = line.chomp.split(",")
       if data[0] == "PR"
@@ -288,6 +310,10 @@ libs.each do |lib|
           tcs_V1V3 = data[1].to_i
           pi_V1V3 = data[6].to_f
           dist20_V1V3 = data[7].to_f
+      elsif data[0] == "P17"
+          tcs_P17 = data[4].to_i
+          pi_P17 = data[6].to_f
+          dist20_P17 = data[7].to_f
       end
   end
 
@@ -323,9 +349,13 @@ libs.each do |lib|
     tcs_RT: tcs_RT,
     tcs_IN: tcs_IN,
     tcs_V1V3: tcs_V1V3,
+    tcs_P17: tcs_P17,
     pi_RT: pi_RT,
+    pi_V1V3: pi_V1V3,
+    pi_P17: pi_P17,
     dist20_RT: dist20_RT,
     dist20_V1V3: dist20_V1V3,
+    dist20_P17: dist20_P17,
     recency: recency,
     sdrm_PR: sdrm_PR,
     sdrm_RT: sdrm_RT,

data/docs/dr.json

@@ -62,6 +62,21 @@
       "ref_end": 7208,
       "indel": true,
       "trim": false
+    },
+    {
+      "region": "P17",
+      "cdna": "GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTNNNNNNNNNNNCAGTCAACAAGGTTTCTGTCATCCAATTTTTTAC",
+      "forward": "GCCTCCCTCGCGCCATCAGAGATGTGTATAAGAGACAGNNNNGTCAGCCAAAATTACCCTATAGTGC",
+      "majority": 0.5,
+      "end_join": true,
+      "end_join_option": 1,
+      "overlap": 0,
+      "TCS_QC": true,
+      "ref_genome": "HXB2",
+      "ref_start": 1196,
+      "ref_end": 1725,
+      "indel": true,
+      "trim": false
     }
   ]
 }

data/lib/viral_seq/hivdr.rb

@@ -5,7 +5,7 @@ module ViralSeq
     # functions to identify SDRMs from a ViralSeq::SeqHash object at HIV PR region.
     #   works for MPID-DR protocol (dx.doi.org/10.17504/protocols.io.useewbe)
     #   PR codon 1-99
-    #   RT codon 34-122 (HXB2 2650-2914) and 152-236(3001-3257)
+    #   RT codon 34-122 (HXB2 2649-2914) and 152-236(3001-3257)
     #   IN codon 53-174 (HXB2 4384-4751)
     # @param cutoff [Integer] cut-off for minimal abundance of a mutation to be called as valid mutation,
     #   can be obtained using ViralSeq::SeqHash#poisson_minority_cutoff function

data/lib/viral_seq/muscle.rb

@@ -28,6 +28,8 @@ module ViralSeq
     # align a sequence with reference sequence Strings
     # @param ref_seq [String] reference sequence
     # @param test_seq [String] test sequence
+    # @param algorithm [Symbol], algorithm for MUSCLE5 only. Choose from :PPP or :Super5. 
+    # @param path_to_muscle [String], path to MUSCLE excutable. if not provided (as default), it will use RubyGem::MuscleBio
     # @param path_to_muscle [String], path to MUSCLE excutable. if not provided (as default), it will use RubyGem::MuscleBio
     # @return [Array] a pair of [:ref_seq_aligned, :test_seq_aligned] or nil
     #   if the cannot find MUSCLE excutable
@@ -37,7 +39,7 @@ module ViralSeq
     #   aligned_seqs = ViralSeq::Muscle.align(seq1,seq2)
     #   => ["AAGGCGTAGGAC-", "-AAGCTTAGGACG"]
 
-    def self.align(ref_seq = "", test_seq = "", path_to_muscle = false)
+    def self.align(ref_seq = "", test_seq = "", algorithm = :PPP, path_to_muscle = false)
       temp_dir = Dir.home
       temp_name = "_"  + SecureRandom.alphanumeric
       temp_file = File.join(temp_dir, temp_name)
@@ -56,7 +58,11 @@ module ViralSeq
         end
         print `#{path_to_muscle} -in #{temp_file} -out #{temp_aln} -quiet`
       else
-        MuscleBio.run("muscle -in #{temp_file} -out #{temp_aln} -quiet")
+        if MuscleBio::VERSION.to_f < 0.5
+          MuscleBio.run("muscle -in #{temp_file} -out #{temp_aln} -quiet")
+        else
+          MuscleBio.exec(temp_file, temp_aln, algorithm)
+        end
       end
       aln_seq_hash = ViralSeq::SeqHash.fa(temp_aln).dna_hash
       File.unlink(temp_file)

data/lib/viral_seq/seq_hash.rb

@@ -223,7 +223,7 @@ module ViralSeq
 
     # check the size range of the DNA sequences of the SeqHash object
     # @return [Hash] Hash of {max: MAX_SIZE, min: MIN_SIZE}
-    
+
     def check_nt_size
       dna_hash = self.dna_hash
       size_array = []
@@ -450,7 +450,7 @@ module ViralSeq
     # function to determine if the sequences have APOBEC3g/f hypermutation.
     #   # APOBEC3G/F pattern: GRD -> ARD
     #   # control pattern: G[YN|RC] -> A[YN|RC]
-    #   # use the sample consensus to determine potential a3g sites
+    #   # use the sample consensus to determine potential a3g sites (default) or provide external reference sequences as a `String`
     #   # Two criteria to identify hypermutation
     #   # 1. Fisher's exact test on the frequencies of G to A mutation at A3G positions vs. non-A3G positions
     #   # 2. Poisson distribution of G to A mutations at A3G positions, outliers sequences
@@ -486,7 +486,7 @@ module ViralSeq
     #   # but it is still called as hypermutation sequence b/c it's Poisson outlier sequence.
     # @see https://www.hiv.lanl.gov/content/sequence/HYPERMUT/hypermut.html LANL Hypermut
 
-    def a3g_hypermut
+    def a3g_hypermut(ref = nil)
       # mut_hash number of apobec3g/f mutations per sequence
       mut_hash = {}
       hm_hash = {}
@@ -495,8 +495,10 @@ module ViralSeq
       # total G->A mutations at apobec3g/f positions.
       total = 0
 
-      # make consensus sequence for the input sequence hash
-      ref = self.consensus
+      unless ref 
+        # make consensus sequence for the input sequence hash
+        ref = self.consensus
+      end
 
       # obtain apobec3g positions and control positions
       apobec = apobec3gf(ref)
@@ -509,7 +511,6 @@ module ViralSeq
         c = 0 # control muts
         d = 0 # potenrial controls
         mut.each do |n|
-          next if v[n] == "-"
           if v[n] == "A"
             a += 1
             b += 1
@@ -521,7 +522,6 @@ module ViralSeq
         total += a
 
         control.each do |n|
-          next if v[n] == "-"
           if v[n] == "A"
             c += 1
             d += 1
@@ -544,7 +544,7 @@ module ViralSeq
         end
       end
 
-      if self.dna_hash.size > 20
+      if self.dna_hash.size > 200
         rate = total.to_f/(self.dna_hash.size)
         count_mut = mut_hash.values.count_freq
         maxi_count = count_mut.values.max
@@ -566,10 +566,12 @@ module ViralSeq
           end
         end
       end
+
       hm_seq_hash = ViralSeq::SeqHash.new
       hm_hash.each do |k,_v|
         hm_seq_hash.dna_hash[k] = self.dna_hash[k]
       end
+    
       hm_seq_hash.title = self.title + "_hypermut"
       hm_seq_hash.file = self.file
       filtered_seq_hash = self.sub(self.dna_hash.keys - hm_hash.keys)
@@ -711,10 +713,11 @@ module ViralSeq
 
 
     # align the @dna_hash sequences, return a new ViralSeq::SeqHash object with aligned @dna_hash using MUSCLE
+    # @param algorithm [Symbol], algorithm for MUSCLE5 only. Choose from :PPP or :Super5. 
     # @param path_to_muscle [String], path to MUSCLE excutable. if not provided (as default), it will use RubyGem::MuscleBio
     # @return [SeqHash] new SeqHash object of the aligned @dna_hash, the title has "_aligned"
 
-    def align(path_to_muscle = false)
+    def align(algorithm = :PPP, path_to_muscle = false)
       seq_hash = self.dna_hash
       if self.file.size > 0
         temp_dir = File.dirname(self.file)
@@ -732,7 +735,11 @@ module ViralSeq
         end
         print `#{path_to_muscle} -in #{temp_file} -out #{temp_aln} -quiet`
       else
-        MuscleBio.run("muscle -in #{temp_file} -out #{temp_aln} -quiet")
+        if MuscleBio::VERSION.to_f < 0.5
+          MuscleBio.run("muscle -in #{temp_file} -out #{temp_aln} -quiet")
+        else
+          MuscleBio.exec(temp_file, temp_aln, algorithm)
+        end
       end
       out_seq_hash = ViralSeq::SeqHash.fa(temp_aln)
       out_seq_hash.title = self.title + "_aligned"
@@ -1351,7 +1358,7 @@ module ViralSeq
     # APOBEC3G/F pattern: GRD -> ARD,
     # control pattern: G[YN|RC] -> A[YN|RC],
     def apobec3gf(seq = '')
-      seq.tr!("-", "")
+      #seq.tr!("-", "")
       seq_length = seq.size
       apobec_position = []
       control_position = []
@@ -1363,6 +1370,7 @@ module ViralSeq
           control_position << n
         end
       end
+
       return [apobec_position,control_position]
     end # end of #apobec3gf
 

data/lib/viral_seq/sequence.rb

@@ -180,7 +180,7 @@ module ViralSeq
         l1 = 0
         l2 = 0
 
-        aln_seq = ViralSeq::Muscle.align(ori_ref, seq, path_to_muscle)
+        aln_seq = ViralSeq::Muscle.align(ori_ref, seq, :PPP, path_to_muscle)
         aln_test = aln_seq[1]
         aln_test =~ /^(\-*)(\w.*\w)(\-*)$/
         gap_begin = $1.size
@@ -214,7 +214,7 @@ module ViralSeq
             l2 = l2 + (post_aln - b2)
           end
 
-          aln_seq = ViralSeq::Muscle.align(ref, seq, path_to_muscle)
+          aln_seq = ViralSeq::Muscle.align(ref, seq, :PPP, path_to_muscle)
           aln_test = aln_seq[1]
           aln_test =~ /^(\-*)(\w.*\w)(\-*)$/
           gap_begin = $1.size
@@ -240,22 +240,22 @@ module ViralSeq
         repeat = 0
 
         if g1 == g2 and (s1 + g1 + s2) == ref.size
-          if s1 > s2 and g2 > 2*s2
+          if s1 > s2 and g2 >= s2
             ref = ref[0..(-g2-1)]
             repeat = 1
             l2 = l2 + g2
-          elsif s1 < s2 and g1 > 2*s1
+          elsif s1 < s2 and g1 >= s1
             ref = ref[g1..-1]
             repeat = 1
             l1 = l1 + g1
           end
         else
-          if g1 > 2*s1
+          if g1 >= s1
             ref = ref[g1..-1]
             repeat = 1
             l1 = l1 + g1
           end
-          if g2 > 2*s2
+          if g2 >= s2
             ref = ref[0..(-g2 - 1)]
             repeat = 1
             l2 = l2 + g2
@@ -263,7 +263,7 @@ module ViralSeq
         end
 
         while repeat == 1
-          aln_seq = ViralSeq::Muscle.align(ref, seq, path_to_muscle)
+          aln_seq = ViralSeq::Muscle.align(ref, seq, :PPP, path_to_muscle)
           aln_test = aln_seq[1]
           aln_test =~ /^(\-*)(\w.*\w)(\-*)$/
           gap_begin = $1.size
@@ -280,12 +280,12 @@ module ViralSeq
           l1 = l1 + gap_begin
           l2 = l2 + gap_end
           repeat = 0
-          if g1 > 2*s1
+          if g1 >= s1
             ref = ref[g1..-1]
             repeat = 1
             l1 = l1 + g1
           end
-          if g2 > 2*s2
+          if g2 >= s2
             ref = ref[0..(-g2 - 1)]
             repeat = 1
             l2 = l2 + g2
@@ -293,8 +293,7 @@ module ViralSeq
         end
         ref = ori_ref[l1..(ori_ref_l - l2 - 1)]
 
-
-        aln_seq = ViralSeq::Muscle.align(ref, seq, path_to_muscle)
+        aln_seq = ViralSeq::Muscle.align(ref, seq, :PPP, path_to_muscle)
         aln_test = aln_seq[1]
         ref = aln_seq[0]
 
@@ -303,12 +302,12 @@ module ViralSeq
         if ref =~ /^(\-+)/
           l1 = l1 - $1.size
         elsif ref =~ /(\-+)$/
-          l2 = l2 + $1.size
+          l2 = l2 - $1.size
         end
 
         if (ori_ref_l - l2 - 1) >= l1
           ref = ori_ref[l1..(ori_ref_l - l2 - 1)]
-          aln_seq = ViralSeq::Muscle.align(ref, seq, path_to_muscle)
+          aln_seq = ViralSeq::Muscle.align(ref, seq, :PPP, path_to_muscle)
           aln_test = aln_seq[1]
           ref = aln_seq[0]
 

data/lib/viral_seq/tcs_dr.rb

@@ -16,7 +16,7 @@ module ViralSeq
                   :ref_genome=>"HXB2",
                   :ref_start=>2648,
                   :ref_end=>3257,
-                  :indel=>false,
+                  :indel=>true,
                   :trim=>false},
                  {:region=>"PR",
                   :cdna=>
@@ -41,7 +41,7 @@ module ViralSeq
                   :forward=>"GCCTCCCTCGCGCCATCAGAGATGTGTATAAGAGACAGNNNNAAAAGGAGAAGCCATGCATG",
                   :majority=>0,
                   :end_join=>true,
-                  :end_join_option=>3,
+                  :end_join_option=>2,
                   :overlap=>171,
                   :TCS_QC=>true,
                   :ref_genome=>"HXB2",
@@ -61,11 +61,26 @@ module ViralSeq
                   :TCS_QC=>true,
                   :ref_genome=>"HXB2",
                   :ref_start=>6585,
-                  :ref_end=>7208,
+                  :ref_end=>7205..7210,
                   :indel=>true,
-                  :trim=>false}
+                  :trim=>false},
+                  {:region=>"P17",
+                   :cdna=>
+                    "GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTNNNNNNNNNNNCAGTCAACAAGGTTTCTGTCATCCAATTTTTTAC",
+                   :forward=>
+                    "GCCTCCCTCGCGCCATCAGAGATGTGTATAAGAGACAGNNNNGTCAGCCAAAATTACCCTATAGTGC",
+                   :majority=>0,
+                   :end_join=>true,
+                   :end_join_option=>1,
+                   :overlap=>0,
+                   :TCS_QC=>true,
+                   :ref_genome=>"HXB2",
+                   :ref_start=>1196,
+                   :ref_end=>1725,
+                   :indel=>true,
+                   :trim=>false}
                   ]
-                }
+              }
   end
 
 end

data/lib/viral_seq/version.rb

@@ -2,6 +2,6 @@
 # version info and histroy
 
 module ViralSeq
-  VERSION = "1.6.1"
-  TCS_VERSION = "2.5.0"
+  VERSION = "1.7.0"
+  TCS_VERSION = "2.5.1"
 end

data/viral_seq.gemspec

@@ -35,7 +35,7 @@ Gem::Specification.new do |spec|
   spec.required_rubygems_version = '>= 1.3.6'
 
   # muscle_bio gem required
-  spec.add_runtime_dependency "muscle_bio", "~> 0.4"
+  spec.add_runtime_dependency "muscle_bio", "~> 0.5"
 
   # colorize gem required
   spec.add_runtime_dependency "colorize", "~> 0.1"

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: viral_seq
 version: !ruby/object:Gem::Version
-  version: 1.6.1
+  version: 1.7.0
 platform: ruby
 authors:
 - Shuntai Zhou
@@ -9,7 +9,7 @@ authors:
 autorequire:
 bindir: bin
 cert_chain: []
-date: 2022-02-02 00:00:00.000000000 Z
+date: 2022-08-25 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler
@@ -59,14 +59,14 @@ dependencies:
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '0.4'
+        version: '0.5'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '0.4'
+        version: '0.5'
 - !ruby/object:Gem::Dependency
   name: colorize
   requirement: !ruby/object:Gem::Requirement