viral_seq 1.6.1 → 1.6.3

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 (1.6.2)
       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

@@ -179,10 +179,16 @@ qc_seqhash.sdrm_hiv_pr(cut_off)
 
 ## Updates
 
+### 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_sdrm

@@ -229,8 +229,9 @@ 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)))
+      puts 'aligned sequence written.'
     end
 
     r_script.gsub!(/PATH_TO_FASTA/,aln_seq_dir)

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 = []
@@ -711,10 +711,11 @@ 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 +733,11 @@ 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"

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",

data/lib/viral_seq/version.rb

@@ -2,6 +2,6 @@
 # version info and histroy
 
 module ViralSeq
-  VERSION = "1.6.1"
+  VERSION = "1.6.3"
   TCS_VERSION = "2.5.0"
 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: 1.6.3
 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: 2022-02-05 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