RubyGems - viral_seq - Versions diffs - 1.6.0 → 1.6.4 - Mend

viral_seq 1.6.0 → 1.6.4

Files changed (16) hide show

checksums.yaml +4 -4
data/Gemfile.lock +3 -3
data/README.md +17 -0
data/bin/tcs +1 -1
data/bin/tcs_log +1 -1
data/bin/tcs_sdrm +32 -2
data/docs/dr.json +15 -0
data/lib/viral_seq/hivdr.rb +1 -1
data/lib/viral_seq/muscle.rb +8 -2
data/lib/viral_seq/seq_hash.rb +8 -3
data/lib/viral_seq/sequence.rb +12 -13
data/lib/viral_seq/tcs_dr.rb +20 -5
data/lib/viral_seq/version.rb +2 -2
data/rc_swans.svc@longleaf.unc.edu +0 -0
data/viral_seq.gemspec +1 -1
metadata +5 -4

checksums.yaml CHANGED Viewed

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

@@ -1,10 +1,10 @@
 PATH
   remote: .
   specs:
-    viral_seq (1.3.0)
+    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 CHANGED Viewed

@@ -179,6 +179,23 @@ qc_seqhash.sdrm_hiv_pr(cut_off)
 ## Updates
+### 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`.
 ### Version 1.6.0-01042022
   1. Update the `ViralSeq::TcsCore::detection_limit` with pre-calculated values to save processing time.

data/bin/tcs CHANGED Viewed

@@ -173,7 +173,7 @@ begin
     unless forward_primer
       log.puts Time.now.to_s + "\t" +  region + " does not have forward primer sequence. #{region} skipped."
     end
-    summary_json[:cdan_primer] = cdna_primer
+    summary_json[:cdna_primer] = cdna_primer
     summary_json[:forward_primer] = forward_primer
     primer[:majority] ? majority_cut_off = primer[:majority] : majority_cut_off = 0

data/bin/tcs_log CHANGED Viewed

@@ -613,7 +613,7 @@ html = '
     <body>
         <div style="display: flex; flex-direction: column; height: 100vh; width: 100vw; position: fixed; overflow: hidden;">
             <div style="display: flex; gap: 4px;">
-                <div id="nav" class="card" style="overflow: auto; min-height: 100vh; text-align: left; margin-top: 0;">
+                <div id="nav" class="card" style="overflow: auto; height: 100vh; text-align: left; margin-top: 0;">
                     <a href="https://primer-id.org" target="_BLANK">
                         <h3 style="margin: 24px; font-weight: 600; color: #333 !important">TCS Log</h3>
                     </a>

data/bin/tcs_sdrm CHANGED Viewed

@@ -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 CHANGED Viewed

@@ -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 CHANGED Viewed

@@ -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 CHANGED Viewed

@@ -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 CHANGED Viewed

@@ -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 CHANGED Viewed

@@ -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 CHANGED Viewed

@@ -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 CHANGED Viewed

@@ -2,6 +2,6 @@
 # version info and histroy
 module ViralSeq
-  VERSION = "1.6.0"
-  TCS_VERSION = "2.5.0"
+  VERSION = "1.6.4"
+  TCS_VERSION = "2.5.1"
 end

data/rc_swans.svc@longleaf.unc.edu ADDED Viewed

Binary file

data/viral_seq.gemspec CHANGED Viewed

@@ -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 CHANGED Viewed

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: viral_seq
 version: !ruby/object:Gem::Version
-  version: 1.6.0
+  version: 1.6.4
 platform: ruby
 authors:
 - Shuntai Zhou
@@ -9,7 +9,7 @@ authors:
 autorequire:
 bindir: bin
 cert_chain: []
-date: 2022-01-18 00:00:00.000000000 Z
+date: 2022-07-19 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
@@ -193,6 +193,7 @@ files:
 - lib/viral_seq/tcs_dr.rb
 - lib/viral_seq/tcs_json.rb
 - lib/viral_seq/version.rb
+- rc_swans.svc@longleaf.unc.edu
 - viral_seq.gemspec
 homepage: https://github.com/ViralSeq/viral_seq
 licenses: