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

viral_seq 1.6.0 → 1.6.4

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

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.tar.gz: 1118ab7b586da98bb2c3533f81c35a02f0efb1978c0b91e15b56218b05342ad83e73f96bd2df53f75e2e6cdd16c591582ebe864562a02d3dd78997678b706233

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: