viral_seq 1.9.0 → 1.10.0

data/lib/viral_seq/pid.rb

@@ -14,10 +14,7 @@ module ViralSeq
       nt = ['A','T','C','G']
       pid_pool = ['A','T','C','G']
       (l-1).times do
-        pid_pool = pid_pool.product(nt)
-        pid_pool.collect! do |v|
-          v.join("")
-        end
+        pid_pool = pid_pool.product(nt).map(&:join)
       end
       return pid_pool
     end # end of .generate_primer_id_pool

data/lib/viral_seq/seq_hash.rb

@@ -656,7 +656,7 @@ module ViralSeq
 
     def nt_variants
       return_obj = {}
-      nt_hash = self.dna_hash
+
       tcs_number = self.size
       dl = ViralSeq::TcsCore.detection_limit(tcs_number)
       fdr_hash = self.fdr
@@ -869,7 +869,7 @@ module ViralSeq
     # @param start_nt [Integer,Range,Array] start nt position(s) on the refernce genome, can be single number (Integer) or a range of Integers (Range), or an Array
     # @param end_nt [Integer,Range,Array] end nt position(s) on the refernce genome,can be single number (Integer) or a range of Integers (Range), or an Array
     # @param indel [Boolean] allow indels or not, `ture` or `false`
-    # @param ref_option [Symbol], name of reference genomes, options are `:HXB2`, `:NL43`, `:MAC239`
+    # @param ref_option [Symbol], name of reference genomes, options are `:HXB2`, `:SIVmm239`
     # @param path_to_muscle [String], path to the muscle executable, if not provided, use MuscleBio to run Muscle
     # @return [ViralSeq::SeqHash] a new ViralSeq::SeqHash object with only the sequences that meet the QC criterias
     # @example QC for sequences in a FASTA files
@@ -880,17 +880,19 @@ module ViralSeq
     #   filtered_seqhash.dna_hash.size
     #   => 4
 
-    def hiv_seq_qc(start_nt, end_nt, indel=true, ref_option = :HXB2, path_to_muscle = false)
-      start_nt = start_nt..start_nt if start_nt.is_a?(Integer)
-      end_nt = end_nt..end_nt if end_nt.is_a?(Integer)
+    def hiv_seq_qc(start_nt, end_nt, indel=true, ref_option = :HXB2)
+      start_nt = position_helper(start_nt)
+      end_nt = position_helper(end_nt)
+
       seq_hash = self.dna_hash.dup
       seq_hash_unique = seq_hash.values.uniq
       seq_hash_unique_pass = []
 
-      seq_hash_unique.each do |seq|
-        next if seq.nil?
-        loc = ViralSeq::Sequence.new('', seq).locator(ref_option, path_to_muscle)
-        next unless loc # if locator tool fails, skip this seq.
+      batch_locator = VirustLocator::Locator.exec(seq_hash_unique.join("\s"), "nt", 1, ref_option).split("\n")
+      seq_hash_unique.each_with_index do |seq, i|
+        loc = batch_locator[i]
+        loc = locator_helper(loc)
+        next unless loc
         if start_nt.include?(loc[0]) && end_nt.include?(loc[1])
           if indel
             seq_hash_unique_pass << seq
@@ -898,8 +900,11 @@ module ViralSeq
             seq_hash_unique_pass << seq
           end
         end
+
       end
+
       seq_pass = []
+
       seq_hash_unique_pass.each do |seq|
         seq_hash.each do |seq_name, orginal_seq|
           if orginal_seq == seq
@@ -909,10 +914,10 @@ module ViralSeq
         end
       end
       self.sub(seq_pass)
-    end # end of #hiv_seq_qc
+    end # end of #hiv_seq_qc # end of #hiv_seq_qc
 
     # sequence locator for SeqHash object, resembling HIV Sequence Locator from LANL
-    # @param ref_option [Symbol], name of reference genomes, options are `:HXB2`, `:NL43`, `:MAC239`
+    # @param ref_option [Symbol], name of reference genomes, options are `:HXB2`, `:SIVmm239`
     # @return [Array] two dimensional array `[[],[],[],...]` for each sequence, including the following information:
     #
     #     title of the SeqHash object (String)
@@ -1341,7 +1346,7 @@ module ViralSeq
       seq_hash_unique = seq_hash.uniq_hash
       trimmed_seq_hash = {}
       seq_hash_unique.each do |seq, names|
-        trimmed_seq = ViralSeq::Sequence.new('', seq).sequence_clip(start_nt, end_nt, ref_option, path_to_muscle).dna
+        trimmed_seq = ViralSeq::Sequence.new('', seq).sequence_clip(start_nt, end_nt, ref_option).dna
         names.each do |name|
           trimmed_seq_hash[name] = trimmed_seq
         end
@@ -1431,6 +1436,37 @@ module ViralSeq
       var_count.sort_by{|key,_value|key}.to_h
     end # end of #varaint_for_poisson
 
+    # helper for start/end position for #hiv_seq_qc
+    def position_helper(position)
+      if position.is_a?(Range)
+        return position
+      elsif position.is_a?(Integer)
+        return position..position
+      elsif position.is_a?(String)
+        return position.to_i..position.to_i
+      elsif position.is_a?(Array)
+        return position[0].to_i..position[1].to_i
+      else
+        raise "Position #{position} not recognized"
+      end
+    end # position_helper
+
+    # helper for batch locator
+    # @param loc [String] the output of batch locator
+    # @return [Array] the locator information in an array
+    def locator_helper(loc)
+      loc = loc.split("\t")
+      loc[0] = loc[0].to_i
+      loc[1] = loc[1].to_i
+      loc[2] = loc[2].to_f.round(1)
+      if loc[3].to_s.downcase == "true"
+        loc[3] = true
+      else
+        loc[3] = false
+      end
+      return loc
+    end
+
   end # end of SeqHash
 
 end # end of ViralSeq

data/lib/viral_seq/sequence.rb

@@ -165,7 +165,7 @@ module ViralSeq
 
     # HIV sequence locator function, resembling HIV Sequence Locator from LANL
     #   # current version only supports nucleotide sequence, not for amino acid sequence.
-    # @param ref_option [Symbol], name of reference genomes, options are `:HXB2`, `:NL43`, `:MAC239`
+    # @param ref_option [Symbol], name of reference genomes, options are `:HXB2`, `:SIVmm239`
     # @param path_to_muscle [String], path to the muscle executable, if not provided, use MuscleBio to run Muscle
     # @return [Array] an array of the following info:
     #
@@ -181,182 +181,32 @@ module ViralSeq
     #
     #   aligned_reference_sequence (String)
     #
-    # @example identify the location of the input sequence on the NL43 genome
+    # @example identify the location of the input sequence on the HXB2 genome
     #   sequence = 'AGCAGATGATACAGTATTAGAAGAAATAAATTTGCCAGGAAGATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAATATGATC'
     #   s = ViralSeq::Sequence.new('my_sequence', sequence)
-    #   loc = s.locator(:NL43)
-    #   h = ViralSeq::SeqHash.new; h.dna_hash['NL43'] = loc[5]; h.dna_hash[s.name] = loc[4]
+    #   loc = s.locator(:HXB2)
+    #   h = ViralSeq::SeqHash.new; h.dna_hash['HXB2'] = loc[5]; h.dna_hash[s.name] = loc[4]
     #   rs_string = h.to_rsphylip.split("\n")[1..-1].join("\n") # get a relaxed phylip format string for display of alignment.
-    #   puts "The input sequence \"#{s.name}\" is located on the NL43 nt sequence from #{loc[0].to_s} to #{loc[1].to_s}.\nIt is #{loc[2].to_s}% similar to the reference.\nIt #{loc[3]? "does" : "does not"} have indels.\nThe alignment is\n#{rs_string}"
-    #   => The input sequence "my_sequence" is located on the NL43 nt sequence from 2333 to 2433.
-    #   => It is 98.0% similar to the reference.
+    #   puts "The input sequence \"#{s.name}\" is located on the HXB2 nt sequence from #{loc[0].to_s} to #{loc[1].to_s}.\nIt is #{loc[2].round(1).to_s}% similar to the reference.\nIt #{loc[3]? "does" : "does not"} have indels.\nThe alignment is\n#{rs_string}"
+    #   => The input sequence "my_sequence" is located on the HXB2 nt sequence from 2333 to 2433.
+    #   => It is 97.0% similar to the reference.
     #   => It does not have indels.
     #   => The alignment is
-    #   => NL43         AGCAGATGAT ACAGTATTAG AAGAAATGAA TTTGCCAGGA AGATGGAAAC CAAAAATGAT AGGGGGAATT GGAGGTTTTA TCAAAGTAAG ACAGTATGAT C
+    #   => HXB2         AGCAGATGAT ACAGTATTAG AAGAAATGAA TTTGCCAGGA AGATGGAAAC CAAAAATGAT AGGGGGAATT GGAGGTTTTA TCAAAGTAAG ACAGTATGAT C
     #   => my_sequence  AGCAGATGAT ACAGTATTAG AAGAAATAAA TTTGCCAGGA AGATGGAAAC CAAAAATGAT AGGGGGAATT GGAGGTTTTA TCAAAGTAAG ACAATATGAT C
     # @see https://www.hiv.lanl.gov/content/sequence/LOCATE/locate.html LANL Sequence Locator
-
-    def locator(ref_option = :HXB2, path_to_muscle = false)
+    def locator(ref_option = :HXB2, algorithm = 1)
       seq = self.dna
-      ori_ref = ViralSeq::RefSeq.get(ref_option)
-
+      ref = ref_option.to_s
       begin
-        ori_ref_l = ori_ref.size
-        l1 = 0
-        l2 = 0
-
-        aln_seq = ViralSeq::Muscle.align(ori_ref, seq, :Super5, path_to_muscle)
-        aln_test = aln_seq[1]
-        aln_test =~ /^(\-*)(\w.*\w)(\-*)$/
-        gap_begin = $1.size
-        gap_end = $3.size
-        aln_test2 = $2
-        ref = aln_seq[0]
-        ref = ref[gap_begin..(-gap_end-1)]
-        ref_size = ref.size
-        if ref_size > 1.3*(seq.size)
-          l1 = l1 + gap_begin
-          l2 = l2 + gap_end
-          max_seq = aln_test2.scan(/[ACGT]+/).max_by(&:length)
-          aln_test2 =~ /#{max_seq}/
-          before_aln_seq = $`
-          before_aln = $`.size
-          post_aln_seq = $'
-          post_aln = $'.size
-          before_aln_seq_size = before_aln_seq.scan(/[ACGT]+/).join("").size
-          b1 = (1.3 * before_aln_seq_size).to_i
-          post_aln_seq_size = post_aln_seq.scan(/[ACGT]+/).join("").size
-          b2 = (1.3 * post_aln_seq_size).to_i
-          if (before_aln > seq.size) and (post_aln <= seq.size)
-            ref = ref[(before_aln - b1)..(ref_size - post_aln - 1)]
-            l1 = l1 + (before_aln - b1)
-          elsif (post_aln > seq.size) and (before_aln <= seq.size)
-            ref = ref[before_aln..(ref_size - post_aln - 1 + b2)]
-            l2 = l2 + post_aln - b2
-          elsif (post_aln > seq.size) and (before_aln > seq.size)
-            ref = ref[(before_aln - b1)..(ref_size - post_aln - 1 + b2)]
-            l1 = l1 + (before_aln - b1)
-            l2 = l2 + (post_aln - b2)
-          end
-
-          aln_seq = ViralSeq::Muscle.align(ref, seq, :Super5, path_to_muscle)
-          aln_test = aln_seq[1]
-          aln_test =~ /^(\-*)(\w.*\w)(\-*)$/
-          gap_begin = $1.size
-          gap_end = $3.size
-          ref = aln_seq[0]
-          ref = ref[gap_begin..(-gap_end-1)]
-        end
-
-        aln_test = aln_seq[1]
-        aln_test =~ /^(\-*)(\w.*\w)(\-*)$/
-        gap_begin = $1.size
-        gap_end = $3.size
-        aln_test = $2
-        aln_test =~ /^(\w+)(\-*)\w/
-        s1 = $1.size
-        g1 = $2.size
-        aln_test =~ /\w(\-*)(\w+)$/
-        s2 = $2.size
-        g2 = $1.size
-
-        l1 = l1 + gap_begin
-        l2 = l2 + gap_end
-        repeat = 0
-
-        if g1 == g2 and (s1 + g1 + s2) == ref.size
-          if s1 > s2 and g2 >= s2
-            ref = ref[0..(-g2-1)]
-            repeat = 1
-            l2 = l2 + g2
-          elsif s1 < s2 and g1 >= s1
-            ref = ref[g1..-1]
-            repeat = 1
-            l1 = l1 + g1
-          end
-        else
-          if g1 >= s1
-            ref = ref[g1..-1]
-            repeat = 1
-            l1 = l1 + g1
-          end
-          if g2 >= s2
-            ref = ref[0..(-g2 - 1)]
-            repeat = 1
-            l2 = l2 + g2
-          end
-        end
-
-        while repeat == 1
-          aln_seq = ViralSeq::Muscle.align(ref, seq, :Super5, path_to_muscle)
-          aln_test = aln_seq[1]
-          aln_test =~ /^(\-*)(\w.*\w)(\-*)$/
-          gap_begin = $1.size
-          gap_end = $3.size
-          aln_test = $2
-          aln_test =~ /^(\w+)(\-*)\w/
-          s1 = $1.size
-          g1 = $2.size
-          aln_test =~ /\w(\-*)(\w+)$/
-          s2 = $2.size
-          g2 = $1.size
-          ref = aln_seq[0]
-          ref = ref[gap_begin..(-gap_end-1)]
-          l1 = l1 + gap_begin
-          l2 = l2 + gap_end
-          repeat = 0
-          if g1 >= s1
-            ref = ref[g1..-1]
-            repeat = 1
-            l1 = l1 + g1
-          end
-          if g2 >= s2
-            ref = ref[0..(-g2 - 1)]
-            repeat = 1
-            l2 = l2 + g2
-          end
-        end
-        ref = ori_ref[l1..(ori_ref_l - l2 - 1)]
-
-        aln_seq = ViralSeq::Muscle.align(ref, seq, :Super5, path_to_muscle)
-        aln_test = aln_seq[1]
-        ref = aln_seq[0]
-
-        #refine alignment
-
-        if ref =~ /^(\-+)/
-          l1 = l1 - $1.size
-        elsif ref =~ /(\-+)$/
-          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, :Super5, path_to_muscle)
-          aln_test = aln_seq[1]
-          ref = aln_seq[0]
-
-          ref_size = ref.size
-          sim_count = 0
-          (0..(ref_size-1)).each do |n|
-            ref_base = ref[n]
-            test_base = aln_test[n]
-            sim_count += 1 if ref_base == test_base
-          end
-          similarity = (sim_count/ref_size.to_f*100).round(1)
-
-          loc_p1 = l1 + 1
-          loc_p2 = ori_ref_l - l2
-          if seq.size != (loc_p2 - loc_p1 + 1)
-              indel = true
-          elsif aln_test.include?("-")
-              indel = true
-          else
-              indel = false
-          end
-          return [loc_p1,loc_p2,similarity,indel,aln_test,ref]
+        loc = VirustLocator::Locator.exec(seq, "nt", algorithm, ref).split("\t")
+        loc[0] = loc[0].to_i
+        loc[1] = loc[1].to_i
+        loc[2] = loc[2].to_f.round(1)
+        if loc[3].to_s.downcase == "true"
+          loc[3] = true
         else
-          return [0,0,0,0,0,0,0]
+          loc[3] = false
         end
       rescue => e
         puts "Unexpected error occured."
@@ -366,12 +216,13 @@ module ViralSeq
         puts "ViralSeq.sequence_locator returns nil"
         return nil
       end
-    end # end of locator
+      return loc
+    end #end of locator
 
     # Given start and end positions on the reference genome, return a sub-sequence of the target sequence in that range
     # @param p1 [Integer] start position number on the reference genome
     # @param p2 [Integer] end position number on the reference genome
-    # @param ref_option [Symbol], name of reference genomes, options are `:HXB2`, `:NL43`, `:MAC239`
+    # @param ref_option [Symbol], name of reference genomes, options are `:HXB2`, `:SIVmm239`
     # @param path_to_muscle [String], path to the muscle executable, if not provided, use MuscleBio to run Muscle
     # @return [ViralSeq::Sequence, nil] a new ViralSeq::Sequence object that of input range on the reference genome or nil
     #   if either the start or end position is beyond the range of the target sequence.
@@ -381,8 +232,8 @@ module ViralSeq
     #   s.sequence_clip(2333, 2433, :HXB2).dna
     #   => "AGCAGATGATACAGTATTAGAAGAAATAAATTTGCCAGGAAGATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAATATGATC"
 
-    def sequence_clip(p1 = 0, p2 = 0, ref_option = :HXB2, path_to_muscle = false)
-      loc = self.locator(ref_option, path_to_muscle)
+    def sequence_clip(p1 = 0, p2 = 0, ref_option = :HXB2)
+      loc = self.locator(ref_option)
       l1 = loc[0]
       l2 = loc[1]
       if (p1 >= l1) & (p2 <= l2)

data/lib/viral_seq/string.rb

@@ -56,13 +56,13 @@ class String
     Regexp.new match
   end
 
-  # parse the nucleotide sequences as an Array of Array 
+  # parse the nucleotide sequences as an Array of Array
   # @return [Array] Array of Array at each position
   # @example parse a sequence with ambiguities to Array of Array
   #   "ATRWCG".nt_to_array
   #   => [["A"], ["T"], ["A", "G"], ["A", "T"], ["C"], ["G"]]
-  
-  def nt_to_array 
+
+  def nt_to_array
     return_array = []
     self.each_char.each do |base|
       base_array = base.to_list
@@ -75,9 +75,6 @@ class String
   # compare the given nt sequence string with the ref sequence string
   # @param ref [String] the ref sequence string to compare with
   # @return [Interger] Number of differences
-  # @example parse a sequence with ambiguities to Array of Array
-  #   "ATRWCG".nt_to_array
-  #   => [["A"], ["T"], ["A", "G"], ["A", "T"], ["C"], ["G"]]
 
   def nt_diff(ref)
     count_diff = 0

data/lib/viral_seq/tcs_core.rb

@@ -331,6 +331,10 @@ module ViralSeq
           return false
         elsif seq[1..-2] =~ /N/ # sequences with ambiguities except the 1st and last position removed
           return false
+        elsif seq =~ /G{11}/ # a string of poly-G indicates poor quanlity in 2-color chemistry
+          return false
+        elsif seq =~ /C{11}/ # a string of poly-C indicates poor quanlity in 2-color chemistry
+          return false
         elsif seq =~ /A{11}/ # a string of poly-A indicates adaptor sequence
           return false
         elsif seq =~ /T{11}/ # a string of poly-T indicates adaptor sequence

data/lib/viral_seq/tcs_dr.rb

@@ -186,7 +186,7 @@ module ViralSeq
         :trim=>false},
         {:region=>"PR",
         :cdna=>
-          "GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTNNNNNNNNNTTAACCTTTGGGCCATCCATTCC",
+          "GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTNNNNNNNNNCAGTTTAACTTTTGGGCCATCCATTCC",
         :forward=>
           "GCCTCCCTCGCGCCATCAGAGATGTGTATAAGAGACAGNNNNTCAGAGCAGACCAGAGCCAACAGCCCCA",
         :majority=>0,
@@ -247,6 +247,87 @@ module ViralSeq
         ]
       },
 
+      "v4" => {:platform_error_rate=>0.01,
+      :primer_pairs=>
+      [{:region=>"RT",
+        :cdna=>
+          "GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTNNNNNNNNNNNCAGTAAGGAATGGAGGTTCTTTCTGATG",
+        :forward=>
+          "GCCTCCCTCGCGCCATCAGAGATGTGTATAAGAGACAGNNNNGGCCATTGACAGAAGAAAAAATAAAAGC",
+        :majority=>0,
+        :end_join=>true,
+        :end_join_option=>1,
+        :overlap=>0,
+        :TCS_QC=>true,
+        :ref_genome=>"HXB2",
+        :ref_start=>2648,
+        :ref_end=>3209,
+        :indel=>true,
+        :trim=>false},
+        {:region=>"PR",
+        :cdna=>
+          "GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTNNNNNNNNNCAGTTTAACTTTTGGGCCATCCATTCC",
+        :forward=>
+          "GCCTCCCTCGCGCCATCAGAGATGTGTATAAGAGACAGNNNNTCAGAGCAGACCAGAGCCAACAGCCCCA",
+        :majority=>0,
+        :end_join=>true,
+        :end_join_option=>3,
+        :TCS_QC=>true,
+        :ref_genome=>"HXB2",
+        :ref_start=>0,
+        :ref_end=>2591,
+        :indel=>true,
+        :trim=>true,
+        :trim_ref=>"HXB2",
+        :trim_ref_start=>2253,
+        :trim_ref_end=>2549},
+        {:region=>"IN",
+        :cdna=>
+          "GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTNNNNNNNNNNNCATCACCTGCCATCTGTTTTCCAT",
+        :forward=>"GCCTCCCTCGCGCCATCAGAGATGTGTATAAGAGACAGNNNNGCAGAAGTTATYCCAGCAGAAACA",
+        :majority=>0,
+        :end_join=>true,
+        :end_join_option=>2,
+        :overlap=>3,
+        :TCS_QC=>true,
+        :ref_genome=>"HXB2",
+        :ref_start=>4509,
+        :ref_end=>5040,
+        :indel=>true,
+        :trim=>false},
+        {:region=>"V1V3",
+        :cdna=>
+          "GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTNNNNNNNNNNNCAGTCCATTTTGCTYTAYTRABVTTACAATRTGC",
+        :forward=>
+          "GCCTCCCTCGCGCCATCAGAGATGTGTATAAGAGACAGNNNNTTATGGGATCAAAGCCTAAAGCCATGTGTA",
+        :majority=>0,
+        :end_join=>true,
+        :end_join_option=>1,
+        :overlap=>0,
+        :TCS_QC=>true,
+        :ref_genome=>"HXB2",
+        :ref_start=>6585,
+        :ref_end=>7205..7210,
+        :indel=>true,
+        :trim=>false},
+        {:region=>"CA",
+          :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}
+        ]
+      },
+
 
     }
 

data/lib/viral_seq/util/drm_versions_config.json

@@ -54,6 +54,58 @@
             }
         }
 
+    },
+    {
+        "version": "v4",
+        "DRM_range": {
+            "CAI": [56,57, 66, 67, 70, 74, 105, 107],
+            "PI": [23, 24, 30, 32, 46, 47, 48, 50, 53, 54, 73, 76, 82, 83, 84, 88, 90],
+            "NRTI": [41, 65, 67, 69, 70, 74, 75, 77, 115, 116, 151, 184, 210, 215, 219],
+            "NNRTI": [98, 100, 101, 103, 106, 138, 179, 181, 188, 190],
+            "INSTI": [95, 97, 121, 140, 143, 147, 148, 155, 263]
+        },
+        "seq_coord": {
+            "CA": {
+                "minimum": 1196,
+                "maximum": 1725,
+                "gap": {
+                    "minimum": 1466,
+                    "maximum": 1471
+                }
+            },
+            "PR": {
+                "minimum": 2253,
+                "maximum": 2549
+            },
+            "RT": {
+                "minimum": 2648,
+                "maximum": 3209,
+                "gap": {
+                    "minimum": 2915,
+                    "maximum": 2949
+                }
+            },
+            "IN": {
+                "minimum": 4509,
+                "maximum": 5040
+            }
+        },
+        "seq_drm_correlation": {
+            "CA": ["CAI"],
+            "RT": ["NRTI", "NNRTI"],
+            "PR": ["PI"],
+            "IN": ["INSTI"]
+        },
+        "ref_info": {
+            "ref_type": "HXB2",
+            "ref_coord": {
+                "CA": [1186,1878],
+                "PR": [2253,2549],
+                "RT": [2550,3869],
+                "IN": [4230,5096]
+            }
+        }
+
     },
     {
         "version": "v1",

data/lib/viral_seq/version.rb

@@ -2,6 +2,6 @@
 # version info and histroy
 
 module ViralSeq
-  VERSION = "1.9.0"
-  TCS_VERSION = "2.7.0"
+  VERSION = "1.10.0"
+  TCS_VERSION = "2.7.2"
 end

data/lib/viral_seq.rb

@@ -53,3 +53,5 @@ require "json"
 require "securerandom"
 require "prawn"
 require "colorize"
+require "virust_locator"
+require "shellwords"

data/viral_seq.gemspec

@@ -37,6 +37,9 @@ Gem::Specification.new do |spec|
   # muscle_bio gem required
   spec.add_runtime_dependency "muscle_bio", "= 0.4"
 
+  # virust-locator-ruby required
+  spec.add_runtime_dependency "virust-locator-ruby", "~> 0.3"
+
   # colorize gem required
   spec.add_runtime_dependency "colorize", "~> 0.1"
 
@@ -47,4 +50,6 @@ Gem::Specification.new do |spec|
   spec.add_runtime_dependency "combine_pdf", "~> 1.0", '>= 1.0.0'
 
   spec.requirements << 'R required for some functions'
+
+  spec.add_dependency "shellwords", "~> 0.2"
 end

metadata

@@ -1,15 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: viral_seq
 version: !ruby/object:Gem::Version
-  version: 1.9.0
+  version: 1.10.0
 platform: ruby
 authors:
 - Shuntai Zhou
 - Michael Clark
-autorequire:
 bindir: bin
 cert_chain: []
-date: 2024-11-13 00:00:00.000000000 Z
+date: 1980-01-02 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler
@@ -67,6 +66,20 @@ dependencies:
     - - '='
       - !ruby/object:Gem::Version
         version: '0.4'
+- !ruby/object:Gem::Dependency
+  name: virust-locator-ruby
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.3'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.3'
 - !ruby/object:Gem::Dependency
   name: colorize
   requirement: !ruby/object:Gem::Requirement
@@ -141,6 +154,20 @@ dependencies:
     - - ">="
       - !ruby/object:Gem::Version
         version: 1.0.0
+- !ruby/object:Gem::Dependency
+  name: shellwords
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.2'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.2'
 description: |-
   A Ruby Gem with bioinformatics tools for processing viral NGS data.
                             Specifically for Primer-ID sequencing and HIV drug resistance analysis.
@@ -226,8 +253,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: 1.3.6
 requirements:
 - R required for some functions
-rubygems_version: 3.5.11
-signing_key:
+rubygems_version: 3.6.7
 specification_version: 4
 summary: A Ruby Gem containing bioinformatics tools for processing viral NGS data.
 test_files: []