viral_seq 1.0.4 → 1.0.9

data/lib/viral_seq/seq_hash_pair.rb

@@ -7,7 +7,7 @@ module ViralSeq
   # @example join the paired-end sequences with an overlap of 100 bp
   #   my_seqhashpair.join1(100)
   # @example join the paired-end sequences with unknown overlap, each pair of sequences has its own overlap size
-  #   my_seqhashpair.join1(:indiv)
+  #   my_seqhashpair.join2(model: :indiv)
 
   class SeqHashPair
 
@@ -104,17 +104,21 @@ module ViralSeq
       raise ArgumentError.new(":overlap has to be Integer, input #{overlap} invalid.") unless overlap.is_a? Integer
       raise ArgumentError.new(":diff has to be float or integer, input #{diff} invalid.") unless (diff.is_a? Integer or diff.is_a? Float)
       joined_seq = {}
-      seq_pair_hash.each do |seq_name, seq_pair|
+      seq_pair_hash.uniq_hash.each do |seq_pair, seq_names|
         r1_seq = seq_pair[0]
         r2_seq = seq_pair[1]
         if overlap.zero?
-          joined_seq[seq_name] = r1_seq + r2_seq
+          joined_sequence = r1_seq + r2_seq
         elsif r1_seq[-overlap..-1].compare_with(r2_seq[0,overlap]) <= (overlap * diff)
-          joined_seq[seq_name] = r1_seq + r2_seq[overlap..-1]
+          joined_sequence= r1_seq + r2_seq[overlap..-1]
         else
           next
         end
+        seq_names.each do |seq_name|
+          joined_seq[seq_name] = joined_sequence
+        end
       end
+
       joined_seq_hash = ViralSeq::SeqHash.new
       joined_seq_hash.dna_hash = joined_seq
       joined_seq_hash.title = self.title + "_joined"
@@ -139,7 +143,7 @@ module ViralSeq
     #   my_seqhashpair = ViralSeq::SeqHashPair.new(paired_seq2)
     #   my_seqhashpair.join2.dna_hash
     #   => {">pair4"=>"AAAGGGGGGGGGGTT", ">pair5"=>"AAAAAAGGGGTTTTT", ">pair6"=>"AAACAAGGGGTTTTT"}
-    #   my_seqhashpair.join2(model :indiv).dna_hash
+    #   my_seqhashpair.join2(model: :indiv).dna_hash
     #   => {">pair4"=>"AAAGGGGGGGTT", ">pair5"=>"AAAAAAGGGGTTTTT", ">pair6"=>"AAACAAGGGGTTTTT"}
 
     def join2(model: :con, diff: 0.0)
@@ -207,7 +211,7 @@ module ViralSeq
     # {minimal overlap set to 4. }
     def overlap_matrix(sequence1, sequence2)
       min_overlap = 4
-      max_overlap = [sequence1.size, sequence2.size].max
+      max_overlap = [sequence1.size, sequence2.size].min
       matrix_hash = {}
       (min_overlap..max_overlap).each do |overlap|
         matrix_hash[overlap] = sequence1[-overlap..-1].compare_with(sequence2[0, overlap])

data/lib/viral_seq/version.rb

@@ -2,5 +2,6 @@
 # version info and histroy
 
 module ViralSeq
-  VERSION = "1.0.4"
+  VERSION = "1.0.9"
+  TCS_VERSION = "2.0.1"
 end

data/viral_seq.gemspec

@@ -26,10 +26,14 @@ Gem::Specification.new do |spec|
   spec.post_install_message = "Thanks for installing!"
 
   spec.add_development_dependency "bundler", "~> 2.0"
-  spec.add_development_dependency "rake", "~> 10.0"
+  spec.add_development_dependency "rake", "~> 13.0"
   spec.add_development_dependency "rspec", "~> 3.0"
 
   # muscle_bio gem required
   spec.add_runtime_dependency "muscle_bio", "~> 0.4"
+
+  # colorize gem required
+  spec.add_runtime_dependency "colorize", "~> 0.1"
+
   spec.requirements << 'R required for some functions'
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: viral_seq
 version: !ruby/object:Gem::Version
-  version: 1.0.4
+  version: 1.0.9
 platform: ruby
 authors:
 - Shuntai Zhou
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2019-07-10 00:00:00.000000000 Z
+date: 2020-07-19 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler
@@ -31,14 +31,14 @@ dependencies:
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '10.0'
+        version: '13.0'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '10.0'
+        version: '13.0'
 - !ruby/object:Gem::Dependency
   name: rspec
   requirement: !ruby/object:Gem::Requirement
@@ -67,6 +67,20 @@ dependencies:
     - - "~>"
       - !ruby/object:Gem::Version
         version: '0.4'
+- !ruby/object:Gem::Dependency
+  name: colorize
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.1'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.1'
 description: |-
   A Ruby Gem with bioinformatics tools for processing viral NGS data.
                             Specifically for Primer-ID sequencing and HIV drug resistance analysis.
@@ -75,6 +89,8 @@ email:
 - clarkmu@gmail.com
 executables:
 - locator
+- tcs
+- tcs_json_generator
 extensions: []
 extra_rdoc_files: []
 files:
@@ -88,6 +104,8 @@ files:
 - README.md
 - Rakefile
 - bin/locator
+- bin/tcs
+- bin/tcs_json_generator
 - lib/viral_seq.rb
 - lib/viral_seq/constant.rb
 - lib/viral_seq/enumerable.rb
@@ -124,7 +142,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements:
 - R required for some functions
-rubygems_version: 3.0.3
+rubygems_version: 3.1.2
 signing_key: 
 specification_version: 4
 summary: A Ruby Gem containing bioinformatics tools for processing viral NGS data.