viral_seq 1.0.13 → 1.2.0

data/lib/viral_seq/tcs_core.rb

@@ -102,9 +102,9 @@ module ViralSeq
       end
 
       # sort array of file names to determine if there is potential errors
-      # input name_array array of file names
-      # output hash { }
-      # need to change for each file name have an error code. and a bool to show if all pass
+      # @param name_array [Array] array of file names
+      # @return [hash] name check results
+
       def validate_file_name(name_array)
         errors = {
                    file_type_error: [] ,
@@ -165,6 +165,13 @@ module ViralSeq
           end
         end
 
+        file_name_with_lib_name = {}
+        passed_libs.each do |lib_name, files|
+          files.each do |f|
+            file_name_with_lib_name[f] = lib_name
+          end
+        end
+
         passed_names = []
 
         passed_libs.values.each { |names| passed_names += names}
@@ -175,7 +182,27 @@ module ViralSeq
           pass = true
         end
 
-        return { errors: errors, all_pass: pass, passed_names: passed_names, passed_libs: passed_libs }
+        file_name_with_error_type = {}
+
+        errors.each do |type, files|
+          files.each do |f|
+            file_name_with_error_type[f] ||= []
+            file_name_with_error_type[f] << type.to_s.tr("_", "\s")
+          end
+        end
+
+        file_check = []
+
+        name_array.each do |name|
+          file_check_hash = {}
+          file_check_hash[:fileName] = name
+          file_check_hash[:errors] = file_name_with_error_type[name]
+          file_check_hash[:libName] = file_name_with_lib_name[name]
+
+          file_check << file_check_hash
+        end
+
+        return { allPass: pass, files: file_check }
       end
 
       # filter r1 raw sequences for non-specific primers.
@@ -278,7 +305,9 @@ module ViralSeq
       end
 
       def general_filter(seq)
-        if seq[1..-2] =~ /N/ # sequences with ambiguities except the 1st and last position removed
+        if seq.size < $platform_sequencing_length
+          return false
+        elsif seq[1..-2] =~ /N/ # sequences with ambiguities except the 1st and last position removed
           return false
         elsif seq =~ /A{11}/ # a string of poly-A indicates adaptor sequence
           return false

data/lib/viral_seq/tcs_dr.rb

@@ -0,0 +1,71 @@
+module ViralSeq
+
+  class TcsDr
+    PARAMS = {:platform_error_rate=>0.02,
+               :primer_pairs=>
+                [{:region=>"RT",
+                  :cdna=>
+                   "GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTNNNNNNNNNNNCAGTCACTATAGGCTGTACTGTCCATTTATC",
+                  :forward=>
+                   "GCCTCCCTCGCGCCATCAGAGATGTGTATAAGAGACAGNNNNGGCCATTGACAGAAGAAAAAATAAAAGC",
+                  :majority=>0.5,
+                  :end_join=>true,
+                  :end_join_option=>1,
+                  :overlap=>0,
+                  :TCS_QC=>true,
+                  :ref_genome=>"HXB2",
+                  :ref_start=>2648,
+                  :ref_end=>3257,
+                  :indel=>false,
+                  :trim=>false},
+                 {:region=>"PR",
+                  :cdna=>
+                   "GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTNNNNNNNNNCAGTTTAACTTTTGGGCCATCCATTCC",
+                  :forward=>
+                   "GCCTCCCTCGCGCCATCAGAGATGTGTATAAGAGACAGNNNNTCAGAGCAGACCAGAGCCAACAGCCCCA",
+                  :majority=>0.5,
+                  :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=>
+                   "GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTNNNNNNNNNNNATCGAATACTGCCATTTGTACTGC",
+                  :forward=>"GCCTCCCTCGCGCCATCAGAGATGTGTATAAGAGACAGNNNNAAAAGGAGAAGCCATGCATG",
+                  :majority=>0.5,
+                  :end_join=>true,
+                  :end_join_option=>3,
+                  :overlap=>171,
+                  :TCS_QC=>true,
+                  :ref_genome=>"HXB2",
+                  :ref_start=>4384,
+                  :ref_end=>4751,
+                  :indel=>false,
+                  :trim=>false},
+                 {:region=>"V1V3",
+                  :cdna=>
+                   "GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTNNNNNNNNNNNCAGTCCATTTTGCTYTAYTRABVTTACAATRTGC",
+                  :forward=>
+                   "GCCTCCCTCGCGCCATCAGAGATGTGTATAAGAGACAGNNNNTTATGGGATCAAAGCCTAAAGCCATGTGTA",
+                  :majority=>0.5,
+                  :end_join=>true,
+                  :end_join_option=>1,
+                  :overlap=>0,
+                  :TCS_QC=>true,
+                  :ref_genome=>"HXB2",
+                  :ref_start=>6585,
+                  :ref_end=>7208,
+                  :indel=>true,
+                  :trim=>false}
+                  ]
+                }
+  end
+
+end

data/lib/viral_seq/tcs_json.rb

@@ -13,6 +13,22 @@ module ViralSeq
         print '> '
         param[:raw_sequence_dir] = gets.chomp.rstrip
 
+        puts "Choose MiSeq Platform (1-3):\n1. 150x7x150\n2. 250x7x250\n3. 300x7x300 (default)"
+        print "> "
+        pf_option = gets.chomp.rstrip
+        # while ![1,2,3].include?(pf_option.to_i)
+        #   print "Entered MiSeq Platform #{pf_option.red.bold} not valid (choose 1-3), try again\n> "
+        #   pf_option = gets.chomp.rstrip
+        # end
+        case pf_option.to_i
+        when 1
+          param[:platform_format] = 150
+        when 2
+          param[:platform_format] = 250
+        else
+          param[:platform_format] = 300
+        end
+
         puts 'Enter the estimated platform error rate (for TCS cut-off calculation), default as ' + '0.02'.red.bold
         print '> '
         input_error = gets.chomp.rstrip.to_f
@@ -52,12 +68,12 @@ module ViralSeq
           if ej =~ /y|yes/i
             data[:end_join] = true
 
-            print "End-join option? Choose from (1-4):\n
-            1: simple join, no overlap
-            2: known overlap \n
-            3: unknow overlap, use sample consensus to determine overlap, all sequence pairs have same overlap\n
-            4: unknow overlap, determine overlap by individual sequence pairs, sequence pairs can have different overlap\n
-            > "
+            puts "End-join option? Choose from (1-4):"
+            puts "1: simple join, no overlap"
+            puts "2: known overlap"
+            puts "3: unknow overlap, use sample consensus to determine overlap, all sequence pairs have same overlap"
+            puts "4: unknow overlap, determine overlap by individual sequence pairs, sequence pairs can have different overlap"
+            print "> "
             ej_option = gets.chomp.rstrip
             while ![1,2,3,4].include?(ej_option.to_i)
               puts "Entered end-join option #{ej_option.red.bold} not valid (choose 1-4), try again"
@@ -138,7 +154,12 @@ module ViralSeq
         if save_option =~ /y|yes/i
           print "Path to save JSON file:\n> "
           path = gets.chomp.rstrip
-          File.open(path, 'w') {|f| f.puts JSON.pretty_generate(param)}
+          while !validate_path_name(path)
+            print "Entered path no valid, try again.\n".red.bold
+            print "Path to save JSON file:\n> "
+            path = gets.chomp.rstrip
+          end
+          File.open(validate_path_name(path), 'w') {|f| f.puts JSON.pretty_generate(param)}
         end
 
         print "\nDo you wish to execute tcs pipeline with the input params now? Y/N \n> "
@@ -147,7 +168,7 @@ module ViralSeq
         if rsp =~ /y/i
           return param
         else
-          abort "Params json file generated. You can execute tcs pipeline using `tcs -p [params.json]`"
+          abort "Params json file generated. You can execute tcs pipeline using `tcs -p [params.json]`".blue
         end
 
       end
@@ -172,7 +193,17 @@ module ViralSeq
               when 3
                 :MAC239
               end
-      end
-    end
+      end # end of get_ref
+
+      def validate_path_name(path)
+        if path.empty?
+          return false
+        elsif File.directory? path
+          return File.join(path, 'params.json')
+        elsif File.directory?(File.dirname(path))
+          return path
+        end
+      end # end of validate_path_name
+    end # end of class << self
   end # end TcsJson
 end # end main module

data/lib/viral_seq/version.rb

@@ -2,6 +2,6 @@
 # version info and histroy
 
 module ViralSeq
-  VERSION = "1.0.13"
-  TCS_VERSION = "2.1.1"
+  VERSION = "1.2.0"
+  TCS_VERSION = "2.3.1"
 end

data/viral_seq.gemspec

@@ -29,11 +29,22 @@ Gem::Specification.new do |spec|
   spec.add_development_dependency "rake", "~> 13.0"
   spec.add_development_dependency "rspec", "~> 3.0"
 
+  # This gem will work with Ruby version 2.5.0 or greater...
+  spec.required_ruby_version = '>= 2.5'
+  # This gem will work with RubyGem version 1.3.6 or greater...
+  spec.required_rubygems_version = '>= 1.3.6'
+
   # muscle_bio gem required
   spec.add_runtime_dependency "muscle_bio", "~> 0.4"
 
   # colorize gem required
   spec.add_runtime_dependency "colorize", "~> 0.1"
 
+  spec.add_runtime_dependency "prawn", "~> 2.3", '>= 2.3.0'
+
+  spec.add_runtime_dependency "prawn-table", "~> 0.2", '>= 0.2.0'
+
+  spec.add_runtime_dependency "combine_pdf", "~> 1.0", '>= 1.0.0'
+
   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: 1.0.13
+  version: 1.2.0
 platform: ruby
 authors:
 - Shuntai Zhou
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2021-03-04 00:00:00.000000000 Z
+date: 2021-05-11 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler
@@ -81,6 +81,66 @@ dependencies:
     - - "~>"
       - !ruby/object:Gem::Version
         version: '0.1'
+- !ruby/object:Gem::Dependency
+  name: prawn
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '2.3'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 2.3.0
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '2.3'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 2.3.0
+- !ruby/object:Gem::Dependency
+  name: prawn-table
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.2'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 0.2.0
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.2'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 0.2.0
+- !ruby/object:Gem::Dependency
+  name: combine_pdf
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.0'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.0.0
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.0'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.0.0
 description: |-
   A Ruby Gem with bioinformatics tools for processing viral NGS data.
                             Specifically for Primer-ID sequencing and HIV drug resistance analysis.
@@ -90,6 +150,8 @@ email:
 executables:
 - locator
 - tcs
+- tcs_log
+- tcs_sdrm
 extensions: []
 extra_rdoc_files: []
 files:
@@ -104,6 +166,12 @@ files:
 - Rakefile
 - bin/locator
 - bin/tcs
+- bin/tcs_log
+- bin/tcs_sdrm
+- docs/assets/img/cover.jpg
+- docs/dr.json
+- docs/sample_miseq_data/hivdr_control/r1.fastq.gz
+- docs/sample_miseq_data/hivdr_control/r2.fastq.gz
 - lib/viral_seq.rb
 - lib/viral_seq/constant.rb
 - lib/viral_seq/enumerable.rb
@@ -112,6 +180,7 @@ files:
 - lib/viral_seq/math.rb
 - lib/viral_seq/muscle.rb
 - lib/viral_seq/pid.rb
+- lib/viral_seq/recency.rb
 - lib/viral_seq/ref_seq.rb
 - lib/viral_seq/rubystats.rb
 - lib/viral_seq/sdrm.rb
@@ -120,6 +189,7 @@ files:
 - lib/viral_seq/sequence.rb
 - lib/viral_seq/string.rb
 - lib/viral_seq/tcs_core.rb
+- lib/viral_seq/tcs_dr.rb
 - lib/viral_seq/tcs_json.rb
 - lib/viral_seq/version.rb
 - viral_seq.gemspec
@@ -135,12 +205,12 @@ required_ruby_version: !ruby/object:Gem::Requirement
   requirements:
   - - ">="
     - !ruby/object:Gem::Version
-      version: '0'
+      version: '2.5'
 required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
   - - ">="
     - !ruby/object:Gem::Version
-      version: '0'
+      version: 1.3.6
 requirements:
 - R required for some functions
 rubygems_version: 3.2.2