viral_seq 1.0.0 → 1.0.1

checksums.yaml

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

@@ -1,7 +1,7 @@
 PATH
   remote: .
   specs:
-    viral_seq (1.0.0)
+    viral_seq (1.0.1)
       muscle_bio (~> 0.4)
 
 GEM
@@ -34,4 +34,4 @@ DEPENDENCIES
   viral_seq!
 
 BUNDLED WITH
-   2.0.1
+   2.0.2

data/README.md

@@ -15,8 +15,45 @@ Load all ViralSeq classes by requiring 'viral_seq.rb'
     #!/usr/bin/env ruby
     require 'viral_seq'
 
+## Some Examples
+
+Load nucleotide sequences from a FASTA format sequence file
+
+    my_seqhash = ViralSeq::SeqHash.fa('my_seq_file.fasta')
+
+Make an alignment (using MUSCLE)
+
+    aligned_seqhash = my_seqhash.align
+
+Filter nucleotide sequences with the reference coordinates (HIV Protease)
+
+    qc_seqhash = aligned_seqhash.hiv_seq_qc(2253, 2549, false, :HXB2)
+
+Further filter out sequences with Apobec3g/f hypermutations
+
+    qc_seqhash = qc_seqhash.a3g
+
+Calculate nucleotide diveristy π
+
+    qc_seqhash.pi
+
+Calculate cut-off for minority variants based on Poisson model
+
+    cut_off = qc_seqhash.pm
+
+Examine for drug resistance mutations for HIV PR region
+
+    qc_seqhash.sdrm_hiv_pr(cut_off)
+
 ## Updates
 
+Version 1.0.1-07102019:
+
+    1. Add keyword argument :model to ViralSeq::SeqHashPair#join2.
+    2. Add method ViralSeq::SeqHash#sequence_locator (also: #loc), a function to locate sequences on HIV/SIV reference genomes, as HIV Sequence Locator from LANL.
+    3. Add executable 'locator'. An HIV/SIV sequence locator tool similar to LANL Sequence Locator.
+    4. update documentations
+
 Version 1.0.0-07092019:
 
     1. Rewrote the whole ViralSeq gem, grouping methods into modules and classes under main Module::ViralSeq

data/bin/locator

@@ -0,0 +1,102 @@
+#!/usr/bin/env ruby
+
+require 'viral_seq'
+require 'csv'
+require 'optparse'
+
+module ViralSeq
+  class SeqHash
+
+    def sequence_locator(ref_option = :HXB2)
+      out_array = []
+      dna_seq = self.dna_hash
+      title = self.title
+
+      uniq_dna = dna_seq.uniq_hash
+
+      uniq_dna.each do |seq,names|
+        s = ViralSeq::Sequence.new('',seq)
+        loc = s.locator(ref_option)
+        names.each do |name|
+          out_array << ([title, name, ref_option.to_s] + loc)
+        end
+      end
+      return out_array
+    end # end of locator
+    alias_method :loc, :sequence_locator
+  end
+end
+
+def myparser
+  options = {}
+  OptionParser.new do |opts|
+    opts.banner = "Usage: locator -i [nt_sequence_fasta_file] -o [locator_info_csv_file] -r [reference_genome_option]"
+
+    opts.on('-i', '--infile FASTA_FILE', 'nt sequence file in FASTA format') do |i|
+      options[:infile] = i
+    end
+
+    opts.on('-o', '--outfile CSV_FILE', 'output .csv file for locator info') do |o|
+      options[:outfile] = o
+    end
+
+    opts.on('-r', '--ref_option OPTION', 'reference genome option, choose from `HXB2` (default), `NL43`, `MAC239`') do |o|
+      options[:ref_option] = o.to_sym
+    end
+
+    opts.on("-h", "--help", "Prints this help") do
+      puts opts
+      exit
+    end
+  end.parse!
+  return options
+end
+
+puts "\nSequence Locator (RubyGem::ViralSeq) v1.0.1 by Shuntai Zhou"
+puts "See details at https://github.com/ViralSeq/viral_seq\n"
+puts "Resembling Sequence Locator from LANL (https://www.hiv.lanl.gov/content/sequence/LOCATE/locate.html)\n\n"
+
+ARGV << '-h' if ARGV.size == 0
+
+options = myparser
+
+begin
+  if options[:infile]
+    seq_file = options[:infile]
+  else
+    raise StandardError.new("Input file sequence file not found")
+  end
+
+  if options[:outfile]
+    csv_file = options[:outfile]
+  else
+    raise StandardError.new("Please provide path to output csv file")
+  end
+
+  unless File.exist?(seq_file)
+    raise StandardError.new("Input file sequence file not found")
+  end
+
+  seqs = ViralSeq::SeqHash.fa(seq_file)
+  opt =  options[:ref_option] ? options[:ref_option] : :HXB2
+
+  unless [:HXB2, :NL43, :MAC239].include? opt
+    puts "Reference option #{opt} not recognized, using `:HXB2` as the reference genome."
+    opt = :HXB2
+  end
+
+  locs = seqs.loc(opt)
+  head = ["title", "sequence", "ref", "start", "end", "similarity", "indel", "aligned_input", "aligned_ref"]
+  locs.unshift(head)
+  data = CSV.generate do |csv|
+    locs.each {|loc| csv << loc}
+  end
+
+  File.write(csv_file, data)
+rescue StandardError => e
+  puts e.message
+  puts "\n"
+  ARGV.clear
+  ARGV << '-h'
+  myparser
+end

data/lib/viral_seq/seq_hash.rb

@@ -713,6 +713,43 @@ module ViralSeq
       self.sub(seq_pass)
     end # 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`
+    # @return [Array] two dimensional array `[[],[],[],...]` for each sequence, including the following information:
+    #
+    #     title of the SeqHash object (String)
+    #
+    #     sequence taxa (String)
+    #
+    #     start_location (Integer)
+    #
+    #     end_location (Integer)
+    #
+    #     percentage_of_similarity_to_reference_sequence (Float)
+    #
+    #     containing_indel? (Boolean)
+    #
+    #     aligned_input_sequence (String)
+    #
+    #     aligned_reference_sequence (String)
+    # @see https://www.hiv.lanl.gov/content/sequence/LOCATE/locate.html LANL Sequence Locator
+    def sequence_locator(ref_option = :HXB2)
+      out_array = []
+      dna_seq = self.dna_hash
+      title = self.title
+
+      uniq_dna = dna_seq.uniq_hash
+
+      uniq_dna.each do |seq,names|
+        s = ViralSeq::Sequence.new('',seq)
+        loc = s.locator(ref_option)
+        names.each do |name|
+          out_array << ([title, name, ref_option.to_s] + loc)
+        end
+      end
+      return out_array
+    end # end of locator
+    alias_method :loc, :sequence_locator
 
     # Remove squences with residual offspring Primer IDs.
     #   Compare PID with sequences which have identical sequences.

data/lib/viral_seq/seq_hash_pair.rb

@@ -139,10 +139,10 @@ module ViralSeq
     #   my_seqhashpair = ViralSeq::SeqHashPair.new(paired_seq2)
     #   my_seqhashpair.join2.dna_hash
     #   => {">pair4"=>"AAAGGGGGGGGGGTT", ">pair5"=>"AAAAAAGGGGTTTTT", ">pair6"=>"AAACAAGGGGTTTTT"}
-    #   my_seqhashpair.join2(:indiv).dna_hash
+    #   my_seqhashpair.join2(model :indiv).dna_hash
     #   => {">pair4"=>"AAAGGGGGGGTT", ">pair5"=>"AAAAAAGGGGTTTTT", ">pair6"=>"AAACAAGGGGTTTTT"}
 
-    def join2(model = :con, diff = 0.0)
+    def join2(model: :con, diff: 0.0)
       seq_pair_hash = self.dna_hash
       begin
         raise ArgumentError.new(":diff has to be float or integer, input #{diff} invalid.") unless (diff.is_a? Integer or diff.is_a? Float)

data/lib/viral_seq/sequence.rb

@@ -142,13 +142,20 @@ module ViralSeq
     #   # 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 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
-    #   #   start_location (Integer)
-    #   #   end_location (Integer)
-    #   #   percentage_of_similarity_to_reference_sequence (Float)
-    #   #   containing_indel? (Boolean)
-    #   #   aligned_input_sequence (String)
-    #   #   aligned_reference_sequence (String)
+    # @return [Array] an array of the following info:
+    #
+    #   start_location (Integer)
+    #
+    #   end_location (Integer)
+    #
+    #   percentage_of_similarity_to_reference_sequence (Float)
+    #
+    #   containing_indel? (Boolean)
+    #
+    #   aligned_input_sequence (String)
+    #
+    #   aligned_reference_sequence (String)
+    #
     # @example identify the location of the input sequence on the NL43 genome
     #   sequence = 'AGCAGATGATACAGTATTAGAAGAAATAAATTTGCCAGGAAGATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAATATGATC'
     #   s = ViralSeq::Sequence.new('my_sequence', sequence)
@@ -349,7 +356,7 @@ module ViralSeq
     #   s = ViralSeq::Sequence.new('my_seq', seq)
     #   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)
       l1 = loc[0]

data/lib/viral_seq/version.rb

@@ -2,5 +2,5 @@
 # version info and histroy
 
 module ViralSeq
-  VERSION = "1.0.0"
+  VERSION = "1.0.1"
 end

data/viral_seq.gemspec

@@ -20,8 +20,8 @@ Gem::Specification.new do |spec|
   spec.files         = Dir.chdir(File.expand_path('..', __FILE__)) do
     `git ls-files -z`.split("\x0").reject { |f| f.match(%r{^(test|spec|features)/}) }
   end
-  spec.bindir        = "exe"
-  # spec.executables   = spec.files.grep(%r{^exe/}) { |f| File.basename(f) }\
+  spec.bindir        = "bin"
+  spec.executables   = spec.files.grep(%r{^bin/}) { |f| File.basename(f) }
   spec.require_paths = ["lib"]
   spec.post_install_message = "Thanks for installing!"
 
@@ -31,8 +31,5 @@ Gem::Specification.new do |spec|
 
   # muscle_bio gem required
   spec.add_runtime_dependency "muscle_bio", "~> 0.4"
-
-
-  spec.requirements << 'MUSCLE (http://www.drive5.com/muscle) required for some functions'
   spec.requirements << 'R required for some functions'
 end

metadata

@@ -1,15 +1,15 @@
 --- !ruby/object:Gem::Specification
 name: viral_seq
 version: !ruby/object:Gem::Version
-  version: 1.0.0
+  version: 1.0.1
 platform: ruby
 authors:
 - Shuntai Zhou
 - Michael Clark
 autorequire: 
-bindir: exe
+bindir: bin
 cert_chain: []
-date: 2019-07-09 00:00:00.000000000 Z
+date: 2019-07-10 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler
@@ -73,7 +73,8 @@ description: |-
 email:
 - shuntai.zhou@gmail.com
 - clarkmu@gmail.com
-executables: []
+executables:
+- locator
 extensions: []
 extra_rdoc_files: []
 files:
@@ -86,8 +87,7 @@ files:
 - LICENSE.txt
 - README.md
 - Rakefile
-- bin/console
-- bin/setup
+- bin/locator
 - lib/viral_seq.rb
 - lib/viral_seq/Integer.rb
 - lib/viral_seq/constant.rb
@@ -124,7 +124,6 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements:
-- MUSCLE (http://www.drive5.com/muscle) required for some functions
 - R required for some functions
 rubygems_version: 3.0.3
 signing_key: 

data/bin/console

@@ -1,14 +0,0 @@
-#!/usr/bin/env ruby
-
-require "bundler/setup"
-require "viral_seq"
-
-# You can add fixtures and/or initialization code here to make experimenting
-# with your gem easier. You can also use a different console, if you like.
-
-# (If you use this, don't forget to add pry to your Gemfile!)
-# require "pry"
-# Pry.start
-
-require "irb"
-IRB.start(__FILE__)

data/bin/setup

@@ -1,8 +0,0 @@
-#!/usr/bin/env bash
-set -euo pipefail
-IFS=$'\n\t'
-set -vx
-
-bundle install
-
-# Do any other automated setup that you need to do here