viral_seq 1.0.4 → 1.0.5

checksums.yaml

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

@@ -1,7 +1,7 @@
 PATH
   remote: .
   specs:
-    viral_seq (1.0.2)
+    viral_seq (1.0.5)
       muscle_bio (~> 0.4)
 
 GEM

data/README.md

@@ -17,36 +17,46 @@ Load all ViralSeq classes by requiring 'viral_seq.rb'
 
 ## Some Examples
 
-Load nucleotide sequences from a FASTA format sequence file
+### Load nucleotide sequences from a FASTA format sequence file
 
     my_seqhash = ViralSeq::SeqHash.fa('my_seq_file.fasta')
 
-Make an alignment (using MUSCLE)
+### Make an alignment (using MUSCLE)
 
     aligned_seqhash = my_seqhash.align
 
-Filter nucleotide sequences with the reference coordinates (HIV Protease)
+### 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
+### Further filter out sequences with Apobec3g/f hypermutations
 
     qc_seqhash = qc_seqhash.a3g
 
-Calculate nucleotide diveristy π
+### Calculate nucleotide diveristy π
 
     qc_seqhash.pi
 
-Calculate cut-off for minority variants based on Poisson model
+### Calculate cut-off for minority variants based on Poisson model
 
     cut_off = qc_seqhash.pm
 
-Examine for drug resistance mutations for HIV PR region
+### Examine for drug resistance mutations for HIV PR region
 
     qc_seqhash.sdrm_hiv_pr(cut_off)
 
+### Use executable `locator` to get the coordinates of the sequences on HIV/SIV reference genome from a FASTA file through a terminal
+
+    $ locator -i sequence.fasta -o sequence.fasta.csv
+
 ## Updates
 
+Version 1.0.5-07112019:
+
+    1. Update ViralSeq::SeqHash#sequence_locator.
+       Program will try to determine the direction (`+` or `-` of the query sequence)
+    2. update executable `locator` to have a column of `direction` in output .csv file
+
 Version 1.0.4-07102019:
 
     1. Use home directory (Dir.home) instead of the directory of the script file for temp MUSCLE file.

data/bin/locator

@@ -4,29 +4,6 @@ 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|
@@ -36,7 +13,7 @@ def myparser
       options[:infile] = i
     end
 
-    opts.on('-o', '--outfile CSV_FILE', 'output .csv file for locator info') do |o|
+    opts.on('-o', '--outfile CSV_FILE', "output .csv file for locator info, default as \#\{infile\}.csv") do |o|
       options[:outfile] = o
     end
 
@@ -48,11 +25,17 @@ def myparser
       puts opts
       exit
     end
+
+    opts.on("-v", "--version", "Version number of RubyGem::ViralSeq") do
+      puts opts
+      exit
+    end
+
   end.parse!
   return options
 end
 
-puts "\nSequence Locator (RubyGem::ViralSeq) #{ViralSeq::VERSION} by Shuntai Zhou"
+puts "\nSequence Locator (RubyGem::ViralSeq Version #{ViralSeq::VERSION}) 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"
 
@@ -70,7 +53,7 @@ begin
   if options[:outfile]
     csv_file = options[:outfile]
   else
-    raise StandardError.new("Please provide path to output csv file")
+    csv_file = seq_file + ".csv"
   end
 
   unless File.exist?(seq_file)
@@ -86,7 +69,7 @@ begin
   end
 
   locs = seqs.loc(opt)
-  head = ["title", "sequence", "ref", "start", "end", "similarity", "indel", "aligned_input", "aligned_ref"]
+  head = ["title", "sequence", "ref", "direction", "start", "end", "similarity", "indel", "aligned_input", "aligned_ref"]
   locs.unshift(head)
   data = CSV.generate do |csv|
     locs.each {|loc| csv << loc}

data/lib/viral_seq/seq_hash.rb

@@ -729,6 +729,8 @@ module ViralSeq
     #
     #     containing_indel? (Boolean)
     #
+    #     direction ('forward' or 'reverse')
+    #
     #     aligned_input_sequence (String)
     #
     #     aligned_reference_sequence (String)
@@ -742,9 +744,13 @@ module ViralSeq
 
       uniq_dna.each do |seq,names|
         s = ViralSeq::Sequence.new('',seq)
-        loc = s.locator(ref_option)
+        loc1 = s.locator(ref_option)
+        s.rc!
+        loc2 = s.locator(ref_option)
+        loc1[2] >= loc2[2] ? (direction = :+; loc = loc1): (direction = :-; loc = loc2)
+    
         names.each do |name|
-          out_array << ([title, name, ref_option.to_s] + loc)
+          out_array << ([title, name, ref_option.to_s, direction.to_s] + loc)
         end
       end
       return out_array

data/lib/viral_seq/version.rb

@@ -2,5 +2,5 @@
 # version info and histroy
 
 module ViralSeq
-  VERSION = "1.0.4"
+  VERSION = "1.0.5"
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: viral_seq
 version: !ruby/object:Gem::Version
-  version: 1.0.4
+  version: 1.0.5
 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: 2019-07-11 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler