orf_finder 0.1.2 → 0.1.4

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 8f48e6149b1ea707c2b01bc7aee4365170ffad5c
-  data.tar.gz: 9b5bc776cefd1a134f235523191a5fe8890c0f01
+  metadata.gz: ae74e9c90fae051a04bfafe5930dfd240fd44a9f
+  data.tar.gz: dd333404439214b4584a4fe99b70f737c3acf269
 SHA512:
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+  data.tar.gz: 5a0fa12da4db509ac1d1e090bd4778aff7521ec3b565a0ab8c8265f029440e8c7e8d33061f30be91f70a83f11282b070752c6b82bcbcf2e07f29a870fb1fa321

data/lib/orf.rb

@@ -9,10 +9,11 @@ class ORF
   #
   include ORF::ORFCommon
   #
+  DEFAULT_CODON_TABLE = 1
   #
   attr_reader :logger, :options, :seq, :sequence
   attr_writer :options
-
+  #
   # class initializer that normalizes sequence to Bio::Sequence,
   #  merges given options and creates logger
   def initialize(sequence, options = {}, logger_file = nil)
@@ -47,20 +48,20 @@ class ORF
 
   #
   # return aminoacid sequence
-  def aa
+  def aa(codon_table = DEFAULT_CODON_TABLE)
     # return already generated aa sequence
     return @res_aa unless @res_aa.nil?
     # save result
-    l = longest
+    l = longest(codon_table)
     return l if @res_aa.nil?
     @res_aa
   end
 
   #
   # return nucletotide sequence
-  def nt
+  def nt(codon_table = DEFAULT_CODON_TABLE)
     return @res_nt unless @res_nt.nil?
-    longest
+    longest(codon_table)
   end
 
   #
@@ -128,7 +129,7 @@ class ORF
   #
   # get the longest sequence in each frame and translate
   #  to aminoacid
-  def longest
+  def longest(codon_table = DEFAULT_CODON_TABLE)
     # run find method if search has not been done
     find if @orf.nil?
     #
@@ -144,7 +145,11 @@ class ORF
     # translate to aa sequence
     unless @res_nt.nil?
       @res_nt.each do |key, val|
-        res_aa[key] = val.translate
+        res_aa[key] = if val.nil? || val.empty?
+                        ''
+                      else
+                        val.translate(1, codon_table)
+                      end
       end
     end
     @res_aa = res_aa

data/lib/orf_finder.rb

@@ -4,6 +4,8 @@ require_relative 'orf'
 #
 # Wrapper class that processes the direct and reverse sequences
 class ORFFinder
+  #
+  attr_reader :codon_table
   #
   DEFAULT_OPTIONS = { start: %w(atg),
                       stop:  %w(tag taa tga),
@@ -12,7 +14,7 @@ class ORFFinder
                       min: 6,
                       debug: false }
 
-  def initialize(sequence, options = {}, logger = nil)
+  def initialize(sequence, codon_table = 1, options = {}, logger = nil)
     #
     sequence = Bio::Sequence::NA.new(sequence) if sequence.class == String
     options = DEFAULT_OPTIONS.merge(options.nil? ? {} : options)
@@ -20,15 +22,18 @@ class ORFFinder
     @output = {}
     @output[:direct] = ORF.new(sequence, options, logger) if options[:direct]
     #
-    return unless options[:reverse]
-    compl = sequence.complement
-    @output[:reverse] = ORF.new(compl, options, logger)
+    if options[:reverse]
+      compl = sequence.complement
+      @output[:reverse] = ORF.new(compl, options, logger)
+    end
+    #
+    @codon_table = codon_table
   end
 
   def nt
     res = {}
     @output.each do |key, value|
-      res[key] = value.nt
+      res[key] = value.nt(@codon_table)
       res[key][:sequence] = value.seq
     end
     res
@@ -37,8 +42,8 @@ class ORFFinder
   def aa
     res = {}
     @output.each do |key, value|
-      res[key] = value.aa
-      res[key][:sequence] = value.sequence.translate.to_s
+      res[key] = value.aa(@codon_table)
+      res[key][:sequence] = value.sequence.translate(@codon_table).to_s
     end
     res
   end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: orf_finder
 version: !ruby/object:Gem::Version
-  version: 0.1.2
+  version: 0.1.4
 platform: ruby
 authors:
 - André Veríssimo