parse_fasta 1.3.0 → 1.4.0

checksums.yaml

@@ -1,7 +1,7 @@
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data/README.md

@@ -29,7 +29,7 @@ and over.
 ## Documentation ##
 
 Checkout
-[parse_fasta docs](http://rubydoc.info/gems/parse_fasta/1.3.0/frames)
+[parse_fasta docs](http://rubydoc.info/gems/parse_fasta/1.4.0/frames)
 to see the full documentation.
 
 ## Usage ##
@@ -58,6 +58,13 @@ Now we can parse fastq files as well!
 
 ## Versions ##
 
+### 1.4.0 ###
+
+Added methods:
+
+    Sequence.base_counts
+	Sequence.base_frequencies
+
 ### 1.3.0 ###
 
 Add additional functionality to `each_record` method.

data/lib/parse_fasta/sequence.rb

@@ -25,7 +25,8 @@ class Sequence < String
   # Calculates GC content by dividing count of G + C divided by count
   # of G + C + T + A + U. If there are both T's and U's in the
   # Sequence, things will get weird, but then again, that wouldn't
-  # happen, now would it!
+  # happen, now would it! Ambiguous bases are ignored similar to
+  # BioRuby.
   #
   # @example Get GC of a Sequence
   #   Sequence.new('ACTg').gc #=> 0.5
@@ -46,7 +47,77 @@ class Sequence < String
     u = s.count('u')
     
     return 0 if c + g + t + a + u == 0
-    return (c + g).quo(c + g + t + a + u).to_f
+    return (c + g) / (c + g + t + a + u).to_f
   end
 
+  # Returns a map of base counts
+  #
+  # This method will check if the sequence is DNA or RNA and return a
+  # count map appropriate for each. If a truthy argument is given, the
+  # count of ambiguous bases will be returned as well.
+  #
+  # If a sequence has both T and U present, will warn the user and
+  # keep going. Will return a map with counts of both, however.
+  #
+  # @example Get base counts of DNA sequence without ambiguous bases
+  #   Sequence.new('AcTGn').base_counts
+  #   #=> { a: 1, c: 1, t: 1, g: 1 }
+  # @example Get base counts of DNA sequence with ambiguous bases
+  #   Sequence.new('AcTGn').base_counts(true)
+  #   #=> { a: 1, c: 1, t: 1, g: 1, n: 1 }
+  # @example Get base counts of RNA sequence without ambiguous bases
+  #   Sequence.new('AcUGn').base_counts
+  #   #=> { a: 1, c: 1, u: 1, g: 1 }
+  # @example Get base counts of DNA sequence with ambiguous bases
+  #   Sequence.new('AcUGn').base_counts(true)
+  #   #=> { a: 1, c: 1, u: 1, g: 1, n: 1 }
+  #
+  # @return [Hash] A hash with base as key, count as value
+  def base_counts(count_ambiguous_bases=nil)
+    s = self.downcase
+    t = s.count('t')
+    u = s.count('u')
+    counts = { a: s.count('a'), c: s.count('c'), g: s.count('g') }
+
+    if t > 0 && u == 0
+      counts[:t] = t
+    elsif t == 0 && u > 0
+      counts[:u] = u
+    elsif t > 0 && u > 0
+      warn('ERROR: A sequence contains both T and U')
+      counts[:t], counts[:u] = t, u
+    end
+    
+    counts[:n] = s.count('n') if count_ambiguous_bases
+    
+    counts
+  end
+
+  # Returns a map of base frequencies
+  #
+  # Counts bases with the `base_counts` method, then divides each
+  # count by the total bases counted to give frequency for each
+  # base. If a truthy argument is given, ambiguous bases will be
+  # included in the total and their frequency reported. Can discern
+  # between DNA and RNA.
+  #
+  # If default or falsy argument is given, ambiguous bases will not be
+  # counted in the total base count and their frequency will not be
+  # given.
+  #
+  # @example Get base frequencies of DNA sequence without ambiguous bases
+  #   Sequence.new('AcTGn').base_counts
+  #   #=> { a: 0.25, c: 0.25, t: 0.25, g: 0.25 }
+  # @example Get base counts of DNA sequence with ambiguous bases
+  #   Sequence.new('AcTGn').base_counts(true)
+  #   #=> { a: 0.2, c: 0.2, t: 0.2, g: 0.2, n: 0.2 }
+  #
+  # @return [Hash] A hash with base as key, frequency as value
+  def base_frequencies(count_ambiguous_bases=nil)
+    base_counts = self.base_counts(count_ambiguous_bases)
+    total_bases = base_counts.values.reduce(:+).to_f
+    base_freqs = 
+      base_counts.map { |base, count| [base, count/total_bases] }.flatten
+    Hash[*base_freqs]
+  end
 end

data/lib/parse_fasta/version.rb

@@ -17,5 +17,5 @@
 # along with parse_fasta.  If not, see <http://www.gnu.org/licenses/>.
 
 module ParseFasta
-  VERSION = "1.3.0"
+  VERSION = "1.4.0"
 end

data/parse_fasta.gemspec

@@ -9,7 +9,7 @@ Gem::Specification.new do |spec|
   spec.authors       = ["Ryan Moore"]
   spec.email         = ["moorer@udel.edu"]
   spec.summary       = %q{Easy-peasy parsing of fasta files}
-  spec.description   = %q{So you want to parse a fasta file...}
+  spec.description   = %q{So you want to parse a fasta or fastq file...}
   spec.homepage      = "https://github.com/mooreryan/parse_fasta"
   spec.license       = "GPLv3: http://www.gnu.org/licenses/gpl.txt"
 

data/spec/lib/sequence_spec.rb

@@ -53,4 +53,71 @@ describe Sequence do
       end
     end
   end
+
+  describe "#base_counts" do
+    context "for a DNA sequence with default or falsy argument" do
+      it "returns a map of A, C, T, and G counts" do
+        s = Sequence.new('ACTGactg')
+        expect(s.base_counts).to eq({ a: 2, c: 2, t: 2, g: 2 })
+      end
+    end
+
+    context "for a DNA sequence with truthy argument" do
+      it "returns a map of A, C, T, G and N counts" do
+        s = Sequence.new('ACTGNactgn')
+        expect(s.base_counts(1)).to eq({ a: 2, c: 2, t: 2, g: 2, n: 2 })
+      end
+    end
+
+    context "for an RNA sequence with falsy or default argument" do
+      it "returns a map of A, C, U, G counts" do
+        s = Sequence.new('ACUGacug')
+        expect(s.base_counts).to eq({ a: 2, c: 2, u: 2, g: 2 })
+      end
+    end
+    
+    context "for an RNA sequence with truthy argument" do
+      it "returns a map of A, C, U, G and N counts" do
+        s = Sequence.new('ACUGNacugn')
+        expect(s.base_counts(1)).to eq({ a: 2, c: 2, u: 2, g: 2, n: 2 })
+      end
+    end
+
+    context "for a sequence with both U and T present" do
+      s = Sequence.new('AaCcTtGgNnUu')
+      err_message = 'ERROR: A sequence contains both T and U'
+
+      it "warns the user about having both U and T present" do
+        expect(s).to receive(:warn).with(err_message)
+        s.base_counts
+      end
+
+      it "returns a map that counts both U's and T's" do
+        expect(s.base_counts).to eq({ a: 2, c: 2, t: 2, u: 2, g: 2 })
+      end
+
+      it "returns a map with T, U and N if truthy argument given" do
+        base_counts = { a: 2, c: 2, t: 2, u: 2, g: 2, n: 2 }
+        expect(s.base_counts(1)).to eq(base_counts)
+      end
+    end
+  end
+
+  describe "#base_frequencies" do
+    context "with falsy argument" do
+      it "doesn't count ambiguous bases in total bases" do
+        s = Sequence.new('ACTTn')
+        base_freqs = { a: 0.25, c: 0.25, t: 0.5, g: 0.0 }
+        expect(s.base_frequencies).to eq(base_freqs)
+      end
+    end
+
+    context "when counting ambiguous bases" do
+      it "does count ambiguous bases in total bases" do
+        s = Sequence.new('ACTTn')
+        base_freqs = { a: 0.2, c: 0.2, t: 0.4, g: 0.0, n: 0.2 }
+        expect(s.base_frequencies(1)).to eq(base_freqs)
+      end
+    end
+  end
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: parse_fasta
 version: !ruby/object:Gem::Version
-  version: 1.3.0
+  version: 1.4.0
 platform: ruby
 authors:
 - Ryan Moore
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-07-24 00:00:00.000000000 Z
+date: 2014-08-13 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler
@@ -80,7 +80,7 @@ dependencies:
     - - "~>"
       - !ruby/object:Gem::Version
         version: '0.8'
-description: So you want to parse a fasta file...
+description: So you want to parse a fasta or fastq file...
 email:
 - moorer@udel.edu
 executables: []