parse_fasta 1.1.2 → 1.2.0

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data/README.md

@@ -32,6 +32,8 @@ to see the full documentation.
 
 ## Usage ##
 
+Some examples...
+
 A little script to print header and length of each record.
 
 	require 'parse_fasta'
@@ -54,6 +56,17 @@ Now we can parse fastq files as well!
 
 ## Versions ##
 
+### 1.2.0 ###
+
+Added `mean_qual` method to the `Quality` class.
+
+### 1.1.2 ###
+
+Dropped Ruby requirement to 1.9.3
+
+(Note, if you want to build the docs with yard and you're using
+Ruby 1.9.3, you may have to install the redcarpet gem.)
+
 ### 1.1.0 ###
 
 Added: Fastq and Quality classes

data/lib/parse_fasta/fastq_file.rb

@@ -35,7 +35,7 @@ class FastqFile < File
   # @yieldparam sequence [Sequence] The sequence of the fastq record
   # @yieldparam description [String] The description line of the fastq
   #   record without the leading '+'
-  # @yieldparam quality string [Quality] The quality string of the
+  # @yieldparam quality_string [Quality] The quality string of the
   #   fastq record
   def each_record
     count = 0

data/lib/parse_fasta/quality.rb

@@ -19,9 +19,19 @@
 # Provide some methods for dealing with common tasks regarding
 # quality strings.
 class Quality < String
+  # Returns the mean quality for the record. This will be a good deal
+  # faster than getting the average with `qual_scores` and reduce.
+  #
+  # @example Get mean quality score for a record
+  #   Quality.new("!+5?I").mean_qual #=> 20.0
+  #
+  # @return [Float] Mean quality score for record
+  def mean_qual
+    (self.sum - (self.length * 33)) / self.length.to_f
+  end
 
   # Returns an array of illumina style quality scores. The quality
-  # scores generated will be Phred+33.
+  # scores generated will be Phred+33 (i.e., new Illumina).
   #
   # @example Get quality score array of a Quality
   #   Quality.new("!+5?I").qual_scores #=> [0, 10, 20, 30, 40]

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 = "1.1.2"
+  VERSION = "1.2.0"
 end

data/spec/lib/quality_spec.rb

@@ -32,4 +32,12 @@ describe Quality do
       end
     end
   end
+
+  describe "#mean_qual" do
+    it "returns the mean quality for the quality string" do
+      len = qual_string.length.to_f
+      mean_quality = qual_string.qual_scores.reduce(:+) / len
+      expect(qual_string.mean_qual).to eq mean_quality
+    end
+  end             
 end

metadata

@@ -1,83 +1,83 @@
 --- !ruby/object:Gem::Specification
 name: parse_fasta
 version: !ruby/object:Gem::Version
-  version: 1.1.2
+  version: 1.2.0
 platform: ruby
 authors:
 - Ryan Moore
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-07-01 00:00:00.000000000 Z
+date: 2014-07-03 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '1.6'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '1.6'
 - !ruby/object:Gem::Dependency
   name: rake
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '10.3'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '10.3'
 - !ruby/object:Gem::Dependency
   name: rspec
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '2.14'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '2.14'
 - !ruby/object:Gem::Dependency
   name: bio
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '1.4'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '1.4'
 - !ruby/object:Gem::Dependency
   name: yard
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '0.8'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '0.8'
 description: So you want to parse a fasta file...
@@ -87,7 +87,7 @@ executables: []
 extensions: []
 extra_rdoc_files: []
 files:
-- .gitignore
+- ".gitignore"
 - COPYING
 - Gemfile
 - README.md
@@ -109,7 +109,7 @@ files:
 - test_files/test.fq
 homepage: https://github.com/mooreryan/parse_fasta
 licenses:
-- ! 'GPLv3: http://www.gnu.org/licenses/gpl.txt'
+- 'GPLv3: http://www.gnu.org/licenses/gpl.txt'
 metadata: {}
 post_install_message: 
 rdoc_options: []
@@ -117,12 +117,12 @@ require_paths:
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement
   requirements:
-  - - ! '>='
+  - - ">="
     - !ruby/object:Gem::Version
       version: 1.9.3
 required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
-  - - ! '>='
+  - - ">="
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []