dna 0.2.0 → 0.2.1

data/dna.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = "dna"
-  s.version = "0.2.0"
+  s.version = "0.2.1"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Austin G. Davis-Richardson"]
-  s.date = "2012-12-14"
+  s.date = "2012-12-19"
   s.description = "Simple FASTA/FASTQ/QSEQ parser library for Ruby."
   s.email = "harekrishna@gmail.com"
   s.executables = ["dna"]

data/lib/dna/dna.rb

@@ -7,9 +7,9 @@ class Dna
 
   attr_reader :format
 
-  def initialize(handle)
+  def initialize(handle, args = {})
     @handle = handle
-    @format = detect_format
+    @format = args[:format] || detect_format
     @iterator =
       case @format
       when :fasta

data/lib/dna/phred.rb

@@ -38,7 +38,7 @@ module Phred
   private
 
   def qualities_with_offset(offset)
-    @qualities.each_byte.map { |q| q - offset }
+    @quality.each_byte.map { |q| q - offset }
   end
 
   def probabilities_with_offset(offset, func)

data/lib/dna/version.rb

@@ -2,7 +2,7 @@ class Dna
   class Version
   MAJOR = 0
   MINOR = 2
-  PATCH = 0
+  PATCH = 1
 
   STRING = [MAJOR, MINOR, PATCH].join('.')
   end

data/readme.md

@@ -53,9 +53,10 @@ File.open('sequences.qseq') do |handle|
   puts records.first.inspect
 end
 
-# Even supports Gzip 
+# Even supports Gzip but you must specify the format
+# (can't rewind in Gzip)
 File.open('sequences.fasta.gz') do |handle|
-  records = Dna.new handle
+  records = Dna.new handle, :format => :fasta
 
   records.each do |record|
     puts record.length
@@ -63,6 +64,31 @@ File.open('sequences.fasta.gz') do |handle|
 end
 ```
 
+## Support for PHRED score parsing
+
+```ruby
+
+# Illumina > 1.3)
+
+record.illumina_qualities # => [31, ..., 37]
+
+# Error probabilities
+
+record.illumina_probabilities
+# => [1.0, 0.7943282347242815, ...,  0.3981071705534972]
+
+# Solexa + Illumina =< 1.3
+
+record.solexa_qualities
+record.solexa_probabilities
+
+# Sanger
+
+record.sanger_qualities
+record.sanger_probabilities
+
+```
+
 ## Bonus Feature
 
 The DNA gem is also a command-line tool with grep-like capabilities. Print records with (Ruby) regexp match in header.

data/spec/phred_spec.rb

@@ -1,6 +1,7 @@
+# XXX should probably use the actual record objects
 class TestRecord
   include Phred
-  attr_accessor :qualities
+  attr_accessor :quality
 end
 
 ##
@@ -62,12 +63,12 @@ describe Phred do
   format_definitions.each_pair do |type, properties|
 
     it "should properly convert #{type} raw ascii PHRED scores to integers" do
-      test_record.qualities = properties[:string]
+      test_record.quality = properties[:string]
       test_record.send(:"#{type}_scores").should == properties[:scores]
     end
 
     it "should properly convert #{type.to_s} raw ascii PHRED scores to probabilities" do
-      test_record.qualities = properties[:string]
+      test_record.quality = properties[:string]
       test_record.send(:"#{type}_probabilities").should == properties[:probabilities]
     end
   end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: dna
 version: !ruby/object:Gem::Version
-  version: 0.2.0
+  version: 0.2.1
   prerelease: 
 platform: ruby
 authors:
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-12-14 00:00:00.000000000 Z
+date: 2012-12-19 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: jeweler
@@ -74,7 +74,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: -74029819579817896
+      hash: 1149140625798689145
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements: