dna 0.3.0 → 0.3.1

checksums.yaml

@@ -0,0 +1,7 @@
+---
+SHA1:
+  metadata.gz: ad48f8e0c0cb16eb16b15aac96835dd3cf14f95f
+  data.tar.gz: d93f3466c1de438e5241af282cc33fbf4a050c7e
+SHA512:
+  metadata.gz: fbd9a6b2ac10635db59dbb23078fbc17889df5a49601ff59abcc0b1ce0d2a1fc157c9d2340487a58f9bb276ee3154b9633a9aae7df5c66b53dc3a11da56821b4
+  data.tar.gz: 0db717cea0f96fedbe4c33175e2f0b3a72a7421716f8feea4aa4783473d99036635486e781efe3f849a20a1694ee65d01313f4350ab7856622d2db4ff4ff391e

data/.travis.yml

@@ -1,4 +1,5 @@
 language: ruby
 rvm:
   - 1.9.3
+  - 2.0.0
 script: bundle exec rspec

data/Gemfile

@@ -2,6 +2,7 @@ source "https://rubygems.org"
 
 group :test do
   gem 'rspec', '~> 2.11.0'
+  gem 'coveralls', require: false
 end
 
 group :development do

data/dna.gemspec

@@ -2,17 +2,22 @@
 # DO NOT EDIT THIS FILE DIRECTLY
 # Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
 # -*- encoding: utf-8 -*-
+# stub: dna 0.3.1 ruby lib
 
 Gem::Specification.new do |s|
   s.name = "dna"
-  s.version = "0.3.0"
+  s.version = "0.3.1"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
+  s.require_paths = ["lib"]
   s.authors = ["Austin G. Davis-Richardson"]
-  s.date = "2013-08-02"
+  s.date = "2015-10-30"
   s.description = "Simple FASTA/FASTQ/QSEQ parser library for Ruby."
   s.email = "harekrishna@gmail.com"
   s.executables = ["dna"]
+  s.extra_rdoc_files = [
+    "readme.md"
+  ]
   s.files = [
     ".rspec",
     ".rvmrc",
@@ -31,6 +36,7 @@ Gem::Specification.new do |s|
     "lib/dna/version.rb",
     "readme.md",
     "spec/data/empty.txt",
+    "spec/data/single.fasta",
     "spec/data/test.fasta",
     "spec/data/test.fasta.gz",
     "spec/data/test.fastq",
@@ -42,12 +48,11 @@ Gem::Specification.new do |s|
   ]
   s.homepage = "http://audy.github.com/dna"
   s.licenses = ["MIT"]
-  s.require_paths = ["lib"]
-  s.rubygems_version = "1.8.25"
+  s.rubygems_version = "2.4.5.1"
   s.summary = "Simple FASTA/FASTQ/QSEQ parser library for Ruby"
 
   if s.respond_to? :specification_version then
-    s.specification_version = 3
+    s.specification_version = 4
 
     if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
       s.add_development_dependency(%q<jeweler>, ["~> 1.8.4"])

data/lib/dna.rb

@@ -1,6 +1,8 @@
 require 'zlib'
 
-[ 'version.rb', 'dna.rb', 'phred.rb', 'record.rb'].each do |f|
-  fp = File.join(File.dirname(__FILE__), 'dna', f)
-  require fp
-end
+$:.unshift(File.join(File.expand_path(File.dirname(__FILE__)), 'dna'))
+
+require 'version'
+require 'dna'
+require 'phred'
+require 'record'

data/lib/dna/parsers/fasta.rb

@@ -7,12 +7,16 @@ class FastaParser
   def each
     sequence, header = nil, nil
     @handle.each do |line|
+
+      line.strip!
+      next if line.strip.empty? # skip blank lines
+
       if line[0].chr == '>'
         yield Fasta.new(:name => header, :sequence => sequence) if sequence
         sequence = ''
-        header = line[1..-1].strip
+        header = line[1..-1]
       else
-        sequence << line.strip.tr(' ','')
+        sequence << line.tr(' ','')
       end
     end
     yield Fasta.new(:name => header, :sequence => sequence)

data/lib/dna/version.rb

@@ -2,7 +2,7 @@ class Dna
   class Version
   MAJOR = 0
   MINOR = 3
-  PATCH = 0
+  PATCH = 1
 
   STRING = [MAJOR, MINOR, PATCH].join('.')
   end

data/readme.md

@@ -1,7 +1,4 @@
-# DNA
-
-[![Build Status](https://secure.travis-ci.org/audy/dna.png?branch=master)](http://travis-ci.org/audy/dna)
-
+# DNA [![Gem Version](https://badge.fury.io/rb/dna.png)](http://badge.fury.io/rb/dna) [![Build Status](https://secure.travis-ci.org/audy/dna.png?branch=master)](http://travis-ci.org/audy/dna) [![Coverage Status](https://coveralls.io/repos/audy/dna/badge.png)](https://coveralls.io/r/audy/dna)
 A biological sequence file parser for Ruby
 
 Austin G. Davis-Richardson
@@ -12,9 +9,8 @@ Features
     - [fasta](http://en.wikipedia.org/wiki/FASTA)
     - [fastq](http://en.wikipedia.org/wiki/Fastq)
     - [qseq](http://blog.kokocinski.net/index.php/qseq-files-format?blog=2)
-  - Autodetection of file formats so your scripts can be format agnostic
-  - Automatic Gzip support
-  - Files are read from disk (not stored in memory)
+  - Automatic format detection
+  - Lazy iteration
 
 ## Installation
 
@@ -53,9 +49,12 @@ File.open('sequences.qseq') do |handle|
   puts records.first.inspect
 end
 
-# Even supports Gzip but you must specify the format
-# (can't rewind in Gzip)
-File.open('sequences.fasta.gz') do |handle|
+# **caveat:** If you are reading from a compressed file
+# or `stdin` you MUST specify the sequence format:
+
+require 'zlib'
+
+Zlib::GzipReader('sequences.fasta.gz') do |handle|
   records = Dna.new handle, :format => :fasta
 
   records.each do |record|

data/spec/data/single.fasta

@@ -0,0 +1,2 @@
+>a single record
+GATC

data/spec/data/test.fasta

@@ -9,4 +9,6 @@ CGAAG
 GAGACAUAUC
 
 CNNNA
-A
+A
+
+

data/spec/dna_spec.rb

@@ -13,6 +13,13 @@ describe Dna do
     fasta.format == :empty
   end
 
+  it 'can read a single record' do
+    File.open('spec/data/single.fasta') do |handle|
+      records = Dna.new(handle).to_a
+      records.first.sequence.should == 'GATC'
+    end
+  end
+
   it 'can automatically parse gzipped files' do
     gzipped.format.should == :fasta
   end
@@ -59,4 +66,4 @@ describe Dna do
   it 'generates qseq objects from a qseq file' do
     qseq.first.class.should == QSEQ
   end
-end
+end

data/spec/spec_helper.rb

@@ -1,8 +1,12 @@
 $LOAD_PATH << File.join(File.dirname(__FILE__), 'lib')
 
+require 'coveralls'
+Coveralls.wear!
+
 require 'rspec'
 require 'dna'
 
+
 path = File.dirname(__FILE__)
 fasta_file = File.readlines(File.join(path, 'data/test.fasta'))
 fastq_file = File.readlines(File.join(path, 'data/test.fastq'))
@@ -17,4 +21,4 @@ shared_context "parser stuff" do
     @empty_file = empty_file
     @gzip_file = File.open(File.join(path, 'data/test.fasta.gz'))
   end
-end
+end

metadata

@@ -1,30 +1,27 @@
 --- !ruby/object:Gem::Specification
 name: dna
 version: !ruby/object:Gem::Version
-  version: 0.3.0
-  prerelease: 
+  version: 0.3.1
 platform: ruby
 authors:
 - Austin G. Davis-Richardson
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-08-02 00:00:00.000000000 Z
+date: 2015-10-30 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: jeweler
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: 1.8.4
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: 1.8.4
 description: Simple FASTA/FASTQ/QSEQ parser library for Ruby.
@@ -32,11 +29,12 @@ email: harekrishna@gmail.com
 executables:
 - dna
 extensions: []
-extra_rdoc_files: []
+extra_rdoc_files:
+- readme.md
 files:
-- .rspec
-- .rvmrc
-- .travis.yml
+- ".rspec"
+- ".rvmrc"
+- ".travis.yml"
 - Gemfile
 - Rakefile
 - bin/dna
@@ -51,6 +49,7 @@ files:
 - lib/dna/version.rb
 - readme.md
 - spec/data/empty.txt
+- spec/data/single.fasta
 - spec/data/test.fasta
 - spec/data/test.fasta.gz
 - spec/data/test.fastq
@@ -62,29 +61,25 @@ files:
 homepage: http://audy.github.com/dna
 licenses:
 - MIT
+metadata: {}
 post_install_message: 
 rdoc_options: []
 require_paths:
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement
-  none: false
   requirements:
-  - - ! '>='
+  - - ">="
     - !ruby/object:Gem::Version
       version: '0'
-      segments:
-      - 0
-      hash: -3491596072416341887
 required_rubygems_version: !ruby/object:Gem::Requirement
-  none: false
   requirements:
-  - - ! '>='
+  - - ">="
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 1.8.25
+rubygems_version: 2.4.5.1
 signing_key: 
-specification_version: 3
+specification_version: 4
 summary: Simple FASTA/FASTQ/QSEQ parser library for Ruby
 test_files: []