dna 0.3.0 → 0.3.1
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- checksums.yaml +7 -0
- data/.travis.yml +1 -0
- data/Gemfile +1 -0
- data/dna.gemspec +10 -5
- data/lib/dna.rb +6 -4
- data/lib/dna/parsers/fasta.rb +6 -2
- data/lib/dna/version.rb +1 -1
- data/readme.md +9 -10
- data/spec/data/single.fasta +2 -0
- data/spec/data/test.fasta +3 -1
- data/spec/dna_spec.rb +8 -1
- data/spec/spec_helper.rb +5 -1
- metadata +15 -20
checksums.yaml
ADDED
@@ -0,0 +1,7 @@
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---
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SHA1:
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metadata.gz: ad48f8e0c0cb16eb16b15aac96835dd3cf14f95f
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data.tar.gz: d93f3466c1de438e5241af282cc33fbf4a050c7e
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SHA512:
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metadata.gz: fbd9a6b2ac10635db59dbb23078fbc17889df5a49601ff59abcc0b1ce0d2a1fc157c9d2340487a58f9bb276ee3154b9633a9aae7df5c66b53dc3a11da56821b4
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7
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data.tar.gz: 0db717cea0f96fedbe4c33175e2f0b3a72a7421716f8feea4aa4783473d99036635486e781efe3f849a20a1694ee65d01313f4350ab7856622d2db4ff4ff391e
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data/.travis.yml
CHANGED
data/Gemfile
CHANGED
data/dna.gemspec
CHANGED
@@ -2,17 +2,22 @@
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# DO NOT EDIT THIS FILE DIRECTLY
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# Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
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# -*- encoding: utf-8 -*-
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# stub: dna 0.3.1 ruby lib
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Gem::Specification.new do |s|
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s.name = "dna"
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8
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-
s.version = "0.3.
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9
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s.version = "0.3.1"
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s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
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s.require_paths = ["lib"]
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s.authors = ["Austin G. Davis-Richardson"]
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-
s.date = "
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+
s.date = "2015-10-30"
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s.description = "Simple FASTA/FASTQ/QSEQ parser library for Ruby."
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s.email = "harekrishna@gmail.com"
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s.executables = ["dna"]
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s.extra_rdoc_files = [
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"readme.md"
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]
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s.files = [
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".rspec",
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".rvmrc",
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@@ -31,6 +36,7 @@ Gem::Specification.new do |s|
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"lib/dna/version.rb",
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"readme.md",
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"spec/data/empty.txt",
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"spec/data/single.fasta",
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"spec/data/test.fasta",
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"spec/data/test.fasta.gz",
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"spec/data/test.fastq",
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@@ -42,12 +48,11 @@ Gem::Specification.new do |s|
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]
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s.homepage = "http://audy.github.com/dna"
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s.licenses = ["MIT"]
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-
s.
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-
s.rubygems_version = "1.8.25"
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+
s.rubygems_version = "2.4.5.1"
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s.summary = "Simple FASTA/FASTQ/QSEQ parser library for Ruby"
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if s.respond_to? :specification_version then
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s.specification_version =
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s.specification_version = 4
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if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
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s.add_development_dependency(%q<jeweler>, ["~> 1.8.4"])
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data/lib/dna.rb
CHANGED
@@ -1,6 +1,8 @@
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require 'zlib'
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-
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-
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-
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-
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$:.unshift(File.join(File.expand_path(File.dirname(__FILE__)), 'dna'))
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require 'version'
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require 'dna'
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require 'phred'
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require 'record'
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data/lib/dna/parsers/fasta.rb
CHANGED
@@ -7,12 +7,16 @@ class FastaParser
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def each
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sequence, header = nil, nil
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@handle.each do |line|
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line.strip!
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next if line.strip.empty? # skip blank lines
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if line[0].chr == '>'
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yield Fasta.new(:name => header, :sequence => sequence) if sequence
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sequence = ''
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-
header = line[1..-1]
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header = line[1..-1]
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else
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sequence << line.
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sequence << line.tr(' ','')
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end
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end
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yield Fasta.new(:name => header, :sequence => sequence)
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data/lib/dna/version.rb
CHANGED
data/readme.md
CHANGED
@@ -1,7 +1,4 @@
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1
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# DNA
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-
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[![Build Status](https://secure.travis-ci.org/audy/dna.png?branch=master)](http://travis-ci.org/audy/dna)
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-
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1
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# 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)
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A biological sequence file parser for Ruby
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Austin G. Davis-Richardson
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@@ -12,9 +9,8 @@ Features
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- [fasta](http://en.wikipedia.org/wiki/FASTA)
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- [fastq](http://en.wikipedia.org/wiki/Fastq)
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- [qseq](http://blog.kokocinski.net/index.php/qseq-files-format?blog=2)
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-
-
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-
-
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-
- Files are read from disk (not stored in memory)
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- Automatic format detection
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- Lazy iteration
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## Installation
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@@ -53,9 +49,12 @@ File.open('sequences.qseq') do |handle|
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puts records.first.inspect
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end
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-
#
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-
#
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-
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# **caveat:** If you are reading from a compressed file
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# or `stdin` you MUST specify the sequence format:
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require 'zlib'
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Zlib::GzipReader('sequences.fasta.gz') do |handle|
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records = Dna.new handle, :format => :fasta
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records.each do |record|
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data/spec/data/test.fasta
CHANGED
data/spec/dna_spec.rb
CHANGED
@@ -13,6 +13,13 @@ describe Dna do
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fasta.format == :empty
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end
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it 'can read a single record' do
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File.open('spec/data/single.fasta') do |handle|
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records = Dna.new(handle).to_a
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records.first.sequence.should == 'GATC'
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end
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end
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it 'can automatically parse gzipped files' do
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gzipped.format.should == :fasta
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end
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@@ -59,4 +66,4 @@ describe Dna do
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it 'generates qseq objects from a qseq file' do
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qseq.first.class.should == QSEQ
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end
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-
end
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end
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data/spec/spec_helper.rb
CHANGED
@@ -1,8 +1,12 @@
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$LOAD_PATH << File.join(File.dirname(__FILE__), 'lib')
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require 'coveralls'
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Coveralls.wear!
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require 'rspec'
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require 'dna'
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path = File.dirname(__FILE__)
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fasta_file = File.readlines(File.join(path, 'data/test.fasta'))
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fastq_file = File.readlines(File.join(path, 'data/test.fastq'))
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@@ -17,4 +21,4 @@ shared_context "parser stuff" do
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@empty_file = empty_file
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@gzip_file = File.open(File.join(path, 'data/test.fasta.gz'))
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end
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-
end
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end
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metadata
CHANGED
@@ -1,30 +1,27 @@
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--- !ruby/object:Gem::Specification
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name: dna
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version: !ruby/object:Gem::Version
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version: 0.3.
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prerelease:
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version: 0.3.1
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platform: ruby
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authors:
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- Austin G. Davis-Richardson
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autorequire:
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bindir: bin
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cert_chain: []
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date:
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date: 2015-10-30 00:00:00.000000000 Z
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dependencies:
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- !ruby/object:Gem::Dependency
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name: jeweler
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requirement: !ruby/object:Gem::Requirement
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none: false
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requirements:
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-
- - ~>
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- - "~>"
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- !ruby/object:Gem::Version
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version: 1.8.4
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type: :development
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prerelease: false
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version_requirements: !ruby/object:Gem::Requirement
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none: false
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requirements:
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-
- - ~>
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- - "~>"
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- !ruby/object:Gem::Version
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version: 1.8.4
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description: Simple FASTA/FASTQ/QSEQ parser library for Ruby.
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@@ -32,11 +29,12 @@ email: harekrishna@gmail.com
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executables:
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- dna
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extensions: []
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-
extra_rdoc_files:
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extra_rdoc_files:
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- readme.md
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files:
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-
- .rspec
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-
- .rvmrc
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-
- .travis.yml
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- ".rspec"
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- ".rvmrc"
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- ".travis.yml"
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- Gemfile
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- Rakefile
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- bin/dna
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@@ -51,6 +49,7 @@ files:
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- lib/dna/version.rb
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- readme.md
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- spec/data/empty.txt
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- spec/data/single.fasta
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- spec/data/test.fasta
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- spec/data/test.fasta.gz
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- spec/data/test.fastq
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@@ -62,29 +61,25 @@ files:
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homepage: http://audy.github.com/dna
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licenses:
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- MIT
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metadata: {}
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post_install_message:
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rdoc_options: []
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require_paths:
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- lib
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required_ruby_version: !ruby/object:Gem::Requirement
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none: false
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requirements:
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-
- -
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- - ">="
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- !ruby/object:Gem::Version
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version: '0'
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-
segments:
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-
- 0
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hash: -3491596072416341887
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required_rubygems_version: !ruby/object:Gem::Requirement
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none: false
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requirements:
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-
- -
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- - ">="
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- !ruby/object:Gem::Version
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version: '0'
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requirements: []
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rubyforge_project:
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rubygems_version:
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rubygems_version: 2.4.5.1
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signing_key:
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specification_version:
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specification_version: 4
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summary: Simple FASTA/FASTQ/QSEQ parser library for Ruby
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test_files: []
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