bio-faidx 0.0.1

checksums.yaml

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+SHA1:
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+  data.tar.gz: 131d2aceda2d2be6df0686fb525b9883c97643ae
+SHA512:
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data/.document

@@ -0,0 +1,5 @@
+lib/**/*.rb
+bin/*
+- 
+features/**/*.feature
+LICENSE.txt

data/.travis.yml

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+language: ruby
+rvm:
+  - 1.9.2
+  - 1.9.3
+  - jruby-19mode # JRuby in 1.9 mode
+
+# - rbx-19mode
+#  - 1.8.7
+#  - jruby-18mode # JRuby in 1.8 mode
+#  - rbx-18mode
+
+# uncomment this line if your project needs to run something other than `rake`:
+# script: bundle exec rspec spec

data/Gemfile

@@ -0,0 +1,15 @@
+source "http://rubygems.org"
+# Add dependencies required to use your gem here.
+# Example:
+#   gem "activesupport", ">= 2.3.5"
+
+# Add dependencies to develop your gem here.
+# Include everything needed to run rake, tests, features, etc.
+group :development do
+  gem "shoulda", ">= 0"
+  gem "rdoc", "~> 3.12"
+  gem "simplecov", ">= 0"
+  gem "jeweler", "~> 2.0.1", :git => "https://github.com/technicalpickles/jeweler.git"
+  gem "bundler", ">= 1.0.21"
+  gem "bio", ">= 1.4.2"
+end

data/LICENSE.txt

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+Copyright (c) 2014 homonecloco
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

data/README.md

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+# bio-faidx
+
+[![Build Status](https://secure.travis-ci.org/homonecloco/bioruby-faidx.png)](http://travis-ci.org/homonecloco/bioruby-faidx)
+
+API to work with the fai format produced to samtools. Useful if you don't want to rely on all the samtools component. 
+Can query sequences from the fasta file. At the minute, it uses bio-samtools, but the idea is to make this self-sufficient. 
+
+
+## Installation
+
+```sh
+gem install bio-faidx
+```
+
+## Usage
+
+```ruby
+require 'bio-faidx'
+```
+
+The API doc is online. For more code examples see the test files in
+the source tree.
+        
+## Project home page
+
+Information on the source tree, documentation, examples, issues and
+how to contribute, see
+
+  http://github.com/homonecloco/bioruby-faidx
+
+The BioRuby community is on IRC server: irc.freenode.org, channel: #bioruby.
+
+## Cite
+
+If you use this software, please cite one of
+  
+* [BioRuby: bioinformatics software for the Ruby programming language](http://dx.doi.org/10.1093/bioinformatics/btq475)
+* [Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics](http://dx.doi.org/10.1093/bioinformatics/bts080)
+
+## Biogems.info
+
+This Biogem is published at (http://biogems.info/index.html#bio-faidx)
+
+## Copyright
+
+Copyright (c) 2014 homonecloco. See LICENSE.txt for further details.
+

data/README.rdoc

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+= bio-faidx
+
+{<img
+src="https://secure.travis-ci.org/homonecloco/bioruby-faidx.png"
+/>}[http://travis-ci.org/#!/homonecloco/bioruby-faidx]
+
+Full description goes here
+
+Note: this software is under active development!
+
+== Installation
+
+        gem install bio-faidx
+
+== Usage
+
+== Developers
+
+To use the library 
+
+        require 'bio-faidx'
+
+The API doc is online. For more code examples see also the test files in
+the source tree.
+        
+== Project home page
+
+Information on the source tree, documentation, issues and how to contribute, see
+
+  http://github.com/homonecloco/bioruby-faidx
+
+The BioRuby community is on IRC server: irc.freenode.org, channel: #bioruby.
+
+== Cite
+
+  If you use this software, please cite one of
+ 
+* [BioRuby: bioinformatics software for the Ruby programming language](http://dx.doi.org/10.1093/bioinformatics/btq475)
+* [Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics](http://dx.doi.org/10.1093/bioinformatics/bts080)
+
+== Biogems.info
+
+This Biogem is published at http://biogems.info/index.html#bio-faidx
+
+== Copyright
+
+Copyright (c) 2014 homonecloco. See LICENSE.txt for further details.
+

data/Rakefile

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+# encoding: utf-8
+
+require 'rubygems'
+require 'bundler'
+begin
+  Bundler.setup(:default, :development)
+rescue Bundler::BundlerError => e
+  $stderr.puts e.message
+  $stderr.puts "Run `bundle install` to install missing gems"
+  exit e.status_code
+end
+require 'rake'
+
+require 'jeweler'
+Jeweler::Tasks.new do |gem|
+  # gem is a Gem::Specification... see http://guides.rubygems.org/specification-reference/ for more options
+  gem.name = "bio-faidx"
+  gem.homepage = "http://github.com/homonecloco/bioruby-faidx"
+  gem.license = "MIT"
+  gem.summary = %Q{Tools to work with fasta files, indexed with samtools}
+  gem.description = %Q{ools to work with fasta files, indexed with samtools. The initial releases depend on bio-samtools, but that will change}
+  gem.email = "ricardo.ramirez-gonzalez@tgac.ac.uk"
+  gem.authors = ["homonecloco"]
+  # dependencies defined in Gemfile
+end
+Jeweler::RubygemsDotOrgTasks.new
+
+require 'rake/testtask'
+Rake::TestTask.new(:test) do |test|
+  test.libs << 'lib' << 'test'
+  test.pattern = 'test/**/test_*.rb'
+  test.verbose = true
+end
+
+desc "Code coverage detail"
+task :simplecov do
+  ENV['COVERAGE'] = "true"
+  Rake::Task['test'].execute
+end
+
+task :default => :test
+
+require 'rdoc/task'
+Rake::RDocTask.new do |rdoc|
+  version = File.exist?('VERSION') ? File.read('VERSION') : ""
+
+  rdoc.rdoc_dir = 'rdoc'
+  rdoc.title = "bio-faidx #{version}"
+  rdoc.rdoc_files.include('README*')
+  rdoc.rdoc_files.include('lib/**/*.rb')
+end

data/VERSION

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+0.0.1

data/lib/bio-faidx.rb

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+# Please require your code below, respecting the naming conventions in the
+# bioruby directory tree.
+#
+# For example, say you have a plugin named bio-plugin, the only uncommented
+# line in this file would be 
+#
+#   require 'bio/bio-plugin/plugin'
+#
+# In this file only require other files. Avoid other source code.
+
+require 'bio-faidx/faidx.rb'
+

data/lib/bio-faidx/faidx.rb

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+require 'csv'
+require 'bio-samtools'
+
+
+class Bio::DB::Faidx
+
+	class Entry
+		attr_accessor :name, :length, :offset, :linebases, :linewidth
+	end
+	def initialize(opts)
+		@cache = false
+		@cache = opts[:cache] if opts[:cache]
+		@filename = opts[:filename]
+		@inited = false
+	end
+
+	def init_cache
+		@inited = true
+		@entries = Hash.new
+		@entries_order = Array.new
+		read_entries do |e|
+			@entries[e.name] = e
+			@entries_order << e.name 
+		end
+	end
+
+	def entries
+		init_cache unless @inited
+		@entries
+	end
+
+	def [](entry)
+		init_cache unless @inited
+	 @entries[entry]
+	end
+	
+
+	def entries_order
+		init_cache unless @inited
+		return @entries_order
+	end
+
+	def read_entries
+		CSV.foreach(@filename, :col_sep => "\t", :skip_lines=>/^#/, :skip_blanks=>true) do |row|
+		fasta_entry = Bio::DB::Faidx::Entry.new
+		[:name, :length, :offset, :linebases, :linewidth].each_with_index do |sym, i|
+			answer = row[i]
+			answer = answer.to_i if [:length, :offset, :linebases, :linewidth].include?(sym)
+			fasta_entry.send("#{sym}=".to_sym, answer)
+			yield fasta_entry
+		end
+	end
+
+	def each_entry
+		unless @cache
+			read_entries { |e| yield e }
+		else
+			entries_order.each { |e|  yield @entries[e] }
+		end
+	end
+end
+
+
+class Bio::DB::Fasta::Region
+	def overlaps (other)
+		return false if other.entry != @entry
+		return true if other.start >= @start and other.start <= @end
+		return true if other.end   >= @start and other.end   <= @end
+		return false
+	end
+
+	def subset (other)
+		return false if other.entry != @entry
+		return true if other.start >= @start and other.end <= @end
+	end
+
+	def joinRegion (other)
+		return nil unless self.overlaps(other)
+		out = self.clone 
+		out.start = other.start if other.start < out.start
+		out.end = other.end if other.end > out.end
+		return out 
+	end
+
+	def overlap_in_set(set) 
+		overlap_set = Set.new 
+		set.each do |e| 
+			overlap_set << e if self.overlaps(e)
+		end
+		overlap_set
+	end
+end
+	#class Faidx
+	class Entry
+		attr_accessor :name, :length, :offset, :linebases, :linewidth
+	end
+	def initialize(opts)
+		@cache = false
+		@cache = opts[:cache] if opts[:cache]
+		@filename = opts[:filename]
+		@inited = false
+	end
+
+	def init_cache
+		@inited = true
+		@entries = Hash.new
+		@entries_order = Array.new
+		read_entries do |e|
+			@entries[e.name] = e
+			@entries_order << e.name 
+		end
+	end
+
+	def entries
+		init_cache unless @inited
+		@entries
+
+	end
+
+	def entries_order
+		init_cache unless @inited
+		return @entries_order
+	end
+
+	def read_entries
+		CSV.foreach(@filename, :col_sep => "\t", :skip_lines=>/^#/, :skip_blanks=>true) do |row|
+		fasta_entry = Bio::DB::Faidx::Entry.new
+		[:name, :length, :offset, :linebases, :linewidth].each_with_index do |sym, i|
+			answer = row[i]
+			answer = answer.to_i if [:length, :offset, :linebases, :linewidth].include?(sym)
+			fasta_entry.send("#{sym}=".to_sym, answer)
+			yield fasta_entry
+		end
+	end
+
+	def each_entry
+		unless @cache
+			read_entries { |e| yield e }
+		else
+			entries_order.each { |e|  yield @entries[e] }
+		end
+	end
+end
+end
+
+class Bio::DB::Fasta::Region
+	def overlaps (other)
+		return false if other.entry != @entry
+		return true if other.start >= @start and other.start <= @end
+		return true if other.end   >= @start and other.end   <= @end
+		return false
+	end
+
+	def subset (other)
+		return false if other.entry != @entry
+		return true if other.start >= @start and other.end <= @end
+	end
+
+	def joinRegion (other)
+		return nil unless self.overlaps(other)
+		out = self.clone 
+		out.start = other.start if other.start < out.start
+		out.end = other.end if other.end > out.end
+		return out 
+	end
+
+	def overlap_in_set(set) 
+		overlap_set = Set.new 
+		set.each do |e| 
+			overlap_set << e if self.overlaps(e)
+		end
+		overlap_set
+	end
+end

data/test/helper.rb

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+require 'simplecov'
+
+module SimpleCov::Configuration
+  def clean_filters
+    @filters = []
+  end
+end
+
+SimpleCov.configure do
+  clean_filters
+  load_adapter 'test_frameworks'
+end
+
+ENV["COVERAGE"] && SimpleCov.start do
+  add_filter "/.rvm/"
+end
+require 'rubygems'
+require 'bundler'
+begin
+  Bundler.setup(:default, :development)
+rescue Bundler::BundlerError => e
+  $stderr.puts e.message
+  $stderr.puts "Run `bundle install` to install missing gems"
+  exit e.status_code
+end
+require 'test/unit'
+require 'shoulda'
+
+$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
+$LOAD_PATH.unshift(File.dirname(__FILE__))
+require 'bio-faidx'
+
+class Test::Unit::TestCase
+end

data/test/test_bio-faidx.rb

@@ -0,0 +1,7 @@
+require 'helper'
+
+class TestBioFaidx < Test::Unit::TestCase
+  should "probably rename this file and start testing for real" do
+    flunk "hey buddy, you should probably rename this file and start testing for real"
+  end
+end

metadata

@@ -0,0 +1,143 @@
+--- !ruby/object:Gem::Specification
+name: bio-faidx
+version: !ruby/object:Gem::Version
+  version: 0.0.1
+platform: ruby
+authors:
+- homonecloco
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2014-10-07 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: shoulda
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: rdoc
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.12'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.12'
+- !ruby/object:Gem::Dependency
+  name: simplecov
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: jeweler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 2.0.1
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 2.0.1
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.0.21
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.0.21
+- !ruby/object:Gem::Dependency
+  name: bio
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.4.2
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.4.2
+description: ools to work with fasta files, indexed with samtools. The initial releases
+  depend on bio-samtools, but that will change
+email: ricardo.ramirez-gonzalez@tgac.ac.uk
+executables: []
+extensions: []
+extra_rdoc_files:
+- LICENSE.txt
+- README.md
+- README.rdoc
+files:
+- ".document"
+- ".travis.yml"
+- Gemfile
+- LICENSE.txt
+- README.md
+- README.rdoc
+- Rakefile
+- VERSION
+- lib/bio-faidx.rb
+- lib/bio-faidx/faidx.rb
+- test/helper.rb
+- test/test_bio-faidx.rb
+homepage: http://github.com/homonecloco/bioruby-faidx
+licenses:
+- MIT
+metadata: {}
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 2.2.1
+signing_key: 
+specification_version: 4
+summary: Tools to work with fasta files, indexed with samtools
+test_files: []