bio-svgenes 0.1.1

data/.document

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

data/Gemfile

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+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 "bundler", "~> 1.0.0"
+  gem "jeweler", "~> 1.6.4"
+  gem "rcov", ">= 0"
+  gem "bio", ">= 1.4.2"
+end

data/Gemfile.lock

@@ -0,0 +1,22 @@
+GEM
+  remote: http://rubygems.org/
+  specs:
+    bio (1.4.3)
+    git (1.2.5)
+    jeweler (1.6.4)
+      bundler (~> 1.0)
+      git (>= 1.2.5)
+      rake
+    rake (0.9.2.2)
+    rcov (0.9.11)
+    shoulda (2.11.3)
+
+PLATFORMS
+  ruby
+
+DEPENDENCIES
+  bio (>= 1.4.2)
+  bundler (~> 1.0.0)
+  jeweler (~> 1.6.4)
+  rcov
+  shoulda

data/LICENSE.txt

@@ -0,0 +1,20 @@
+Copyright (c) 2012 Dan MacLean
+
+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.rdoc

@@ -0,0 +1,19 @@
+= bio-svgenes
+
+Description goes here.
+
+== Contributing to bio-svgenes
+ 
+* Check out the latest master to make sure the feature hasn't been implemented or the bug hasn't been fixed yet
+* Check out the issue tracker to make sure someone already hasn't requested it and/or contributed it
+* Fork the project
+* Start a feature/bugfix branch
+* Commit and push until you are happy with your contribution
+* Make sure to add tests for it. This is important so I don't break it in a future version unintentionally.
+* Please try not to mess with the Rakefile, version, or history. If you want to have your own version, or is otherwise necessary, that is fine, but please isolate to its own commit so I can cherry-pick around it.
+
+== Copyright
+
+Copyright (c) 2012 Dan MacLean. See LICENSE.txt for
+further details.
+

data/Rakefile

@@ -0,0 +1,53 @@
+# 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://docs.rubygems.org/read/chapter/20 for more options
+  gem.name = "bio-svgenes"
+  gem.homepage = "http://github.com/danmaclean/bioruby-svgenes"
+  gem.license = "MIT"
+  gem.summary = %Q{Create pretty SVG-format images of features, gene models and data tracks}
+  gem.description = %Q{This bio-gem facilitates the creation of pretty, publication quality SVG images from feature data.}
+  gem.email = "maclean.daniel@gmail.com"
+  gem.authors = ["Dan MacLean"]
+  # 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
+
+require 'rcov/rcovtask'
+Rcov::RcovTask.new do |test|
+  test.libs << 'test'
+  test.pattern = 'test/**/test_*.rb'
+  test.verbose = true
+  test.rcov_opts << '--exclude "gems/*"'
+end
+
+task :default => :test
+
+require 'rake/rdoctask'
+Rake::RDocTask.new do |rdoc|
+  version = File.exist?('VERSION') ? File.read('VERSION') : ""
+
+  rdoc.rdoc_dir = 'rdoc'
+  rdoc.title = "bio-svgenes #{version}"
+  rdoc.rdoc_files.include('README*')
+  rdoc.rdoc_files.include('lib/**/*.rb')
+end

data/VERSION

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+0.1.1

data/bio-svgenes.gemspec

@@ -0,0 +1,83 @@
+# Generated by jeweler
+# DO NOT EDIT THIS FILE DIRECTLY
+# Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
+# -*- encoding: utf-8 -*-
+
+Gem::Specification.new do |s|
+  s.name = "bio-svgenes"
+  s.version = "0.1.1"
+
+  s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
+  s.authors = ["Dan MacLean"]
+  s.date = "2012-11-21"
+  s.description = "This bio-gem facilitates the creation of pretty, publication quality SVG images from feature data."
+  s.email = "maclean.daniel@gmail.com"
+  s.extra_rdoc_files = [
+    "LICENSE.txt",
+    "README.rdoc"
+  ]
+  s.files = [
+    ".DS_Store",
+    ".document",
+    "Gemfile",
+    "Gemfile.lock",
+    "LICENSE.txt",
+    "README.rdoc",
+    "Rakefile",
+    "VERSION",
+    "bio-svgenes.gemspec",
+    "examples/.DS_Store",
+    "examples/annotate_snps.rb",
+    "examples/data.txt",
+    "examples/draw_from_json.rb",
+    "examples/drawn_from_json.svg",
+    "examples/drawn_from_json2.svg",
+    "examples/example.rb",
+    "examples/example.svg",
+    "examples/example_config.json",
+    "examples/gene.gff",
+    "examples/get_coverage_in_windows.rb",
+    "examples/transcripts.gff",
+    "lib/.DS_Store",
+    "lib/bio-svgenes.rb",
+    "lib/bio/.DS_Store",
+    "lib/bio/graphics/glyph.rb",
+    "lib/bio/graphics/mini_feature.rb",
+    "lib/bio/graphics/page.rb",
+    "lib/bio/graphics/primitive.rb",
+    "lib/bio/graphics/svgee.rb",
+    "lib/bio/graphics/track.rb",
+    "test/helper.rb",
+    "test/test_bio-svgenes.rb"
+  ]
+  s.homepage = "http://github.com/danmaclean/bioruby-svgenes"
+  s.licenses = ["MIT"]
+  s.require_paths = ["lib"]
+  s.rubygems_version = "1.8.10"
+  s.summary = "Create pretty SVG-format images of features, gene models and data tracks"
+
+  if s.respond_to? :specification_version then
+    s.specification_version = 3
+
+    if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
+      s.add_development_dependency(%q<shoulda>, [">= 0"])
+      s.add_development_dependency(%q<bundler>, ["~> 1.0.0"])
+      s.add_development_dependency(%q<jeweler>, ["~> 1.6.4"])
+      s.add_development_dependency(%q<rcov>, [">= 0"])
+      s.add_development_dependency(%q<bio>, [">= 1.4.2"])
+    else
+      s.add_dependency(%q<shoulda>, [">= 0"])
+      s.add_dependency(%q<bundler>, ["~> 1.0.0"])
+      s.add_dependency(%q<jeweler>, ["~> 1.6.4"])
+      s.add_dependency(%q<rcov>, [">= 0"])
+      s.add_dependency(%q<bio>, [">= 1.4.2"])
+    end
+  else
+    s.add_dependency(%q<shoulda>, [">= 0"])
+    s.add_dependency(%q<bundler>, ["~> 1.0.0"])
+    s.add_dependency(%q<jeweler>, ["~> 1.6.4"])
+    s.add_dependency(%q<rcov>, [">= 0"])
+    s.add_dependency(%q<bio>, [">= 1.4.2"])
+  end
+end
+

data/examples/annotate_snps.rb

@@ -0,0 +1,86 @@
+#!/usr/bin/env ruby
+#
+#  untitled
+#
+#  Created by Dan MacLean (TSL) on 2012-10-30.
+#  Copyright (c)  . All rights reserved.
+###################################################
+
+require 'ostruct'
+
+class DanGFF
+  attr_accessor :seqname, :source, :attributes, :start, :end, :strand, :feature, :phase, :score
+  
+  def initialize(line)
+    @seqname, @source, @feature, @start, @end, @score, @strand, @phase, @attributes = line.split(/\t/)
+    @start = @start.to_i
+    @end = @end.to_i 
+  end
+
+  def parent
+    self.attributes =~ /Parent=(.*?);/
+    $1
+  end
+  
+  def overlaps?(other)
+    if (self.seqname == other.seqname and self.start >= other.start and self.start <= other.end)
+      return true
+    elsif (self.seqname == other.seqname and self.end >= other.start and self.end <= other.end)
+      return true
+    end
+  end
+  
+  def contains?(other)
+    if self.seqname == other.seqname and self.start <= other.start and self.end >= other.end
+      return true
+    else
+      return false
+    end
+  end
+  
+end
+features_file = ARGV.shift
+bam_file = ARGV.shift
+bgi_snp_file = ARGV.shift
+#rest = data dump files from R
+
+#get SNP list (position, methodd)
+ARGV.each do |file|
+  snps = []
+  file =~ /(.*)_r_dump.csv/
+  id = $1
+  File.open(file,"r").each do |line|
+      next if line=~ /Method/
+      snp = OpenStruct.new
+      snp.index, snp.pos, snp.method =line.chomp.split(/,/)
+      snp.index = snp.index.to_i
+      snp.pos =  snp.pos.to_i
+      snp.seqname = id
+      snp.start = snp.pos
+      snp.end = snp.pos
+      snps << snp
+  end
+  features = []
+  File.open(features_file, "r").each do |line|
+    feature = DanGFF.new(line) 
+    features << feature if feature.seqname == id and feature.feature == "mRNA"
+  end
+
+  features.each do |f|
+    snps.each do |snp|
+      if feature.contains(snp)
+        snp_info = case snp.method
+        when "BGI"
+          get_snp_from_bgi(snp)
+        when "PileUp"
+          get_snp_from_pileup(snp)
+        when "VCF"
+          get_snp_from_vcf(snp)
+        end
+        print snp_out(snp,snp_info)
+      end
+    end
+  end
+  
+end
+

data/examples/data.txt

@@ -0,0 +1,192 @@
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