UCSCBin 0.2.0

data/sample/refseqgene.rb

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+#!/usr/local/bin/ruby
+#
+# = refseqgene.rb, an UCSCBin sample
+# Author:: Hiroyuki Mishima ( missy at be.to / hmishima at nagasaki-u.ac.jp )
+# Copyright:: Hiroyuki Mishima, 2010
+# Licence:: the MIT/X11 licence. See the LICENCE file.
+# Usage:: refseqgene chr1:12345-23456
+# 
+
+DB_URL = "mysql://genome:@genome-mysql.cse.ucsc.edu/hg18"
+
+require 'rubygems'
+require 'UCSCBin'
+require 'sequel'
+
+chr, one_start, one_end = ARGV[0].chomp.split(/:|-/)
+
+zero_start, zero_end = 
+  UCSCBin::Utils.one_to_zero(one_start.to_i, one_end.to_i)
+bins = UCSCBin::BinRange.bin_all(zero_start, zero_end)
+
+db = Sequel.connect(DB_URL)
+dset = db[:refGene].select(:name2)
+dset = dset.filter(:chrom => chr)
+dset = dset.filter(:bin => bins)
+dset = dset.exclude do |o|
+  ((o.txStart < zero_start) & (o.txEnd < zero_start)) |
+  ((o.txStart > zero_end) & (o.txEnd > zero_end))
+end
+
+genes = dset.all.map{|hit| hit[:name2]}.uniq
+genes = ["no hit"] if genes.empty?
+
+puts "#{chr}:#{one_start}-#{one_end}\t#{genes.join("; ")}"
+

data/spec/UCSCBin_BinRange_spec.rb

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+require File.expand_path(File.dirname(__FILE__) + '/spec_helper')
+
+##
+## UCSCBin::Utils
+##
+
+describe UCSCBin::Utils, "#zero_to_one" do 
+  it "(0, 10) should return an array [1, 10]" do
+    UCSCBin::Utils.zero_to_one(0 , 10).should == [1, 10]
+  end
+
+  it "(-1, 10) should raise ArgumentError" do
+    caller = lambda{UCSCBin::Utils.zero_to_one(-1, 10)}
+    caller.should raise_error(ArgumentError)
+  end    
+  
+  it "(10, 1) should raise ArgumentError" do
+    caller = lambda{UCSCBin::Utils.zero_to_one(10, 1)}
+    caller.should raise_error(ArgumentError)
+  end
+
+  it "(0, 0) should raise ArgumentError" do 
+    caller = lambda{UCSCBin::Utils.zero_to_one(10, 1)}
+    caller.should raise_error(ArgumentError)
+  end
+end
+
+describe UCSCBin::Utils, "#one_to_zero" do 
+  it "(1, 10) should return an array [0, 10]" do
+    UCSCBin::Utils.one_to_zero(1, 10).should == [0, 10]
+  end
+
+  it "(-1, 10) should raise ArgumentError" do 
+    caller = lambda{UCSCBin::Utils.one_to_zero(-1, 10)}
+    caller.should raise_error(ArgumentError)
+  end
+
+  it "(0, 10) should raise ArgumentError" do 
+    caller = lambda{UCSCBin::Utils.one_to_zero(0, 10)}
+    caller.should raise_error(ArgumentError)
+  end
+
+  it "(10, 1) should raise ArgumentError" do 
+    caller = lambda{UCSCBin::Utils.one_to_zero(0, 10)}
+    caller.should raise_error(ArgumentError)
+  end
+end

data/spec/UCSCBin_Utils_spec.rb

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+require File.expand_path(File.dirname(__FILE__) + '/spec_helper')
+
+##
+## UCSCBin::BinRange
+##
+
+describe UCSCBin::BinRange, "#bin" do 
+  it "(20,000,000-20,000,999) should be 737" do
+    bin_start = 20_000_000
+    bin_end   = 20_000_999
+    UCSCBin::BinRange.bin(bin_start, bin_end).should == 737
+  end
+
+  it "(2,000,000,000-9,000,000,100) should raise exception" do
+    bin_start = 2_000_000_000
+    bin_end   = 9_000_000_100
+    caller = lambda{UCSCBin::BinRange.bin(bin_start, bin_end)}
+    caller.should raise_error(NotImplementedError)
+  end
+end
+
+  describe UCSCBin::BinRange, "#bin_all" do 
+  it "(20,000,000-20,000,999) should be all bins" do
+    bin_start = 20_000_000
+    bin_end   = 20_000_999
+    UCSCBin::BinRange.bin_all(bin_start, bin_end).should == [737, 92, 11, 1 ,0]
+  end
+
+  it "(2,000,000,000-9,000,000,100) should raise exception" do
+    bin_start = 2_000_000_000
+    bin_end   = 9_000_000_100
+    caller = lambda{UCSCBin::BinRange.bin_all(bin_start, bin_end)}
+    caller.should raise_error(NotImplementedError)
+  end
+
+  it "(20,000,000-20,100,999) should be an array of BINs" do
+    bin_start = 20_000_000
+    bin_end   = 20_100_999
+    UCSCBin::BinRange.bin_all(bin_start, bin_end).should == [737,738,92, 11, 1, 0]
+  end
+
+  it "(20,000,000-21,000,999) should be an array of BINs" do
+    bin_start = 20_000_000
+    bin_end   = 21_000_999
+    UCSCBin::BinRange.bin_all(bin_start, bin_end).should ==
+      [737, 738, 739, 740, 741, 742, 743, 744, 745, 92, 93, 11, 1, 0]
+  end
+end
+

data/spec/spec.opts

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+--color

data/spec/spec_helper.rb

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+$LOAD_PATH.unshift(File.dirname(__FILE__))
+$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
+require 'UCSCBin'
+require 'spec'
+require 'spec/autorun'
+
+Spec::Runner.configure do |config|
+  
+end

metadata

@@ -0,0 +1,132 @@
+--- !ruby/object:Gem::Specification 
+name: UCSCBin
+version: !ruby/object:Gem::Version 
+  hash: -2481588639819700252
+  prerelease: false
+  segments: 
+  - 0
+  - 2
+  - 0
+  version: 0.2.0
+platform: ruby
+authors: 
+- Hiroyuki MISHIMA
+autorequire: 
+bindir: bin
+cert_chain: []
+
+date: 2010-10-28 00:00:00 +09:00
+default_executable: 
+dependencies: 
+- !ruby/object:Gem::Dependency 
+  name: rspec
+  prerelease: false
+  requirement: &id001 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        hash: -1730125512753482917
+        segments: 
+        - 1
+        - 2
+        - 9
+        version: 1.2.9
+  type: :development
+  version_requirements: *id001
+description: |-
+  Utilities for UCSC Bioinfomatics's Genome Browser
+        ( http://g  enome.ucsc.edu ) including calculation of a BIN index
+         from a genomic interval to speed-up SQL queries, and conversion
+         between 1-based full-closed (for humans) and 0-based half-open 
+         (for machienes) intervals
+email: missy@be.to
+executables: []
+
+extensions: []
+
+extra_rdoc_files: 
+- LICENSE
+- README.rdoc
+files: 
+- LICENSE
+- README.rdoc
+- Rakefile
+- UCSCBin.gemspec
+- VERSION
+- lib/UCSCBin.rb
+- rdoc/README_rdoc.html
+- rdoc/UCSCBin.html
+- rdoc/UCSCBin/BinRange.html
+- rdoc/UCSCBin/Utils.html
+- rdoc/created.rid
+- rdoc/images/brick.png
+- rdoc/images/brick_link.png
+- rdoc/images/bug.png
+- rdoc/images/bullet_black.png
+- rdoc/images/bullet_toggle_minus.png
+- rdoc/images/bullet_toggle_plus.png
+- rdoc/images/date.png
+- rdoc/images/find.png
+- rdoc/images/loadingAnimation.gif
+- rdoc/images/macFFBgHack.png
+- rdoc/images/package.png
+- rdoc/images/page_green.png
+- rdoc/images/page_white_text.png
+- rdoc/images/page_white_width.png
+- rdoc/images/plugin.png
+- rdoc/images/ruby.png
+- rdoc/images/tag_green.png
+- rdoc/images/wrench.png
+- rdoc/images/wrench_orange.png
+- rdoc/images/zoom.png
+- rdoc/index.html
+- rdoc/js/darkfish.js
+- rdoc/js/jquery.js
+- rdoc/js/quicksearch.js
+- rdoc/js/thickbox-compressed.js
+- rdoc/lib/UCSCBin_rb.html
+- rdoc/rdoc.css
+- sample/refseqgene.rb
+- spec/UCSCBin_BinRange_spec.rb
+- spec/UCSCBin_Utils_spec.rb
+- spec/spec.opts
+- spec/spec_helper.rb
+has_rdoc: true
+homepage: http://github.com/misshie/UCSCBin
+licenses: []
+
+post_install_message: 
+rdoc_options: 
+- --charset=UTF-8
+require_paths: 
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement 
+  none: false
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      hash: -1944775192741746749
+      segments: 
+      - 0
+      version: "0"
+required_rubygems_version: !ruby/object:Gem::Requirement 
+  none: false
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      hash: -1944775192741746749
+      segments: 
+      - 0
+      version: "0"
+requirements: []
+
+rubyforge_project: 
+rubygems_version: 1.3.7
+signing_key: 
+specification_version: 3
+summary: Calculate BIN indexes on UCSC Bioinformatics's Genome Browser
+test_files: 
+- spec/UCSCBin_Utils_spec.rb
+- spec/spec_helper.rb
+- spec/UCSCBin_BinRange_spec.rb