bio-ucsc-util 0.1.0

data/lib/bio/ucsc/src/Version

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+v268

data/lib/bio/ucsc/util.rb

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+# == ucsc_util.rb
+# This file contains the UcscUtil class implementing the ucsc utility programs
+#
+# == Contact
+#
+# Author::    Nicholas A. Thrower
+# Copyright:: Copyright (c) 2012 Nicholas A Thrower
+# License::   See LICENSE.txt for more details
+
+# :nodoc:
+module Bio 
+# -
+  module Ucsc
+    class Util
+      # UcscUtil implements the utility programs from the ucsc source as class methods.
+      # Names are converted by ruby convention to snake case (underscore) based on the camel case C routines
+      require 'bio/ucsc/binding'
+      # Converts ascii Wig file to binary BigWig
+      # - :wig_file => input wiggle file
+      # - :chrom_file => two column file: <chromosome name> <size in bases> for each entry
+      # - :big_wig_file => output indexed file
+      # Options:
+      # * :blockSize => Number of items to bundle in r-tree [256]
+      # * :itemsPerSlot => Number of data points bundled at lowest level [1024]
+      # * :clip => If set just issue warning messages rather than dying if wig file contains items off end of chromosome
+      # * :unc => If set, do not use compression    
+      def self.wig_to_big_wig(wig_file, chrom_file, big_wig_file, opts={})
+        block_size = opts[:block_size]||256
+        items_per_slot = opts[:items_per_slot]||1024
+        clip = opts[:clip]||false
+        unc = opts[:unc]||false
+        do_compress = !unc
+        Binding::bigWigFileCreate(wig_file,chrom_file,block_size,items_per_slot,clip,do_compress,big_wig_file)
+        return BigWig.open(big_wig_file)
+      end   
+      # Converts ascii bedGraph file to binary bigWig.
+      # The input bedGraph file must be sorted, use the unix sort command:
+      #   sort -k1,1 -k2,2n unsorted.bedGraph > sorted.bedGraph
+      # - :bed_file => input bedGraph
+      # - :chrom_file => two column file: <chromosome name> <size in bases> for each entry
+      # - :big_wig_file => output indexed file
+      def self.bed_graph_to_big_wig(wig_file, chrom_file, big_wig_file, opts={})
+        block_size = opts[:block_size]||256
+        items_per_slot = opts[:items_per_slot]||1024
+        unc = opts[:unc]||false
+        do_compress = !unc
+        Binding::bedGraphToBigWig(wig_file,chrom_file,block_size,items_per_slot,do_compress,big_wig_file)
+        return BigWig.open(big_wig_file)
+      end
+    end
+  end
+end

data/test/1.bed

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+chr1	1	2	1
+chr1	2	3	5
+chr1	3	4	5
+chr1	4	5	10
+chr1	5	6	10
+chr1	9	10	5
+chr1	10	11	1
+chr2	1	2	1
+chr2	2	3	5
+chr2	3	4	5
+chr2	4	5	5
+chr2	5	6	1

data/test/1.wig

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+variableStep chrom=chr1 span=1
+1	1
+2	5
+3	5
+4	10
+5	10
+9	5
+10	1
+variableStep chrom=chr2 span=1
+1	2
+2	5
+3	5
+4	5
+5	8
+variableStep chrom=chr3 span=1
+1	1
+2	1
+3	2
+4	3
+5	3

data/test/chrom.sizes

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+chr1	5000
+chr2	2500
+chr3	10000

data/test/helper.rb

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+require 'rubygems'
+require 'bundler'
+require 'simplecov'
+SimpleCov.start
+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-ucsc-util'
+
+class Test::Unit::TestCase
+end

data/test/test_big_wig.rb

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+require 'helper'
+
+class TestBioUcscUtil < Test::Unit::TestCase
+  include Bio::Ucsc
+  TEST_BW = "test/1.bw"
+  TEST_WIG = "test/1.wig"
+  TEST_BED = "test/1.bed"
+  TEST_WIG_OUT = "test/1.wig.bw"
+  TEST_BED_OUT = "test/2.bed.bw"
+  CHROM_FILE = "test/chrom.sizes"
+  BAD_FILE = 'test/not_existing_file'
+  TEST_SMOOTH_FILE = 'test/1_smoothed.bw'
+  TEST_SMOOTH_OUT_FILE = 'test/smoothed.bw'
+  
+  context "a new big wig" do
+    setup do
+      @bw = BigWig.new
+    end
+    should "not be open and have no filename" do
+      assert_equal nil, @bw.bbi_file
+      assert_equal nil, @bw.filename
+    end
+    should "allowing setting filename" do
+      @bw.filename = TEST_BW
+      assert_equal TEST_BW, @bw.filename
+    end
+    should "report no filename on open" do
+      assert_raise ArgumentError do
+        @bw.open
+      end
+    end
+    should "report bad filename on open" do
+      @bw.filename = BAD_FILE
+      assert_raise NameError do
+        @bw.open
+      end
+    end
+    should "report bad format on open" do
+      @bw.filename = TEST_BED
+      assert_raise LoadError do
+        @bw.open
+      end
+    end
+    should "allow opening a good file" do
+      @bw.filename = TEST_BW
+      assert_nothing_raised do 
+        @bw.open
+      end
+      assert_not_nil @bw.bbi_file
+    end
+  end
+  
+  context "an open big wig" do 
+    setup do
+      @bw = BigWig.open(TEST_BW)
+      @out = StringIO.new
+      $stdout = @out
+    end
+    should "already be open" do 
+      assert_not_nil @bw.bbi_file
+    end
+    should "allow closing a file" do
+      @bw.close
+      assert_nil @bw.bbi_file
+    end
+    should "have detailed info" do
+      @bw.info
+      assert_equal "version: 4\nisCompressed: no\nisSwapped: 0\nprimaryDataSize: 116\nprimaryIndexSize: 6204\nzoomLevels: 1\nchromCount: 1\nbasesCovered: 7\nmean: 52.857143\nmin: 10.000000\nmax: 100.000000\nstd: 36.839420\n", @out.string
+    end
+    should "allow chrom details" do
+      @bw.info({:chroms => true})
+      assert @out.string=~/chr1 0 5000/
+    end
+    should "allow zoom details" do
+      @bw.info({:zooms => true})
+      assert @out.string=~/32	36/
+    end
+    should "allow min/max" do
+      @bw.info({:minMax => true})
+      assert_equal "10.000000 100.000000\n", @out.string
+    end
+  end
+  
+  context "a new big wig from wig" do
+    setup do
+      @bw = Util.wig_to_big_wig(TEST_WIG,CHROM_FILE,TEST_WIG_OUT)
+    end
+    should "have summary data" do
+      assert_same_elements( [5.0,10.0], @bw.summary("chr1",2,4,2,{:type => 'max'}) )
+    end
+    should "have min 1.0" do
+      assert_equal 1.0, @bw.min
+    end
+    should "have max 10.0" do 
+      assert_equal 10.0, @bw.max
+    end
+    should "have std of 2.94.." do
+      assert_equal 2.9480801329998196, @bw.std_dev
+    end
+    should "have a mean of 4.23.." do
+      assert_equal 4.235294117647059, @bw.mean
+    end
+    should "have 17 bases covered" do
+      assert_equal 17, @bw.bases_covered
+    end
+    should "have total chromosome length of 17500" do
+      assert_equal 17500, @bw.chrom_length
+    end
+    should "have total coverage of" do
+      assert_equal 0.0009714285714285714, @bw.coverage
+    end
+    should "have chr1 length of" do
+      assert_equal 5000, @bw.chrom_length('chr1')
+    end
+    should "have chr1 coverage of" do
+      assert_equal 0.0014, @bw.coverage('chr1')
+    end
+    should "have chr2 min of 2" do
+      assert_equal 2, @bw.min('chr2')
+    end
+    should "have chr2 max of 8" do
+      assert_equal 8, @bw.max('chr2')
+    end
+    should "have chr2 mean of 5.0" do
+      assert_equal 5.0, @bw.mean('chr2')
+    end
+    should "have chr3 std of 1.0" do
+      assert_equal 1.0, @bw.std_dev('chr3')
+    end
+    should "allow smoothing" do
+      assert_nothing_raised do
+        @bw.smooth(TEST_SMOOTH_OUT_FILE)
+      end
+      `rm #{TEST_SMOOTH_OUT_FILE}`
+    end
+    teardown do
+      `rm #{TEST_WIG_OUT}`
+    end
+  end
+  
+  context "a new big wig from bed" do
+    setup do
+      @bw = Util.bed_graph_to_big_wig(TEST_BED,CHROM_FILE,TEST_BED_OUT)
+    end
+    should "have summary data" do
+      assert_same_elements [5.0,10.0], @bw.summary("chr1",3,5,2,{:type => 'max'})
+    end
+    should "have min 1.0" do
+      assert_equal 1.0, @bw.min
+    end
+    should "have max 10.0" do 
+      assert_equal 10.0, @bw.max
+    end
+    should "have chr2 length of 2500" do
+      assert_equal 2500, @bw.chrom_length('chr2')
+    end
+    teardown do
+      `rm #{TEST_BED_OUT}`
+    end
+  end
+
+end

metadata

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+--- !ruby/object:Gem::Specification
+name: bio-ucsc-util
+version: !ruby/object:Gem::Version
+  version: 0.1.0
+  prerelease: 
+platform: ruby
+authors:
+- throwern
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2012-08-07 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: ffi
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: rdoc
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '3.12'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '3.12'
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '1.0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '1.0'
+- !ruby/object:Gem::Dependency
+  name: jeweler
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.8.3
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.8.3
+description: ! 'Ruby FFI binding and implmentation of the ucsc utilities: bigWigInfo,
+  bigWigSummary and wigToBigWig'
+email: throwern@msu.edu
+executables: []
+extensions:
+- ext/ucsc-util/mkrf_conf.rb
+extra_rdoc_files:
+- LICENSE.txt
+- README.rdoc
+files:
+- .document
+- .rvmrc
+- Gemfile
+- Gemfile.lock
+- LICENSE.txt
+- README.rdoc
+- Rakefile
+- VERSION
+- bio-ucsc-util.gemspec
+- ext/ucsc-util/README
+- ext/ucsc-util/makefile
+- ext/ucsc-util/mkrf_conf.rb
+- ext/ucsc-util/ucsc-util-src-v268.tgz
+- lib/bio-ucsc-util.rb
+- lib/bio/ucsc/big_wig.rb
+- lib/bio/ucsc/binding.rb
+- lib/bio/ucsc/library.rb
+- lib/bio/ucsc/src/Version
+- lib/bio/ucsc/util.rb
+- test/1.bed
+- test/1.bw
+- test/1.wig
+- test/1_smoothed.bw
+- test/chrom.sizes
+- test/helper.rb
+- test/test_big_wig.rb
+homepage: http://github.com/throwern/bio-ucsc-util
+licenses:
+- MIT
+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: -1186691304766418588
+required_rubygems_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 1.8.24
+signing_key: 
+specification_version: 3
+summary: Ruby binding to the ucsc kent utilities
+test_files: []