exodb 0.0.2

data/lib/exodb/utils.rb

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+# 
+# Exodb
+# Copyright (C) 2014
+#
+# author: Natapol Pornputtapong <natapol.por@gmail.com>
+#
+# Documentation: Natapol Pornputtapong (RDoc'd and embellished by William Webber)
+#
+
+# raise "Please, use ruby 1.9.0 or later." if RUBY_VERSION < "1.9.0"
+
+require 'exodb/utils/upload_generef.rb'
+require 'exodb/utils/upload_var.rb'
+
+module Exodb
+	
+	module Utils
+		
+		module_function
+		
+		# Guess the type of id
+		#
+		# @param [String]  id string
+		# @return [String] a miriam registry or the string itself incase cannot guess
+		def guess_miriam(str)
+			case str
+			when /\A((AC|AP|NC|NG|NM|NP|NR|NT|NW|XM|XP|XR|YP|ZP)_\d+|(NZ\_[A-Z]{4}\d+))(\.\d+)?\z/
+				return "urn:miriam:refseq:#{str}"
+			when /\A((ENS[A-Z]*[FPTG]\d{11}(\.\d+)?)|(FB\w{2}\d{7})|(Y[A-Z]{2}\d{3}[a-zA-Z](\-[A-Z])?)|([A-Z_a-z0-9]+(\.)?(t)?(\d+)?([a-z])?))\z/
+				return "urn:miriam:ensembl:#{str}"
+			when /\A((HGNC|hgnc):)?\d{1,5}\z/
+				return "urn:miriam:hgnc:#{str}"
+			when /\ACCDS\d+\.\d+\z/
+				return "urn:miriam:ccds:#{str}"
+			else
+				return str
+			end
+		end
+		
+	end
+	
+end

data/lib/exodb/vcf.rb

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+
+
+class VCF
+	
+	attr_reader :info_attr, :filter_attr, :format_attr, :meta, :contig, :samples, :variants, :alt_attr
+	
+	def initialize()
+		@info_attr = {}
+		@filter_attr = {}
+		@format_attr = {}
+		@alt_attr = {}
+		@meta = {}
+		@contig = {}
+		@variants = []
+
+	end
+	
+	def open(filename)
+		
+		File.open(filename).each do |line|
+			case line
+			when /^##INFO/
+				parse_info(line.chomp)
+			when /^##FORMAT/
+				parse_format(line.chomp)
+			when /^##FILTER/
+				parse_filter(line.chomp)
+			when /^##contig/
+				parse_contig(line.chomp)
+			when /^##ALT/
+				parse_alt(line.chomp)
+			when /^##/
+				parse_meta(line.chomp)
+			when /^#/
+				@samples = line.split(/\s+/)[9..-1]
+			else
+				@variants.push(Variant.new(line.chomp))
+			end
+			
+		end
+		
+	end
+	
+	def fileformat
+		return @meta[:fileformat]
+	end
+	
+	def parse(line = 4000)
+		@variants.each_index do |ind|
+			break if ind > line
+			Thread.new (ind) {
+				@variants[ind].parse!(@info_attr, @format_attr)
+			}
+		end
+	end
+	
+	def sample_num
+		return @samples.length
+	end
+	
+	def variant_num
+		return @variants.length
+	end
+	
+	class Variant
+		
+		attr_reader :chrom, :pos, :id, :ref, :alt, :qual, :filter, :info, :sample_data, :str
+		
+		CASTING = lambda do |string, type|
+			case type
+			when 'Integer'
+				return string.to_i
+			when 'Float'
+				return string.to_f
+			else
+				return string.to_s
+			end
+		end
+		
+		def initialize(str)
+			@str = str
+		end
+		
+		def parse!(info_attr, format_attr)
+			
+			if @str
+				splited = str.split(/\s+/)
+				@chrom = splited[0]
+				@pos = splited[1].to_i
+				@id = splited[2]
+				@ref = splited[3]
+				@alt = splited[4]
+				@qual = splited[5]
+				@filter = splited[6]
+				@info = {}
+				parse_info(splited[7], info_attr)
+				
+				@formats = splited[8].split(/:/)
+				@sample_data = []
+				splited[9..-1].each {|data| @sample_data.push(parse_format(data, @formats, format_attr))}
+				@str = nil
+			end
+			
+		end
+		
+		private
+		
+		def parse_info(str, info_attr)
+			str.split(/;/).each do |entry|
+				splited = entry.split(/=/)
+				case info_attr[splited[0]][:Number]
+				when '1'
+					@info[splited[0]] = CASTING.call(splited[1], info_attr[splited[0]][:Type])
+				when '0'
+					@info[splited[0]] = true
+				else
+					@info[splited[0]] = []
+					splited[1].split(/,/).each {|e| @info[splited[0]].push(CASTING.call(e, info_attr[splited[0]][:Type]))}
+				end
+			end
+		end
+		
+		def parse_format(str, formats, format_attr)
+			
+			result = {}
+			
+			splited = str.split(/:/)
+			formats.each_index do |ind|
+				case format_attr[formats[ind]][:Number]
+				when '1'
+					result[formats[ind]] = CASTING.call(splited[ind], format_attr[formats[0]][:Type])
+				when '0'
+					result[formats[ind]] = true
+				else
+					result[formats[ind]] = []
+					formats[ind].split(/,/).each {|e| result[formats[ind]].push(CASTING.call(e, format_attr[formats[ind]][:Type]))}
+				end
+			end
+			
+			return result
+		end
+	end
+	
+	private
+	
+	def parse_meta(str)
+		splited = str[2..-1].split(/=/)
+		@meta[splited[0].to_sym] = splited[1]
+	end
+	
+	def parse_contig(str)
+		@contig = parse_data(str[10..-1])
+	end
+	
+	def parse_filter(str)
+		data = parse_data(str[10..-1])
+		@filter_attr[data[:ID]] = data
+	end
+	
+	def parse_info(str)
+		data = parse_data(str[8..-1])
+		@info_attr[data[:ID]] = data
+	end
+	
+	def parse_format(str)
+		data = parse_data(str[10..-1])
+		@format_attr[data[:ID]] = data
+	end
+	
+	def parse_alt(str)
+		data = parse_data(str[7..-1])
+		@alt_attr[data[:ID]] = data
+	end
+	
+	def parse_data(str)
+		result = {}
+		str.scan(/(\w+=\w+|\w+=\".+\")/).each do |entry|
+			splited = entry[0].split(/=/)
+			result[splited[0].to_sym] = splited [1]
+		end
+		return result
+	end
+	
+end
+
+
+	
+vcf = VCF.new()
+vcf.open('./sample.vcf')
+#p vcf.sample_num
+#p vcf.variant_num
+vcf.parse
+p vcf

data/lib/exodb/version.rb

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+# 
+# Exodus
+# Copyright (C) 2014
+#
+# author: Natapol Pornputtapong <natapol.por@gmail.com>
+#
+# Documentation: Natapol Pornputtapong (RDoc'd and embellished by William Webber)
+#
+
+# raise "Please, use ruby 1.9.0 or later." if RUBY_VERSION < "1.9.0"
+
+
+module Exodb
+	VERSION = "0.0.2"
+end

data/lib/exodb.rb

@@ -0,0 +1,44 @@
+# 
+# Exodus
+# Copyright (C) 2014
+#
+# author: Natapol Pornputtapong <natapol.por@gmail.com>
+#
+# Documentation: Natapol Pornputtapong (RDoc'd and embellished by William Webber)
+#
+
+# raise "Please, use ruby 1.9.0 or later." if RUBY_VERSION < "1.9.0"
+
+
+$: << File.join(File.expand_path(File.dirname(__FILE__)))
+
+#specify gem version
+gem 'mongoid', '~> 3.1'
+
+#Internal library
+require 'open-uri'
+require 'json'
+
+#External library
+#require 'bio-vcf'
+require 'highline/import'
+require 'mongoid'
+require 'bio'
+require 'pry'
+
+I18n.enforce_available_locales = false
+
+#library
+require 'exodb/dbconnection.rb'
+require 'exodb/usermanage.rb'
+require 'exodb/datamodel.rb'
+require 'exodb/exception.rb'
+require 'exodb/utils.rb'
+require 'exodb/addon.rb'
+
+
+module Exodb
+	
+	module_function
+	
+end

data/session.yml

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+production:
+ sessions:
+  default:
+   database: exomeid
+   hosts:
+    - localhost:27017

metadata

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+--- !ruby/object:Gem::Specification
+name: exodb
+version: !ruby/object:Gem::Version
+  version: 0.0.2
+platform: ruby
+authors:
+- Natapol Pornputtapong
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2014-10-31 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: mongoid
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '3.1'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '3.1'
+- !ruby/object:Gem::Dependency
+  name: bio
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '1.4'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '1.4'
+- !ruby/object:Gem::Dependency
+  name: highline
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '1.6'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '1.6'
+- !ruby/object:Gem::Dependency
+  name: pry
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '0.10'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '0.10'
+description: A library for exome sequencing data management
+email: natapol.por@gmail.com
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- contributors.txt
+- exodb.gemspec
+- genome/process_genome_seq.rb
+- lib/exodb.rb
+- lib/exodb/addon.rb
+- lib/exodb/addon/string.rb
+- lib/exodb/datamodel.rb
+- lib/exodb/datamodel/locationfield.rb
+- lib/exodb/datamodel/reference.rb
+- lib/exodb/datamodel/region.rb
+- lib/exodb/datamodel/source.rb
+- lib/exodb/datamodel/variant.rb
+- lib/exodb/datamodel/xrefsfield.rb
+- lib/exodb/dbconnection.rb
+- lib/exodb/exception.rb
+- lib/exodb/usermanage.rb
+- lib/exodb/utils.rb
+- lib/exodb/utils/upload_generef.rb
+- lib/exodb/utils/upload_var.rb
+- lib/exodb/vcf.rb
+- lib/exodb/version.rb
+- session.yml
+homepage: http://rubygems.org/gems/dactyls
+licenses:
+- GPL
+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: 2.0.14
+signing_key: 
+specification_version: 4
+summary: A library for exome sequencing data management development
+test_files: []
+has_rdoc: