exodb 0.0.2 → 0.1.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: bd0cec2b7ef4791ab9686827bf8d31409152af2a
-  data.tar.gz: 117c7eb770d5473a76909af778017f2557288982
+  metadata.gz: f59876f64775ac85fda8bbb7db9a06e253ab39b8
+  data.tar.gz: 978e13f8048b2cabea0cfe4fc96a9da6e42b97fe
 SHA512:
-  metadata.gz: 6b7cd7602e7bda8da25c1799e5fbc0fd3221e04397b52a54cb4c1b5b2691b6cfea96d1e114bfc1f218529d747614544876da7eb78d8258ef3ee41a082d22eee2
-  data.tar.gz: 5699679e8fb8834af7c4e7f42ca2f399c549c015b1fa07781240a9a9f76d01a56951ba72af04645254232d588a6c1c9424034f23ec03791098bd57a0e3d5bf3c
+  metadata.gz: ceca94da8429c39dee7e1baa9d96f5a88f8860cbf1c185ee2439845d0c93d3a63605bc4d2e6bc7c33c3e1d5c0c424e1d37a1f7557ce8a96baa303ca692a78f55
+  data.tar.gz: 1d20bb30b30b1aea8a612abd255c02f985a2b6fdcc6dd38431f387c2fc3335e56fd5261b38adefb58655d064cb6fef074e11d725af871768269b4bef2b44e9ee

data/lib/exodb.rb

@@ -17,6 +17,8 @@ gem 'mongoid', '~> 3.1'
 
 #Internal library
 require 'open-uri'
+require 'net/http'
+require 'uri'
 require 'json'
 
 #External library

data/lib/exodb/datamodel/locationfield.rb

@@ -11,12 +11,14 @@
 
 module Exodb
     
-	module LocationField
+	module GenomeLocationField
 		
 		extend ActiveSupport::Concern
 		
 		included do
 			field :location,		type: Hash #{chromosome: '', start: x, stop: x}
+			field :strand,			type: String
+
 			index({location: 1}, background: true)
 		end
 		
@@ -73,7 +75,19 @@ module Exodb
 			self[:location]['stop']
 		end
 		
-		alias_method :end, :stop
+		# get the start position of gene rely on the genome
+		#
+		# @return [Integer] start position of gene
+		def begin
+			self[:strand] == '+' ? self[:location]['start'] : self[:location]['stop']
+		end
+		
+		# get the start position of gene rely on the genome
+		#
+		# @return [Integer] start position of gene
+		def end
+			self[:strand] == '+' ? self[:location]['stop'] : self[:location]['start']
+		end
 		
 		# get the chromosome
 		#

data/lib/exodb/datamodel/reference.rb

@@ -28,14 +28,14 @@ module Exodb
 		PATTERN = /(?<gene>[A-Z0-9]+)-?(?<position>[0-9,]*|[is]?)(?<to>[A-Z=]*)/
 		SILENTSIGN = '='
 		
-		include Exodb::LocationField
+		include Exodb::GenomeLocationField
 		
 		field :reference,			type: String
 		field :alternate,			type: String
 		
 	end
 	
-	class Incidence
+	class Occurrent
 		
 		include Mongoid::Document
 		
@@ -50,19 +50,18 @@ module Exodb
 	
 	class Generef < Reference
 		
-		include Exodb::LocationField
+		include Exodb::GenomeLocationField
 		
 		field :sequence,			type: String
 		field :chrrefseq,			type: String # refseq id of chromomose
-		field :strand,				type: String
 		field :psuedo,				type: Boolean
 		field :genomeref,			type: String
 		
 		index({sequence: 'text'}, background: true)
 		
 		has_many :genes
-		embeds_many :splices
-		embeds_many :incidences
+		embeds_many :isoforms
+		embeds_many :occurrents
 		
 		validates_format_of :chrrefseq, with: /\A(urn:miriam:refseq)/
 		
@@ -114,7 +113,7 @@ module Exodb
 		
 		# Download incident data from TCGA
 		#
-		def dl_incidence!
+		def dl_occurrent!
 			
 			if self.get_xref('urn:miriam:hgnc.symbol')
 				
@@ -124,7 +123,7 @@ module Exodb
 					f.each_line {|line| cancerstudies.push(line.chomp.split("\t")[0])}
 				}
 				
-				incidents = {}
+				occurrents = {}
 				totalcase = {}
 				
 				cancerstudies.each do |study|
@@ -137,7 +136,7 @@ module Exodb
 						end
 					end
 					
-					incidents[study] = {} if !incidents.has_key?(study)
+					occurrents[study] = {} if !occurrents.has_key?(study)
 					
 					open("http://www.cbioportal.org/public-portal/webservice.do?cmd=getMutationData&genetic_profile_id=#{study}_mutations&gene_list=#{self.get_xref('urn:miriam:hgnc.symbol').id}") do |f|
 						f.each_line do |line|
@@ -145,8 +144,8 @@ module Exodb
 							
 							if dat[5] == 'Missense_Mutation'
 								
-								incidents[study][dat[7].split(/(\d+)/)[1]] = [] if !incidents[study].has_key?(dat[7].split(/(\d+)/)[1])
-								incidents[study][dat[7].split(/(\d+)/)[1]].push(dat[2])
+								occurrents[study][dat[7].split(/(\d+)/)[1]] = [] if !occurrents[study].has_key?(dat[7].split(/(\d+)/)[1])
+								occurrents[study][dat[7].split(/(\d+)/)[1]].push(dat[2])
 								
 							end
 							
@@ -156,11 +155,11 @@ module Exodb
 					end
 				end
 				
-				self.incidences.clear if self.incidences
+				self.occurrents.clear if self.occurrents
 				
-				incidents.each_pair do |cancertype, v|
+				occurrents.each_pair do |cancertype, v|
 					v.each_pair do |position, occur|
-						self.incidences << Incidence.new({cancertype: cancertype, position: position, occur: occur.uniq.sort, casenumber: totalcase[cancertype]})
+						self.occurrents << Occurrent.new({cancertype: cancertype, position: position, occur: occur.uniq.sort, casenumber: totalcase[cancertype]})
 					end
 				end
 				
@@ -181,7 +180,7 @@ module Exodb
 		def longest_splice()
 			length = 0
 			longest = nil
-			self.splices.each do |e|
+			self.isoforms.each do |e|
 				
 				if e.prot_len > length
 					length = e.prot_len
@@ -197,7 +196,7 @@ module Exodb
 		#
 		# @return [Boolean] true if has any splices
 		def has_splices?
-			return self.splices.exists?
+			return self.isoforms.exists?
 		end
 		
 		# Check if Generef has sequence
@@ -231,7 +230,7 @@ module Exodb
 		
 	end
 	
-	class Splice
+	class Isoform
 		
 		include Mongoid::Document
 		
@@ -375,7 +374,7 @@ module Exodb
 			
 			seqlen = self.get_cds_seq(pos).length
 			if seqlen != 0
-				return [(seqlen - 1) / 3, (seqlen - 1) % 3]
+				return [((seqlen - 1) / 3) + 1, ((seqlen - 1) % 3) + 1]
 			else
 				return []
 			end

data/lib/exodb/datamodel/region.rb

@@ -22,29 +22,56 @@ module Exodb
 	class Gene < Region
 		
 		include Mongoid::Versioning
-		include Exodb::LocationField
+		include Exodb::GenomeLocationField
 		
 		field :symbol,				type: String
 		field :loh,					type: Boolean
 		
-		embeds_many :aacids
+		embeds_many :changes
 		belongs_to :generef
 		belongs_to :cell
 		
 		index({'symbol' => 1, 'aacids.position' => 1}, background: true)
 	end
 	
-	class Aacid < Region
+	class Change
 		
-		field :position,			type: Integer # position referenced to the first codon from the longest splice variant
+		include Mongoid::Document
+		include Mongoid::Timestamps
+		
+		embedded_in :gene
+		has_many :variants
+		
+	end
+	
+	class Onexon < Change
+		
+		field :aaposition,			type: Integer # position referenced to the first codon from the longest splice variant
 		field :refcodon,			type: String
 		field :refaa,				type: String
 		field :altcodon,			type: Hash
 		field :inhcodon,			type: Hash
 		field :isoform,				type: Array
 		
-		embedded_in :gene
-		has_many :variants
+	end
+	
+	class Aa < Onexon
+		
+	end
+	
+	class Lossgain < Onexon
+		
+	end
+	
+	class Offexon < Change
+		
+	end
+	
+	class Splice < Offexon
+		
+	end
+	
+	class Utr < Offexon
 		
 	end
 	

data/lib/exodb/datamodel/source.rb

@@ -99,7 +99,6 @@ module Exodb
 								position = splice.get_prot_pos(variant.start)
 								aacid.isoform.push("#{generef.get_xref()}:p.#{mainsplice.get_codon(position[0]).translate}#{position[0]}") if !position.empty?
 							end
-							aacid.save!
 							gene.save!
 						end
 					end

data/lib/exodb/datamodel/variant.rb

@@ -17,7 +17,7 @@ module Exodb
 		include Mongoid::Versioning
 		include Mongoid::Timestamps
 		
-		include Exodb::LocationField
+		include Exodb::GenomeLocationField
 		
 		#max_versions 5
 		
@@ -74,11 +74,7 @@ module Exodb
 		
 	end
 	
-	class SV < Variant #
-		
-	end
-	
-	class Indel < Variant
+	class Indel < Variant #
 		
 	end
 	

data/lib/exodb/exception.rb

@@ -14,5 +14,9 @@ module Exodb
 	class CreateUserError < Exception
 		
 	end
+	
+	class InvalidResponse < Exception
+		
+	end
 
 end

data/lib/exodb/usermanage.rb

@@ -68,16 +68,16 @@ module Exodb
 	# @param [String] database that user created
 	def create_rwuser(username)
 		
-		create_user(username, Mongoid.session.options[:database], "readWrite")
+		create_user(username, Mongoid.session(:default).options[:database], "readWrite")
 		
 	end
 	
 	# To create a read-only user
 	#
 	# @param (see #create_rwuser)
-	def create_ruser(username)
+	def create_rouser(username)
 		
-		create_user(username, Mongoid.session.options[:database], "read")
+		create_user(username, Mongoid.session(:default).options[:database], "read")
 		
 	end
 	

data/lib/exodb/utils.rb

@@ -11,6 +11,7 @@
 
 require 'exodb/utils/upload_generef.rb'
 require 'exodb/utils/upload_var.rb'
+require 'exodb/utils/ensemblrest.rb'
 
 module Exodb
 	

data/lib/exodb/utils/upload_generef.rb

@@ -140,13 +140,13 @@ module Exodb
 					
 					v[:childs].each do |child|
 						
-						rna = Splice.new()
+						rna = Isoform.new()
 						data = genes[child]
 						rna.xrefs = data[:xrefs]
 						rna.exon = data[:exon].sort
 						rna.cds = data[:cds].sort
 						
-						gene.splices.push(rna)
+						gene.isoforms.push(rna)
 						
 					end
 					

data/lib/exodb/utils/upload_var.rb

@@ -51,6 +51,16 @@ module Exodb
 				
 			end
 		end
+		
+		def load_variant_from_ann(annfile)
+			
+			File.open(annfile).each do |line|
+				record = line.chomp.split("\t")
+				p record
+			end
+			
+		end
+		
 	end
 	
 end

data/lib/exodb/version.rb

@@ -11,5 +11,5 @@
 
 
 module Exodb
-	VERSION = "0.0.2"
+	VERSION = "0.1.0"
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: exodb
 version: !ruby/object:Gem::Version
-  version: 0.0.2
+  version: 0.1.0
 platform: ruby
 authors:
 - Natapol Pornputtapong