exodb 0.1.2 → 0.1.3

checksums.yaml

@@ -1,7 +1,7 @@
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data/lib/exodb.rb

@@ -36,12 +36,35 @@ require 'exodb/dbconnection.rb'
 require 'exodb/usermanage.rb'
 require 'exodb/datamodel.rb'
 require 'exodb/exception.rb'
+require 'exodb/constant.rb'
 require 'exodb/utils.rb'
 require 'exodb/addon.rb'
 
+require 'exodb/extra.rb'
 
 module Exodb
 	
+	@@verbose = true
+	
 	module_function
 	
+	def verbose()
+		@@verbose = true
+	end
+	
+	def noverbose()
+		@@verbose = false
+	end
+	
+	def putstv(str)
+		putst(str) if @@verbose == true
+	end
+	
+	def putst(str)
+		puts "Exodb:STATUS #{str}"
+	end
+	
+	def assembly(str)
+		return Exodb::ASSEMBLY[str.downcase]
+	end
 end

data/lib/exodb/addon/string.rb

@@ -11,6 +11,8 @@
 
 class String
 	
+	# For miriam
+	
 	def is_miriam?
 		return self =~ /^urn:miriam:/
 	end
@@ -23,4 +25,141 @@ class String
 		return self.is_miriam? ? self.split(':', 4)[2] : ''
 	end
 	
+	def resolve
+		
+	end
+	
+	# For HGV
+	
+	def is_hgvs?
+		return self =~ Exodb::HGVPATTERN
+	end
+	
+	def parse_hgvs
+		
+		result = {}
+		
+		Exodb::HGVPATTERN.match(self) do |m|
+			
+			if m[1] =~ /^chr/
+				ref = m[1].split(/\./)
+				result[:chr] = ref[0]
+				result[:assembly] = ref[1].blank? ? Exodb::DEFAULTASSEMBLY : Exodb.assembly(ref[1])
+			elsif m[1] =~ /^(\d{0,2}|[MXY])\./
+				ref = m[1].split(/\./)
+				result[:chr] = "chr#{ref[0]}"
+				result[:assembly] = ref[1].blank? ? Exodb::DEFAULTASSEMBLY : Exodb.assembly(ref[1])
+			else
+				result[:chrrefseq] = m[1]
+			end
+			
+			pos = m[2].split(/_/).sort
+			result[:pos] = pos[0].to_i
+			result[:start] = pos[0].to_i
+			result[:stop] = pos[1].blank? ? pos[0].to_i : pos[1].to_i
+			
+			case m[3]
+			when /^ins/
+				result[:type] = 'ins'
+				result[:alt] = m[3][3..-1]
+			when /^del/
+				result[:type] = 'del'
+				result[:alt] = m[3][3..-1]
+			else 
+				result[:type] = 'sub'
+				result[:alt] = m[3].split(/\>/)[1]
+			end
+			
+		end
+		
+		return result
+		
+	end
+	
+	# For Pileup string
+	def count_allele
+		
+		allellset = {
+			'A' => "aA",
+			'T' => "tT",
+			'C' => "cC",
+			'G' => "gG",
+			'.' => "\\.\\,",
+			'*' => "\\*"
+		}
+		
+		tmpstr = self.dup
+		
+		allele = {}
+		
+		self.scan(/([+-])(\d+)([ATCGatcg]+)/) do |a, b, c|
+			pattern = "#{a}#{b}#{c[0,(b.to_i)]}".upcase
+			if !allele.has_key?(pattern)
+				allele[pattern] = 0
+				tmpstr.gsub!(/#{"#{b}#{c[0,(b.to_i)]}"}/, '')
+			end
+			allele[pattern] += 1
+		end
+		
+		allellset.each_pair do |k, v|
+			allele[k] = tmpstr.count(v) if tmpstr.count(v) > 0
+		end
+		
+		return allele
+		
+	end
+	
+	# For pileup var
+	def is_pileup_var?
+		dat = self.split(/\//)
+		return dat[0].is_loc? && dat[1] =~ /[\+\-]?[ATCG]+/
+	end
+	
+	def parse_pileup_var
+		
+		result = {}
+		if self.is_pileup_var?
+			dat = self.split(/\//)
+			result = dat[0].parse_loc
+			dat[1] =~ /([\+\-]?)([ATCG]+)/
+			result[:type] = case $1
+			when '+'
+				'ins'
+			when '-'
+				'del'
+			else
+				'sub'
+			end
+			result[:alt] = dat[1]
+		end
+		
+		return result
+		
+	end
+	
+	# Location String
+	
+	def is_loc?
+		return /^\w+:(\d+|\d+\.\.\d+|\d+-\d+)(:\w+)?$/
+	end
+	# For quality string
+	
+	# Assign gene location in format of chromosome_number:start..stop
+	#
+	# @param [String] gene location in format of chromosome_number:start..stop
+	def parse_loc
+		
+		if self =~ /^[^:]+:(\d+|\d+\.\.\d+|\d+-\d+)(:\w+)?$/
+			dat = self.split(/:/)
+			pos = []
+			dat[1].split(/\.\.|-/).each {|e| pos.push(e.to_i)}
+			pos.sort!
+			return {'chr' => dat[0], 'start' => pos[0], 'pos' => pos[0], 'stop' => pos[1] ? pos[1] : pos[0], 'assembly' => dat[2] ? Exodb::assembly(dat[2]) : Exodb::DEFAULTASSEMBLY}
+		else
+			raise
+		end
+		
+		
+	end
+	
 end

data/lib/exodb/constant.rb

@@ -0,0 +1,64 @@
+# 
+# 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
+	
+	NAIUPAC = {
+		'Y'	=> 'CT',
+		'R'	=> 'AG',
+		'W'	=> 'AT',
+		'S'	=> 'CG',
+		'K'	=> 'GT',
+		'M'	=> 'AC',
+		
+		'B'	=> 'CGT',
+		'D'	=> 'AGT',
+		'H'	=> 'ACT',
+		'V'	=> 'ACG',
+		
+		'N'	=> 'ACGT',
+		
+		'A'	=> 'A',
+		'T'	=> 'T',
+		'G'	=> 'G',
+		'C'	=> 'C',
+		'U'	=> 'U',
+		
+		'CT' => 'Y',
+		'AG' => 'R',
+		'AT' => 'W',
+		'CG' => 'S',
+		'GT' => 'K',
+		'AC' => 'M',
+		
+		'CGT' => 'B',
+		'AGT' => 'D',
+		'ACT' => 'H',
+		'ACG' => 'V',
+		
+		'ACGT' => 'N'
+	}
+	
+	ASSEMBLY = {
+		'hg19' => 'GRCh37',
+		'hg38' => 'GRCh38',
+		'GRCh37' => 'GRCh37',
+		'GRCh38' => 'GRCh38',
+		'grch37' => 'GRCh37',
+		'grch38' => 'GRCh38'
+	}
+	
+	DEFAULTASSEMBLY = 'GRCh37'
+	LATESTASSEMBLY = 'GRCh38'
+	
+	HGVPATTERN = /^([^:]+):g\.([\-_\d]+)([ATGC]>[ATCG]|del[ATCG]*|ins[ATCG]*)$/
+	
+end

data/lib/exodb/datamodel.rb

@@ -11,9 +11,12 @@
 
 require 'mongoid'
 
-require 'exodb/datamodel/locationfield.rb'
+require 'exodb/datamodel/genelocfield.rb'
+require 'exodb/datamodel/varlocfield.rb'
 require 'exodb/datamodel/xrefsfield.rb'
 require 'exodb/datamodel/variant.rb'
 require 'exodb/datamodel/reference.rb'
+require 'exodb/datamodel/generef.rb'
+require 'exodb/datamodel/isoform.rb'
 require 'exodb/datamodel/region.rb'
 require 'exodb/datamodel/source.rb'

data/lib/exodb/datamodel/genelocfield.rb

@@ -0,0 +1,177 @@
+# 
+# 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"
+
+module Exodb
+    
+	module GeneLocationField
+		
+		extend ActiveSupport::Concern
+		
+		included do
+			field :start,				type: Integer
+			field :stop,				type: Integer
+			field :chr,					type: String
+			field :seqstart,			type: Integer
+			field :seqstop,				type: Integer
+			field :strand,				type: String
+			field :assembly,			type: String
+			field :sequence,			type: String
+			field :chrrefseq,			type: String # refseq id of chromosome
+			
+			validates_presence_of :start, message: "start field missing"
+			validates_presence_of :stop, message: "stop field missing"
+			validates_presence_of :chr, message: "chr field missing"
+			validates_presence_of :assembly, message: "assembly field missing"
+			
+			index({start: 1, stop: 1, chr: 1, assembly: 1}, background: true)
+		end
+		
+		module ClassMethods
+			
+			def where_cover(loc_str)
+				
+				dat = parse_locstr(loc_str)
+				
+				return self.where({chr: dat['chr'], assembly: dat['assembly']}).lte(start: dat['start']).gte(stop: dat['stop'])
+				
+			end
+			
+			def where_intersect(loc_str)
+				dat = parse_locstr(loc_str)
+				
+				return self.where({chr: dat['chr'], assembly: dat['assembly']}).or({:start.lte => dat['start'], :stop.gte => dat['start']}, {:start.lte => dat['stop'], :stop.gte => dat['stop']})
+			end
+			
+			def where_in(loc_str)
+				dat = parse_locstr(loc_str)
+				return self.where({chr: dat['chr'], assembly: dat['assembly']}).gte(start: dat['start']).lte(stop: dat['stop'])
+			end
+			
+			def where_ups_cover(loc_str)
+				#code
+			end
+			
+		end
+		
+		# Download sequence from web service please use by caution. NCBI will block scamming sequest
+		#
+		def dl_seq!
+			
+			case self.chrrefseq
+			when /\Aurn:miriam:refseq:/
+				self.sequence = Bio::FastaFormat.new(Bio::NCBI::REST.efetch(self.chrrefseq.split(':', 4), {"db"=>"nucleotide", "rettype"=>"fasta", "retmode"=>"text", "seq_start"=>self.start, "seq_stop"=>self.end})).seq
+			else 
+				self.sequence = Exodb::Ensembl::REST.sequence_region()
+			end
+			
+			self.save!
+			
+		end
+		
+		# get the start position of gene rely on the genome
+		#
+		# @return [Integer] start position of gene
+		def start
+			self[:start]
+		end
+		
+		# get the end position of gene rely on the genome
+		#
+		# @return [Integer] end position of gene
+		def stop
+			self[:stop]
+		end
+		
+		# get the start position of gene rely on the genome
+		#
+		# @return [Integer] start position of gene
+		def begin
+			self[:strand] == '+' ? self[:start] : self[:stop]
+		end
+		
+		# get the start position of gene rely on the genome
+		#
+		# @return [Integer] start position of gene
+		def end
+			self[:strand] == '+' ? self[:stop] : self[:start]
+		end
+		
+		# get the chromosome
+		#
+		# @return [Integer] chromosome
+		def chromosome
+			self[:chr]
+		end
+		
+		# Assign location
+		#
+		# @param [String, Hash] location string in chromosome:start..stop or chromosome:start-stop format
+		def location=(loc)
+			if loc.is_a?(String)
+				
+				begin
+					loc.parse_loc.delete_if {|k, v| k == 'pos'}.each_pair do |k, v|
+						self[k.to_sym] = v
+					end
+				rescue
+					
+				end
+				
+			end
+		end
+		
+		# Return location
+		#
+		# @return [String] location string in chromosome:position
+		def location_str
+			return "#{self.chromosome}:#{[self.start, self.stop].uniq.join('..')}"
+		end
+		
+		alias_method :locstr, :location_str
+		
+		# Return gene sequence
+		#
+		# @return [Bio::Sequence] gene sequence
+		def to_seq
+			whole_seq.splice("#{self[:start] - self[:seqstart] + 1}..#{self[:stop] - self[:seqstart] + 1}")
+		end
+		
+		# Return whole deposited sequence
+		#
+		# @return [Bio::Sequence] gene sequence
+		def whole_seq
+			Bio::Sequence::NA.new(self[:sequence])
+		end
+		
+		# join exon or cds position into a string
+		#
+		# @param [Array] input array exon or cds
+		# @param [Interger] Position to stop positive value for forward read negative value for complement
+		#
+		# @return [String] a string in start..end,start..end,...
+		def get_splice(arr, strand = nil)
+			
+			strand = strand || self[:strand]
+			
+			reducer = self[:seqlocation]['start'] - 1
+			
+			str = []
+			
+			arr.each do |e|
+				str.push("#{e[0] - reducer}..#{e[1] - reducer}")
+			end
+			
+			return strand == '+' ? self.to_seq.splicing("join(#{str.join(',')})") : self.to_seq.splicing("complement(join(#{str.join(',')}))")
+			
+		end
+	end
+    
+end