Class: Exodb::Mapping

Inherits:
Object
  • Object
show all
Includes:
Mongoid::Document
Defined in:
lib/exodb/extra/upload.rb,
lib/exodb/datamodel/reference.rb

Class Method Summary collapse

Instance Method Summary collapse

Class Method Details

.convert(locstr, target = Exodb::LATESTASSEMBLY) ⇒ Object 



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# File 'lib/exodb/datamodel/reference.rb', line 67

def self.convert(locstr, target = Exodb::LATESTASSEMBLY)
	begin
		query = parse_locstr(locstr)
		return self.where({from: query['assembly'], to: target, :start.lte => query[:pos], :stop.gte => query[:pos]}).first.convert(query[:pos])
	rescue
		
	end
end

.load_assembly_mapping!(from, to) ⇒ Object 



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# File 'lib/exodb/extra/upload.rb', line 17

def self.load_assembly_mapping!(from, to)
	
	self.where(from: Exodb::assembly(from), to: Exodb::assembly(to))
	
	Exodb::Chrref.where({:assembly => Exodb::assembly(from), 'location.chr' => /\Achr/}).each do |chr|
		
		Exodb::Ensembl::REST.assembly_map(chr.locstr =~ /\Achr/ ? chr.locstr[3..-1] : chr.locstr,  Exodb::assembly(to),  Exodb::assembly(from))["mappings"].each do |map|
			
			#map = {"original"=>{"seq_region_name"=>"1", "strand"=>1, "coordinate_system"=>"chromosome", "end"=>235674528, "start"=>235669016, "assembly"=>"GRCh37"}, "mapped"=>{"seq_region_name"=>"1", "strand"=>1, "coordinate_system"=>"chromosome", "end"=>235511225, "start"=>235505713, "assembly"=>"GRCh38"}}
			
			mapping = self.new()
			mapping.chr = "#{map['original']["coordinate_system"] == "chromosome" ? 'chr' : ''}#{map['original']["seq_region_name"]}"
			mapping.start = map['original']["start"]
			mapping.stop = map['original']["end"]
			mapping.from = map['original']["assembly"]
			mapping.tchr = "#{map['mapped']["coordinate_system"] == "chromosome" ? 'chr' : ''}#{map['mapped']["seq_region_name"]}"
			mapping.tstart = map['mapped']["start"]
			mapping.tstop = map['mapped']["end"]
			mapping.coeff = map['mapped']["strand"]
			mapping.to = map['mapped']["assembly"]
			
			p mapping.save!
		end
	end
end

Instance Method Details

#convert(pos) ⇒ Object 



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# File 'lib/exodb/datamodel/reference.rb', line 76

def convert(pos)
	return  "#{self[:tchr]}:#{(coeff > 0 ? tstart : tstop) + ((pos - self[:start]) * coeff)}:#{to}"
end