Module: Exodb::GenomeLocationField

Extended by:
ActiveSupport::Concern
Included in:
Gene, Generef, Variant, Variantref
Defined in:
lib/exodb/datamodel/locationfield.rb

Defined Under Namespace

Modules: ClassMethods

Instance Method Summary collapse

Instance Method Details

#begin ⇒ Integer

get the start position of gene rely on the genome

Returns:

  • (Integer) —

    start position of gene



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# File 'lib/exodb/datamodel/locationfield.rb', line 81

def begin
	self[:strand] == '+' ? self[:location]['start'] : self[:location]['stop']
end

#chromosome ⇒ Integer

get the chromosome

Returns:

  • (Integer) —

    chromosome



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# File 'lib/exodb/datamodel/locationfield.rb', line 95

def chromosome
	self[:location]['chromosome']
end

#end ⇒ Integer

get the start position of gene rely on the genome

Returns:

  • (Integer) —

    start position of gene



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# File 'lib/exodb/datamodel/locationfield.rb', line 88

def end
	self[:strand] == '+' ? self[:location]['stop'] : self[:location]['start']
end

#location_str ⇒ Object 



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# File 'lib/exodb/datamodel/locationfield.rb', line 111

def location_str
	return "#{self.chromosome}:#{[self.start, self.stop].uniq.join('..')}"
end

#parse_location(loc_str) ⇒ Object

Assign gene location in format of chromosome_number:start..stop

Parameters:

  • gene (String) —

    location in format of chromosome_number:start..stop



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# File 'lib/exodb/datamodel/locationfield.rb', line 102

def parse_location(loc_str)
	dat = loc_str.split(/(:|\.\.|-)/)
	if dat[4]
		self[:location] = {'chromosome' => dat[0], 'start' => dat[2].to_i, 'stop' => dat[4].to_i}
	else
		self[:location] = {'chromosome' => dat[0], 'start' => dat[2].to_i, 'stop' => dat[2].to_i}
	end
end

#start ⇒ Integer

get the start position of gene rely on the genome

Returns:

  • (Integer) —

    start position of gene



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

def start
	self[:location]['start']
end

#stop ⇒ Integer

get the end position of gene rely on the genome

Returns:

  • (Integer) —

    end position of gene



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# File 'lib/exodb/datamodel/locationfield.rb', line 74

def stop
	self[:location]['stop']
end