Class: String

Inherits:
Object
  • Object
show all
Defined in:
lib/exodb/addon/string.rb

Overview

raise “Please, use ruby 1.9.0 or later.” if RUBY_VERSION < “1.9.0”

Instance Method Summary collapse

Instance Method Details

#count_allele ⇒ Object

For Pileup string



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# File 'lib/exodb/addon/string.rb', line 80

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

#id ⇒ Object 



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# File 'lib/exodb/addon/string.rb', line 20

def id
	return self.is_miriam? ? self.split(':', 4)[-1] : ''
end

#is_hgvs? ⇒ Boolean

For HGV

Returns:

  • (Boolean) 


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# File 'lib/exodb/addon/string.rb', line 34

def is_hgvs?
	return self =~ Exodb::HGVPATTERN
end

#is_loc? ⇒ Boolean

Location String

Returns:

  • (Boolean) 


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# File 'lib/exodb/addon/string.rb', line 142

def is_loc?
	return /^\w+:(\d+|\d+\.\.\d+|\d+-\d+)(:\w+)?$/
end

#is_miriam? ⇒ Boolean

For miriam

Returns:

  • (Boolean) 


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# File 'lib/exodb/addon/string.rb', line 16

def is_miriam?
	return self =~ /^urn:miriam:/
end

#is_pileup_var? ⇒ Boolean

For pileup var

Returns:

  • (Boolean) 


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# File 'lib/exodb/addon/string.rb', line 113

def is_pileup_var?
	dat = self.split(/\//)
	return dat[0].is_loc? && dat[1] =~ /[\+\-]?[ATCG]+/
end

#namespace ⇒ Object 



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# File 'lib/exodb/addon/string.rb', line 24

def namespace
	return self.is_miriam? ? self.split(':', 4)[2] : ''
end

#parse_hgvs ⇒ Object 



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# File 'lib/exodb/addon/string.rb', line 38

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

#parse_loc ⇒ 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/addon/string.rb', line 150

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

#parse_pileup_var ⇒ Object 



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# File 'lib/exodb/addon/string.rb', line 118

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

#resolve ⇒ Object 



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# File 'lib/exodb/addon/string.rb', line 28

def resolve
	
end