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