Class: Cytogenetics::Aberration

Inherits:
Object
  • Object
show all
Defined in:
lib/cytogenetics/aberration.rb

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(str) ⇒ Aberration

Returns a new instance of Aberration.



55
56
57
58
59
60
61
62
63
64
65
66
 
# File 'lib/cytogenetics/aberration.rb', line 55

def initialize(str)
  config_logging()

  @abr = str
  @breakpoints = []; @fragments = []

  #regex = Aberration.regex[@type.to_sym]
  # make sure it really is an inversion first
  #raise StructureError, "#{str} does not appear to be a #{self.class}" unless str.match(self.regex)
  get_breakpoints() #(@abr)
  @breakpoints.flatten!
end

Instance Attribute Details

#ab_objs ⇒ Object (readonly)

Returns the value of attribute ab_objs.



7
8
9
 
# File 'lib/cytogenetics/aberration.rb', line 7

def ab_objs
  @ab_objs
end

#abr ⇒ Object (readonly)

Returns the value of attribute abr.



7
8
9
 
# File 'lib/cytogenetics/aberration.rb', line 7

def abr
  @abr
end

#breakpoints ⇒ Object

Returns the value of attribute breakpoints.



6
7
8
 
# File 'lib/cytogenetics/aberration.rb', line 6

def breakpoints
  @breakpoints
end

#fragments ⇒ Object (readonly)

Returns the value of attribute fragments.



7
8
9
 
# File 'lib/cytogenetics/aberration.rb', line 7

def fragments
  @fragments
end

Class Method Details

.aberration_objs ⇒ Object

instantiate these



38
39
40
 
# File 'lib/cytogenetics/aberration.rb', line 38

def self.aberration_objs
  @ab_objs ||= self.instantiate_aberrations
end

.aberration_type ⇒ Object 



42
43
44
45
46
 
# File 'lib/cytogenetics/aberration.rb', line 42

def self.aberration_type
  abr_breaks = Aberration.all_regex.keys
  abr_breaks.delete_if { |c| c.to_s.match(/gain|loss/) }
  return abr_breaks
end

.all_regex ⇒ Object 



28
29
30
31
32
33
34
35
 
# File 'lib/cytogenetics/aberration.rb', line 28

def self.all_regex
  rx = {}
  ChromosomeAberrations.constants.each do |ca|
    ca_obj = ChromosomeAberrations.const_get(ca)
    rx[ca_obj.type.to_sym] = ca_obj.regex
  end
  return rx
end

.classify_aberration(abr) ⇒ Object 



48
49
50
51
52
53
 
# File 'lib/cytogenetics/aberration.rb', line 48

def self.classify_aberration(abr)
  Aberration.all_regex.each_pair do |k, regex|
    return k if abr.match(regex)
  end
  return "unk".to_sym
end

.instantiate_aberrations ⇒ Object 



10
11
12
13
14
15
16
17
 
# File 'lib/cytogenetics/aberration.rb', line 10

def instantiate_aberrations
  aberration_obj = {}
  ChromosomeAberrations.constants.each do |ca|
    abr_obj = ChromosomeAberrations.const_get(ca)
    aberration_obj[abr_obj.type.to_sym] = abr_obj
  end
  return aberration_obj
end

.regex ⇒ Object 



24
25
26
 
# File 'lib/cytogenetics/aberration.rb', line 24

def self.regex
  return @rx
end

.type ⇒ Object 



20
21
22
 
# File 'lib/cytogenetics/aberration.rb', line 20

def self.type
  return @kt
end

Instance Method Details

#config_logging ⇒ Object 



150
151
152
153
 
# File 'lib/cytogenetics/aberration.rb', line 150

def config_logging
  @log = Cytogenetics.logger
  #@log.progname = self.class.name
end

#find_bands(str, index) ⇒ Object 



112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
 
# File 'lib/cytogenetics/aberration.rb', line 112

def find_bands(str, index)
  band_info = nil
  #raise StructureError, "No bands defined in #{str}" if str.length.eql?(index+1)
  if str.length.eql?(index+1)
    @log.warn("No bands defined in #{str}, skipped.")
    return
  end

  ei = str.index(/\(/, index)
  if str.match(/(q|p)(\d+|\?)/) and str[ei-1..ei].eql?(")(") # has bands and is not a translocation
    band_s = str.index(/\(/, index)
    band_e = str.index(/\)/, band_s)
    band_e = str.length-1 if band_e.nil?
    bands = str[band_s+1..band_e-1].split(/;|:/)

    if str[band_s+1..band_e-1].match(/::/)
      @log.warn("Aberration defined using different language, not currently parsed skipping: #{@abr}")
      return band_info
    else
      bands.map! { |b| b.sub(/-[q|p]\d+$/, "") } # sometimes bands are given a range, for our purposes we'll take the first one (CyDas appears to do this as well)
      bands.each do |b|
        unless b.match(/^[p|q]\d+(\.\d)?$/)
          @log.warn("Bands incorrectly defined in #{str}")
          return band_info
        end
      end
      band_info = {:start_index => band_s, :end_index => band_e, :bands => bands}
    end
  end
  return band_info
end

#find_chr(str) ⇒ Object

Parsing aberration strings to pull out the chromosome and band definitions These will result in breakpoint information



99
100
101
102
103
104
105
106
107
108
109
110
 
# File 'lib/cytogenetics/aberration.rb', line 99

def find_chr(str)
  chr_s = str.index(/\(/, 0)
  chr_e = str.index(/\)/, chr_s)
  chrs = str[chr_s+1..chr_e-1].split(/;|:/)
  chrs.each do |chr|
    unless chr.match(/^\d+|X|Y$/)
      @log.warn("No chromosome defined from #{str}, skipped.")
      return
    end
  end
  return {:start_index => chr_s, :end_index => chr_e, :chr => chrs}
end

#find_fragments(str) ⇒ Object

sometimes bands are defined for a single chr as p13q22



145
146
147
 
# File 'lib/cytogenetics/aberration.rb', line 145

def find_fragments(str)
  return str.scan(/([p|q]\d+)/).collect { |a| a[0] }
end

#get_breakpoints ⇒ Object 



80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
 
# File 'lib/cytogenetics/aberration.rb', line 80

def get_breakpoints
  chr_i = find_chr(@abr)
  return if chr_i.nil?

  band_i = find_bands(@abr, chr_i[:end_index])

  unless band_i.nil? # breakpoints aren't added if there is no band information
    chr_i[:chr].each_with_index do |c, i|
      fragments = find_fragments(band_i[:bands][i])
      fragments.each { |f| @breakpoints << Breakpoint.new(c, f, self.class.type) }
    end
  else
    ## No band --> TODO add this as information somewhere but not as a breakpoint
    #@breakpoints << Breakpoint.new(c, "", @type)
  end
end

#remove_breakpoint(bp) ⇒ Object 



68
69
70
71
72
 
# File 'lib/cytogenetics/aberration.rb', line 68

def remove_breakpoint(bp)
  removed = @breakpoints.index(bp)
  @breakpoints.delete_at(removed) if removed
  return removed
end

#to_s ⇒ Object 



74
75
76
 
# File 'lib/cytogenetics/aberration.rb', line 74

def to_s
  "#{@abr}: #{@breakpoints.join(',')}"
end