cytogenetics 0.0.1 → 0.0.2
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- data/lib/cytogenetics.rb +19 -1
- data/lib/cytogenetics/aberration.rb +6 -6
- data/lib/cytogenetics/breakpoint.rb +1 -1
- data/lib/cytogenetics/chromosome.rb +4 -1
- data/lib/cytogenetics/chromosome_aberrations.rb +2 -2
- data/lib/cytogenetics/fragment.rb +1 -1
- data/lib/cytogenetics/karyotype.rb +4 -3
- data/lib/cytogenetics/utils/band_reader.rb +1 -0
- data/lib/cytogenetics/utils/karyotype_reader.rb +0 -1
- data/lib/cytogenetics/version.rb +2 -2
- metadata +1 -2
- data/lib/cytogenetics/karyotype_error.rb +0 -4
data/lib/cytogenetics.rb
CHANGED
@@ -4,7 +4,7 @@ require 'cytogenetics/chromosome'
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4
4
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require 'cytogenetics/chromosome_aberrations'
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5
5
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require 'cytogenetics/fragment'
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6
6
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require 'cytogenetics/karyotype'
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7
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-
require 'cytogenetics/karyotype_error'
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7
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+
#require 'cytogenetics/karyotype_error'
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8
8
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9
9
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10
10
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require 'cytogenetics/utils/karyotype_reader'
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@@ -27,10 +27,28 @@ module Cytogenetics
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27
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end
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28
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@clog
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29
29
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end
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30
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+
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31
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+
#def haploid=(hp)
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32
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+
# @sp_ploidy=hp
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33
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+
#end
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34
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+
#
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35
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+
#def haploid
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36
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+
# unless @sp_ploidy
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37
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+
#
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38
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# end
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39
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+
#end
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40
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+
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end
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31
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32
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def self.karyotype(kary_str)
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return Karyotype.new(kary_str)
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34
45
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end
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46
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47
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+
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48
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+
class StructureError < StandardError
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49
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end
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50
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+
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51
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+
class KaryotypeError < StandardError
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52
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end
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53
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+
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end
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@@ -60,7 +60,7 @@ module Cytogenetics
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#regex = Aberration.regex[@type.to_sym]
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62
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# make sure it really is an inversion first
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63
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-
#raise
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63
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+
#raise StructureError, "#{str} does not appear to be a #{self.class}" unless str.match(self.regex)
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64
64
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get_breakpoints() #(@abr)
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@breakpoints.flatten!
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66
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end
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@@ -102,7 +102,7 @@ module Cytogenetics
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chrs = str[chr_s+1..chr_e-1].split(/;|:/)
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103
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chrs.each do |chr|
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unless chr.match(/^\d+|X|Y$/)
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105
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-
log.warn("No chromosome defined from #{str}, skipped.")
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105
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+
@log.warn("No chromosome defined from #{str}, skipped.")
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106
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return
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107
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end
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108
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end
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@@ -111,9 +111,9 @@ module Cytogenetics
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111
111
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112
112
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def find_bands(str, index)
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113
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band_info = nil
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114
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-
#raise
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114
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+
#raise StructureError, "No bands defined in #{str}" if str.length.eql?(index+1)
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115
115
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if str.length.eql?(index+1)
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116
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-
log.warn("No bands defined in #{str}, skipped.")
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116
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+
@log.warn("No bands defined in #{str}, skipped.")
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117
117
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return
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118
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end
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119
119
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@@ -125,13 +125,13 @@ module Cytogenetics
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bands = str[band_s+1..band_e-1].split(/;|:/)
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126
126
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127
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if str[band_s+1..band_e-1].match(/::/)
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128
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-
log.warn("Aberration defined using different language, not currently parsed skipping: #{@abr}")
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128
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+
@log.warn("Aberration defined using different language, not currently parsed skipping: #{@abr}")
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129
129
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return band_info
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130
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else
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131
131
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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)
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bands.each do |b|
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unless b.match(/^[p|q]\d+(\.\d)?$/)
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134
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-
log.warn("Bands incorrectly defined in #{str}")
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134
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+
@log.warn("Bands incorrectly defined in #{str}")
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135
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return band_info
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136
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end
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137
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end
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@@ -11,7 +11,7 @@ module Cytogenetics
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11
11
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12
12
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unless ((c.is_a? String and c.match(/\d+|X|Y/)) and (b.is_a? String and b.length > 0))
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13
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@log.error("#{c}#{b} is not a valid breakpoint")
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14
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-
raise
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14
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+
raise StructureError, "#{c}#{b} is not a valid breakpoint"
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15
15
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end
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16
16
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@chr = c; @band = b
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end
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@@ -1,5 +1,8 @@
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1
1
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require 'cytogenetics/utils/band_reader'
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2
2
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3
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+
File.expand_path '../../resources', File.dirname(__FILE__)
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+
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5
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+
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3
6
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module Cytogenetics
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4
7
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5
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class Chromosome
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@@ -19,7 +22,7 @@ module Cytogenetics
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raise ArgumentError, "#{chr} is not a valid chromosome identifier." unless (chr.is_a? String and chr.match(/^\d+|X|Y$/))
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23
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@name = chr
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@aberrations = []
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22
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-
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25
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+
#@normal_bands = bands(@name, File.open("HsBands.txt", 'r')) if (args.length > 1 and args[1].eql? true) ## TODO quit hardcoding
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23
26
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end
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24
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25
28
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def to_s
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@@ -91,7 +91,7 @@ module Cytogenetics
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91
91
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abrclass = Aberration.classify_aberration(abn)
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92
92
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93
93
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if abrclass.to_s.eql? 'unk' # not dealing with unknowns
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94
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-
log.warn("Cannot handle #{abn}, incorrect format.")
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94
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+
@log.warn("Cannot handle #{abn}, incorrect format.")
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next
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96
96
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end
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97
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@@ -145,7 +145,7 @@ module Cytogenetics
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145
145
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chr_i = find_chr(@abr)
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146
146
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band_i = find_bands(@abr, chr_i[:end_index])
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147
147
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unless band_i
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148
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-
log.warn("No bands defined in #{@abr}")
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148
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+
@log.warn("No bands defined in #{@abr}")
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149
149
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else
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150
150
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chr_i[:chr].each_with_index do |c, i|
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151
151
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@breakpoints << Breakpoint.new(c, band_i[:bands][i], 'trans')
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@@ -16,7 +16,7 @@ module Cytogenetics
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@chr = @start.chr
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18
18
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unless @start.chr.eql? @end.chr
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19
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-
raise
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19
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+
raise StructureError, "Fragments must be within the same chromosome: #{args}"
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20
20
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end
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end
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22
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@@ -8,7 +8,7 @@ module Cytogenetics
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8
8
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9
9
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@@haploid = 23
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10
10
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11
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-
attr_reader :aberrations, :karyotype, :ploidy, :sex, :abnormal_chr, :normal_chr
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11
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+
attr_reader :aberrations, :karyotype, :ploidy, :sex, :abnormal_chr, :normal_chr, :original_karyotype
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12
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class<<self
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14
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attr_accessor :aberration_objs, :unclear_aberrations, :log
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@@ -20,6 +20,7 @@ module Cytogenetics
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@log.info("Reading karyotype #{karyotype_str}")
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@karyotype = karyotype_str.gsub(/\s/, "")
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+
@original_karyotype = @karyotype # just to keep it around before it gets cleaned up
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@normal_chr = {}; @abnormal_chr = {}; @aberrations = {}; @unclear_aberrations = [];
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setup_abberation_objs()
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prep_karyotype()
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@@ -117,10 +118,10 @@ module Cytogenetics
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117
118
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# determine ploidy & gender, clean up each aberration and drop any "unknown"
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118
119
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def prep_karyotype
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119
120
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@karyotype.gsub!(/\s/, "")
|
120
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-
clones = @karyotype.scan(/(\[\
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121
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+
clones = @karyotype.scan(/(\[\w+\])/).collect { |a| a[0] }
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@log.warn("Karyotype is a collection of clones, analysis may be inaccurate.") if clones.length > 3
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122
123
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123
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-
@karyotype.gsub!(/\[\
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124
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+
@karyotype.gsub!(/\[\w+\]/, "") # don't care about numbers of cells: [5] or [cp10], there are some other problematic things in [] but they are just being ignored currently
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125
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(pl, sc) = @karyotype.split(",")[0..1]
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if (pl and sc)
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data/lib/cytogenetics/version.rb
CHANGED
@@ -1,3 +1,3 @@
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1
1
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module Cytogenetics
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2
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-
VERSION = '0.0.
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3
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-
end
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2
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+
VERSION = '0.0.2'
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3
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+
end
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metadata
CHANGED
@@ -1,7 +1,7 @@
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1
1
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--- !ruby/object:Gem::Specification
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2
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name: cytogenetics
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3
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version: !ruby/object:Gem::Version
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4
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-
version: 0.0.
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4
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+
version: 0.0.2
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5
5
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prerelease:
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platform: ruby
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7
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authors:
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@@ -25,7 +25,6 @@ files:
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25
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- lib/cytogenetics/chromosome_aberrations.rb
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- lib/cytogenetics/fragment.rb
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27
27
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- lib/cytogenetics/karyotype.rb
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28
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-
- lib/cytogenetics/karyotype_error.rb
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29
28
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- lib/cytogenetics/utils/band_reader.rb
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30
29
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- lib/cytogenetics/utils/karyotype_reader.rb
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31
30
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- lib/cytogenetics/version.rb
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