cytogenetics 0.0.1 → 0.0.2

data/lib/cytogenetics.rb

@@ -4,7 +4,7 @@ require 'cytogenetics/chromosome'
 require 'cytogenetics/chromosome_aberrations'
 require 'cytogenetics/fragment'
 require 'cytogenetics/karyotype'
-require 'cytogenetics/karyotype_error'
+#require 'cytogenetics/karyotype_error'
 
 
 require 'cytogenetics/utils/karyotype_reader'
@@ -27,10 +27,28 @@ module Cytogenetics
       end
       @clog
     end
+
+    #def haploid=(hp)
+    #  @sp_ploidy=hp
+    #end
+    #
+    #def haploid
+    #  unless @sp_ploidy
+    #
+    #  end
+    #end
+
   end
 
   def self.karyotype(kary_str)
     return Karyotype.new(kary_str)
   end
 
+
+  class StructureError < StandardError
+  end
+
+  class KaryotypeError < StandardError
+  end
+
 end

data/lib/cytogenetics/aberration.rb

@@ -60,7 +60,7 @@ module Cytogenetics
 
       #regex = Aberration.regex[@type.to_sym]
       # make sure it really is an inversion first
-      #raise KaryotypeError, "#{str} does not appear to be a #{self.class}" unless str.match(self.regex)
+      #raise StructureError, "#{str} does not appear to be a #{self.class}" unless str.match(self.regex)
       get_breakpoints() #(@abr)
       @breakpoints.flatten!
     end
@@ -102,7 +102,7 @@ module Cytogenetics
       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.")
+          @log.warn("No chromosome defined from #{str}, skipped.")
           return
         end
       end
@@ -111,9 +111,9 @@ module Cytogenetics
 
     def find_bands(str, index)
       band_info = nil
-      #raise KaryotypeError, "No bands defined in #{str}" if str.length.eql?(index+1)
+      #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.")
+        @log.warn("No bands defined in #{str}, skipped.")
         return
       end
 
@@ -125,13 +125,13 @@ module Cytogenetics
         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}")
+          @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}")
+              @log.warn("Bands incorrectly defined in #{str}")
               return band_info
             end
           end

data/lib/cytogenetics/breakpoint.rb

@@ -11,7 +11,7 @@ module Cytogenetics
 
       unless ((c.is_a? String and c.match(/\d+|X|Y/)) and (b.is_a? String and b.length > 0))
         @log.error("#{c}#{b} is not a valid breakpoint")
-        raise ArgumentError, "#{c}#{b} is not a valid breakpoint"
+        raise StructureError, "#{c}#{b} is not a valid breakpoint"
       end
       @chr = c; @band = b
     end

data/lib/cytogenetics/chromosome.rb

@@ -1,5 +1,8 @@
 require 'cytogenetics/utils/band_reader'
 
+File.expand_path '../../resources', File.dirname(__FILE__)
+
+
 module Cytogenetics
 
   class Chromosome
@@ -19,7 +22,7 @@ module Cytogenetics
       raise ArgumentError, "#{chr} is not a valid chromosome identifier." unless (chr.is_a? String and chr.match(/^\d+|X|Y$/))
       @name = chr
       @aberrations = []
-      @normal_bands = bands(@name, "resources/HsBands.txt") if (args.length > 1 and args[1].eql? true) ## TODO quit hardcoding
+      #@normal_bands = bands(@name, File.open("HsBands.txt", 'r')) if (args.length > 1 and args[1].eql? true) ## TODO quit hardcoding
     end
 
     def to_s

data/lib/cytogenetics/chromosome_aberrations.rb

@@ -91,7 +91,7 @@ module Cytogenetics
           abrclass = Aberration.classify_aberration(abn)
 
           if abrclass.to_s.eql? 'unk' # not dealing with unknowns
-            log.warn("Cannot handle #{abn}, incorrect format.")
+            @log.warn("Cannot handle #{abn}, incorrect format.")
             next
           end
 
@@ -145,7 +145,7 @@ module Cytogenetics
         chr_i = find_chr(@abr)
         band_i = find_bands(@abr, chr_i[:end_index])
         unless band_i
-          log.warn("No bands defined in #{@abr}")
+          @log.warn("No bands defined in #{@abr}")
         else
           chr_i[:chr].each_with_index do |c, i|
             @breakpoints << Breakpoint.new(c, band_i[:bands][i], 'trans')

data/lib/cytogenetics/fragment.rb

@@ -16,7 +16,7 @@ module Cytogenetics
       @chr = @start.chr
 
       unless @start.chr.eql? @end.chr
-        raise GenomeStructureError, "Fragments must be within the same chromosome: #{args}"
+        raise StructureError, "Fragments must be within the same chromosome: #{args}"
       end
     end
 

data/lib/cytogenetics/karyotype.rb

@@ -8,7 +8,7 @@ module Cytogenetics
 
     @@haploid = 23
 
-    attr_reader :aberrations, :karyotype, :ploidy, :sex, :abnormal_chr, :normal_chr
+    attr_reader :aberrations, :karyotype, :ploidy, :sex, :abnormal_chr, :normal_chr, :original_karyotype
 
     class<<self
       attr_accessor :aberration_objs, :unclear_aberrations, :log
@@ -20,6 +20,7 @@ module Cytogenetics
       @log.info("Reading karyotype #{karyotype_str}")
 
       @karyotype = karyotype_str.gsub(/\s/, "")
+      @original_karyotype = @karyotype # just to keep it around before it gets cleaned up
       @normal_chr = {}; @abnormal_chr = {}; @aberrations = {}; @unclear_aberrations = [];
       setup_abberation_objs()
       prep_karyotype()
@@ -117,10 +118,10 @@ module Cytogenetics
 # determine ploidy & gender, clean up each aberration and drop any "unknown"
     def prep_karyotype
       @karyotype.gsub!(/\s/, "")
-      clones = @karyotype.scan(/(\[\d+\])/).collect { |a| a[0] }
+      clones = @karyotype.scan(/(\[\w+\])/).collect { |a| a[0] }
       @log.warn("Karyotype is a collection of clones, analysis may be inaccurate.") if clones.length > 3
 
-      @karyotype.gsub!(/\[\d+\]/, "") # don't care about numbers of cells: [5]
+      @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
 
       (pl, sc) = @karyotype.split(",")[0..1]
       if (pl and sc)

data/lib/cytogenetics/utils/band_reader.rb

@@ -17,6 +17,7 @@ module Cytogenetics
       band_by_chr = {}
       file.each_line do |line|
         line.chomp!
+        next if line.start_with?"#"
         line.match(/^(\d+|X|Y)([p|q].*)/)
         c = $1; b = $2
         band_by_chr[c] = Array.new unless band_by_chr.has_key? c

data/lib/cytogenetics/utils/karyotype_reader.rb

@@ -1,4 +1,3 @@
-require 'cytogenetics/karyotype_error'
 
 module Cytogenetics
   class KaryotypeReader

data/lib/cytogenetics/version.rb

@@ -1,3 +1,3 @@
 module Cytogenetics
-  VERSION = '0.0.1'
-end
+  VERSION = '0.0.2'
+end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: cytogenetics
 version: !ruby/object:Gem::Version
-  version: 0.0.1
+  version: 0.0.2
   prerelease: 
 platform: ruby
 authors:
@@ -25,7 +25,6 @@ files:
 - lib/cytogenetics/chromosome_aberrations.rb
 - lib/cytogenetics/fragment.rb
 - lib/cytogenetics/karyotype.rb
-- lib/cytogenetics/karyotype_error.rb
 - lib/cytogenetics/utils/band_reader.rb
 - lib/cytogenetics/utils/karyotype_reader.rb
 - lib/cytogenetics/version.rb

data/lib/cytogenetics/karyotype_error.rb

@@ -1,4 +0,0 @@
-module Cytogenetics
-  class KaryotypeError < StandardError
-  end
-end