Class: YouAndMe::DataProcessor

Inherits:
Object
  • Object
show all
Defined in:
lib/youandme/data_processor.rb

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(left, right) ⇒ DataProcessor 



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# File 'lib/youandme/data_processor.rb', line 19

def initialize(left, right)
  @left = left
  @right = right
  # @rsid_same = nil
  # @rsid_diff = nil
  # @both_rsid = nil
  # process
end

Instance Attribute Details

#both_rsid ⇒ Object

Returns the value of attribute both_rsid.



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# File 'lib/youandme/data_processor.rb', line 14

def both_rsid
  @both_rsid
end

#left ⇒ Object

Returns the value of attribute left.



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# File 'lib/youandme/data_processor.rb', line 10

def left
  @left
end

#multimarkdown_text ⇒ Object

Returns the value of attribute multimarkdown_text.



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# File 'lib/youandme/data_processor.rb', line 16

def multimarkdown_text
  @multimarkdown_text
end

#right ⇒ Object

Returns the value of attribute right.



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# File 'lib/youandme/data_processor.rb', line 11

def right
  @right
end

#rsid_diff ⇒ Object

Returns the value of attribute rsid_diff.



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# File 'lib/youandme/data_processor.rb', line 13

def rsid_diff
  @rsid_diff
end

#rsid_same ⇒ Object

Returns the value of attribute rsid_same.



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# File 'lib/youandme/data_processor.rb', line 12

def rsid_same
  @rsid_same
end

Instance Method Details

#process(status = false) ⇒ Object 



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# File 'lib/youandme/data_processor.rb', line 80

def process(status = false)
  puts "Creating indexes..." if status
  puts "\tIndexing left data..." if status
  @left_rsid         = @left.collect do |n| n[:rsid] end
  @left_chromosome   = @left.collect do |n| n[:chromosome] end
  @left_position     = @left.collect do |n| n[:position] end
  @left_genotype     = @left.collect do |n| n[:genotype] end

  puts "\tIndexing right data..." if status
  @right_rsid        = @right.collect do |n| n[:rsid] end
  @right_chromosome  = @right.collect do |n| n[:chromosome] end
  @right_position    = @right.collect do |n| n[:position] end
  @right_genotype    = @right.collect do |n| n[:genotype] end

  puts "Computing stuff..." if status
  puts "\tDetecting basic commonalities..." if status
  @both_rsid         = @left_rsid & @right_rsid
  both_position          = @left_position & @right_position

  puts "\tFinding dissimilar genotypes..." if status
  @rsid_same = []
  @rsid_diff = []
  @both_rsid.each do |rsid|
    l = left[@left_rsid.index(rsid)]
    r = right[@right_rsid.index(rsid)]
    if l[:genotype] == r[:genotype]
      @rsid_same << [l, r]
    else
      @rsid_diff << [l, r]
    end
  end
  
end

#to_multimarkdown(left_file, right_file) ⇒ Object 



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# File 'lib/youandme/data_processor.rb', line 71

def to_multimarkdown(left_file, right_file)
  @left_file = left_file
  @right_file = right_file
  dir = File.dirname(File.expand_path(__FILE__))
  template_file = File.join(dir, 'report.md.erb')
  template = ERB.new(File.read(template_file))
  @multimarkdown_text = template.result(binding)
end

#write_html(path) ⇒ Object 



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# File 'lib/youandme/data_processor.rb', line 45

def write_html(path)
  # Write the default file first.
  file_path = File.join(path, "report.html")
  puts "\tHTML #{file_path}..."
  report = File.open(file_path, 'w')
  mmd = MultiMarkdown.new(@multimarkdown_text, :smart, :filter_html)
  report.write mmd.to_html
  report.close

  # Load the XSL Transform.
  stylesheet_doc = XML::Document.file(File.join(File.dirname(__FILE__), 'xhtml-toc.xslt'))
  stylesheet = LibXSLT::XSLT::Stylesheet.new(stylesheet_doc)

  # Apply it and re-write the document.
  old_html = XML::Document.file(file_path)
  new_html = stylesheet.apply(old_html)
  report = File.open(file_path, 'w')
  report.write new_html
  report.close
  
  # Copy the CSS file into place.
  css_src = File.join(File.dirname(__FILE__), 'report.css')
  css_dest = File.join(path, 'report.css')
  FileUtils.copy(css_src, css_dest)
end

#write_latex(path) ⇒ Object 



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# File 'lib/youandme/data_processor.rb', line 36

def write_latex(path)
  file_path = File.join(path, "report.ltx")
  puts "\tLaTeX #{file_path}..."
  report = File.open(file_path, 'w')
  mmd = MultiMarkdown.new(@multimarkdown_text)
  report.write mmd.to_latex
  report.close 
end

#write_multimarkdown(path) ⇒ Object 



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# File 'lib/youandme/data_processor.rb', line 28

def write_multimarkdown(path)
  file_path = File.join(path, "report.md")
  puts "\tMultiMarkdown #{file_path}..."
  report = File.open(file_path, 'w')
  report.write @multimarkdown_text
  report.close 
end