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

Returns a new instance of 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