youandme 0.2.0

data/.document

@@ -0,0 +1,5 @@
+lib/**/*.rb
+bin/*
+- 
+features/**/*.feature
+LICENSE.txt

data/Gemfile

@@ -0,0 +1,12 @@
+source "http://rubygems.org"
+
+gem 'getopt', "~> 1.4.1"
+gem 'rpeg-multimarkdown',	'~> 0.1.1', :require => 'multimarkdown'
+gem 'libxslt-ruby', '~> 1.0.8	'
+
+group :development do
+  gem "shoulda", ">= 0"
+  gem "bundler", "~> 1.0.0"
+  gem "jeweler", "~> 1.6.4"
+  gem "rcov", ">= 0"
+end

data/Gemfile.lock

@@ -0,0 +1,28 @@
+GEM
+  remote: http://rubygems.org/
+  specs:
+    getopt (1.4.1)
+    git (1.2.5)
+    jeweler (1.6.4)
+      bundler (~> 1.0)
+      git (>= 1.2.5)
+      rake
+    libxml-ruby (2.2.2)
+    libxslt-ruby (1.0.8)
+      libxml-ruby (>= 2.2.2)
+    rake (0.9.2.2)
+    rcov (0.9.11)
+    rpeg-multimarkdown (0.1.1)
+    shoulda (2.11.3)
+
+PLATFORMS
+  ruby
+
+DEPENDENCIES
+  bundler (~> 1.0.0)
+  getopt (~> 1.4.1)
+  jeweler (~> 1.6.4)
+  libxslt-ruby (~> 1.0.8)
+  rcov
+  rpeg-multimarkdown (~> 0.1.1)
+  shoulda

data/LICENSE.txt

@@ -0,0 +1,13 @@
+Copyright 2011 Preston Lee
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+    http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.

data/README.md

@@ -0,0 +1,23 @@
+# youandme
+
+An unofficial Ruby library and command-line application ("youandme") for quickly parsing 23andme raw data files into a plain Ruby structures for quick processing and analysis.
+
+## Installation ##
+
+    gem install youandme
+
+## Command-Line Usage
+
+The primary command-line script is "youandme", which generates a simple side-by-side comparison report for two given 23andme raw data files. To generate the reports, grab a few raw 23andme data files (from 23andme.com, SNPedia etc.), and compare them like so:
+
+    bin/youandme --directory <output_directory> --left <23andme_data_file.txt> --right <23andme_data_file.txt>
+
+For "full" files, this will take a LONG time to run. (As in, probably more than 24 hours.) I recommend breaking down the data files into chromosome-size chunks, and running each comparison through this script individually.
+
+## Authors ##
+
+Preston Lee
+
+## Copyright
+
+Copyright (c) 2011 Preston Lee. See LICENSE.txt for further details.

data/Rakefile

@@ -0,0 +1,53 @@
+# encoding: utf-8
+
+require 'rubygems'
+require 'bundler'
+begin
+  Bundler.setup(:default, :development)
+rescue Bundler::BundlerError => e
+  $stderr.puts e.message
+  $stderr.puts "Run `bundle install` to install missing gems"
+  exit e.status_code
+end
+require 'rake'
+
+require 'jeweler'
+Jeweler::Tasks.new do |gem|
+  # gem is a Gem::Specification... see http://docs.rubygems.org/read/chapter/20 for more options
+  gem.name = "youandme"
+  gem.homepage = "http://github.com/preston/youandme"
+  gem.license = "Apache 2.0"
+  gem.summary = %Q{Data comparison and analysis tools for 23andme raw data files.}
+  gem.description = %Q{An unofficial ruby library for quickly parsing 23andme raw data files into a plain Ruby structures for quick processing and analysis.}
+  gem.email = "conmotto@gmail.com"
+  gem.authors = ["Preston Lee"]
+  # dependencies defined in Gemfile
+end
+Jeweler::RubygemsDotOrgTasks.new
+
+require 'rake/testtask'
+Rake::TestTask.new(:test) do |test|
+  test.libs << 'lib' << 'test'
+  test.pattern = 'test/**/test_*.rb'
+  test.verbose = true
+end
+
+require 'rcov/rcovtask'
+Rcov::RcovTask.new do |test|
+  test.libs << 'test'
+  test.pattern = 'test/**/test_*.rb'
+  test.verbose = true
+  test.rcov_opts << '--exclude "gems/*"'
+end
+
+task :default => :test
+
+require 'rdoc/task'
+Rake::RDocTask.new do |rdoc|
+  version = File.exist?('VERSION') ? File.read('VERSION') : ""
+
+  rdoc.rdoc_dir = 'rdoc'
+  rdoc.title = "youandme #{version}"
+  rdoc.rdoc_files.include('README*')
+  rdoc.rdoc_files.include('lib/**/*.rb')
+end

data/VERSION

@@ -0,0 +1 @@
+0.2.0

data/bin/youandme

@@ -0,0 +1,76 @@
+#!/usr/bin/env ruby
+#
+# An script to compare two 23andme SNP data files.
+#
+# Author: Preston Lee
+# License: Apache 2
+
+# Runtime libraries:
+require 'erb'
+
+# 3rd-party libraries:
+require 'getopt/long'
+require 'multimarkdown'
+
+# Our libraries:
+current_dir = File.dirname(File.expand_path(__FILE__))
+gem_dir = File.join(current_dir, '..')
+lib_path = File.join(gem_dir, 'lib')
+$LOAD_PATH.unshift lib_path
+require 'youandme'
+
+
+def print_help_and_exit
+	puts "Usage:"
+	puts "\t#{$0} --directory <output_directory> --left <23andme_data_file.txt> --right <23andme_data_file.txt>"
+	puts "\t#{$0} -d <output_directory> -l <23andme_data_file.txt> -r <23andme_data_file.txt>"
+	exit(1)
+end
+
+
+begin
+	opt = Getopt::Long.getopts(
+	   ["--left", "-l", Getopt::REQUIRED],
+	   ["--right", "-r", Getopt::REQUIRED],
+	   ["--directory", "-d", Getopt::REQUIRED],
+	   ["--help", "-h", Getopt::BOOLEAN]
+	)
+rescue
+	print_help_and_exit
+end
+
+
+
+if(opt['help'])
+	print_help_and_exit
+end
+
+puts "Checking data file existyness..."
+loader = YouAndMe::RawDataFileLoader.new
+left_file = opt['left']
+right_file = opt['right']
+unless(loader.check_file(left_file) and loader.check_file(right_file))
+	puts "Please specify valid data files!"
+	print_help_and_exit
+end
+
+puts "Parsing data files... (may take a while)"
+max_rows = 1000
+left = loader.load_file(left_file, max_rows).sort{|a,b| a[:rsid] <=> b[:rsid]}
+puts "\tLoaded #{left.length} SNPs from #{left_file}"
+# y left[0..4]
+right = loader.load_file(right_file, max_rows).sort{|a,b| a[:rsid] <=> b[:rsid]}
+puts "\tLoaded #{right.length} SNPs from #{right_file}"
+processor = YouAndMe::DataProcessor.new(left, right)
+processor.process(true)
+
+
+puts "Writing reports..."
+processor.to_multimarkdown(left_file, right_file)
+path = File.expand_path("#{opt['directory']}")
+processor.write_multimarkdown(path)
+processor.write_latex(path)
+processor.write_html(path)
+
+
+puts "Done!"

data/lib/youandme.rb

@@ -0,0 +1,2 @@
+require 'youandme/raw_data_file_loader'
+require 'youandme/data_processor'

data/lib/youandme/data_processor.rb

@@ -0,0 +1,116 @@
+require 'xml'
+require 'libxslt'
+require 'fileutils'
+
+
+module YouAndMe
+	
+	class DataProcessor
+		
+		attr_accessor :left
+		attr_accessor :right
+		attr_accessor :rsid_same
+		attr_accessor :rsid_diff
+		attr_accessor :both_rsid
+		
+		attr_accessor :multimarkdown_text
+		
+		
+		def initialize(left, right)
+			@left = left
+			@right = right
+			# @rsid_same = nil
+			# @rsid_diff = nil
+			# @both_rsid = nil
+			# process
+		end
+		
+		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
+
+		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
+
+		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
+		
+		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
+		
+		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
+		
+	end
+	
+end

data/lib/youandme/raw_data_file_loader.rb

@@ -0,0 +1,48 @@
+# Author: Preston Lee
+
+module YouAndMe
+
+	# Tool for loading raw data files from 23andme into native Ruby structures
+	class RawDataFileLoader
+
+		# Returns Markdown-formatted URLs for the given SNP hash.
+		def markdown_links(snp)
+			 "[dbSNP](http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?rs=#{snp[:rsid]}) [SNPedia](http://www.snpedia.com/index.php/#{snp[:rsid]})"
+		end
+
+		# Returns true if and only if the given file exists and is readable.
+		def check_file(file_name)
+			valid = false
+			if(file_name != nil && File.file?(file_name) && File.readable?(file_name))
+				valid = true
+			end
+			valid
+		end
+
+		# Reads the given raw 23andme data file, parses the data, and shoves it into a native Ruby data structure.
+		# The returned data is an +Array+ full of +Hash+es, where each hash has key/value pairs for the columns in the data file.
+		def load_file(file_name, max = 0)
+			snps = []
+			# Manually spliting seems to be faster than the built-in CSV parser for
+			rows = File.read(file_name).split("\n")
+			rows.each do |n|
+				row = n.chomp.split("\t")
+			# CSV.foreach(file_name, :col_sep => "\t") do |row|
+				# Skip if the the line is a comment
+				next if row[0][0] == '#'
+				break if max > 0 && snps.length >= max
+				snp = {
+					:rsid => row[0],
+					:chromosome => row[1],
+					:position => row[2],
+					:genotype => row[3]				
+				}
+				# y snp
+				snps << snp
+			end
+			snps
+		end
+
+	end
+
+end

data/lib/youandme/report.css

@@ -0,0 +1,235 @@
+
+
+body blockquote {
+margin-top: .75em;
+line-height: 1.5;
+margin-bottom: .75em;
+}
+html {
+background: #f8f8f8;
+}
+html body {
+background: #fff;
+margin: 1em auto 1em auto;
+padding: 40px 100px;
+line-height: 1.8;
+width: 1000px;
+text-align: justify;
+font: 1.2em/2em "Century Gothic","Trebuchet MS",Arial,Helvetica,sans-serif;
+font-size: 18px;
+color: #444;
+}
+
+.legalnotice {
+font-size: small;
+font-variant: small-caps;
+}
+
+body div {
+margin: 0;
+}
+
+dl {
+margin: .8em 0;
+line-height: 1.2;
+}
+
+body form {
+margin: .6em 0;
+}
+
+h1, h2, h4, h5, h6,
+div.example p b,
+.question,
+div.table p b,
+div.procedure p b {
+color: #005599;
+font: bold 1.2em/2em "Century Gothic","Trebuchet MS",Arial,Helvetica,sans-serif;
+margin: 20px 0;
+}
+
+h1 {
+border-bottom: 1px solid black;
+}
+
+
+
+
+body hr {
+margin: .6em;
+border-width: 0 0 1px 0;
+border-style: solid;
+border-color: #cecece;
+}
+
+body img.navheader {
+margin: 0 0 0 -4%;
+}
+
+ol {
+margin: 0 0 0 5%;
+line-height: 1.2;
+}
+
+body pre {
+margin: .75em 0;
+line-height: 1.0;
+font-family: monospace;
+}
+
+body td, body th {
+line-height: 1.2;
+}
+
+ul, body dir, body menu {
+margin: 0 0 0 5%;
+line-height: 1.2;
+}
+
+html {
+margin: 0;
+padding: 0;
+}
+
+body p b.application {
+color: #000000;
+}
+
+.FILENAME {
+color: #007a00;
+}
+
+.GUIMENU, .GUIMENUITEM, .GUISUBMENU,
+.GUILABEL, .INTERFACE,
+.SHORTCUT, .SHORTCUT .KEYCAP {
+font-weight: bold;
+}
+
+.GUIBUTTON {
+background-color: #CFCFCF;
+padding: 2px;
+}
+
+.ACCEL {
+background-color: #F0F0F0;
+text-decoration: underline;
+}
+
+.SCREEN {
+padding: 1ex;
+}
+
+.PROGRAMLISTING {
+padding: 1ex;
+background-color: #eee;
+border: 1px solid #ccc;
+}
+
+@media screen {/* hide from IE3 */
+	a[href]:hover {
+background: #ffa
+}
+
+}
+
+BLOCKQUOTE.NOTE {
+color: #222;
+background: #eee;
+border: 1px solid #ccc;
+padding: 0.4em 0.4em;
+width: 85%;
+}
+
+BLOCKQUOTE.TIP {
+color: #004F00;
+background: #d8ecd6;
+border: 1px solid green;
+padding: 0.2em 2em;
+width: 85%;
+}
+
+BLOCKQUOTE.IMPORTANT {
+font-style: italic;
+border: 1px solid #a00;
+border-left: 12px solid #c00;
+padding: 0.1em 1em;
+}
+
+BLOCKQUOTE.WARNING {
+color: #9F1313;
+background: #f8e8e8;
+border: 1px solid #e59595;
+padding: 0.2em 2em;
+width: 85%;
+}
+
+.EXAMPLE {
+background: #fefde6;
+border: 1px solid #f1bb16;
+margin: 1em 0;
+padding: 0.2em 2em;
+width: 90%;
+}
+
+
+table {
+width: 90%;
+border-top: 1px solid #e5eff8;
+border-right: 1px solid #e5eff8;
+margin: 1em auto;
+border-collapse: collapse;
+}
+caption {
+color: #9ba9b4;
+font-size: .94em;
+letter-spacing: .1em;
+margin: 1em 0 0 0;
+padding: 0;
+caption-side: top;
+text-align: center;
+}
+tr.odd td {
+background: #f7fbff
+}
+tr.odd .column1 {
+background: #f4f9fe;
+}
+.column1 {
+background: #f9fcfe;
+}
+td {
+color: #678197;
+border-bottom: 1px solid #e5eff8;
+border-left: 1px solid #e5eff8;
+padding: .3em 1em;
+text-align: center;
+}
+th {
+font-weight: normal;
+color: #678197;
+text-align: left;
+border-bottom: 1px solid #e5eff8;
+border-left: 1px solid #e5eff8;
+padding: .3em 1em;
+}
+thead th {
+background: #f4f9fe;
+text-align: center;
+font: bold 1.2em/2em "Century Gothic","Trebuchet MS",Arial,Helvetica,sans-serif;
+color: #66a3d3
+}
+tfoot th {
+text-align: center;
+background: #f4f9fe;
+}
+tfoot th strong {
+font: bold 1.2em "Century Gothic","Trebuchet MS",Arial,Helvetica,sans-serif;
+margin: .5em .5em .5em 0;
+color: #66a3d3;
+}
+tfoot th em {
+color: #f03b58;
+font-weight: bold;
+font-size: 1.1em;
+font-style: normal;
+}

data/lib/youandme/report.md.erb

@@ -0,0 +1,37 @@
+Title:			SNV Comparison Report
+Subtitle:		A side-by-side comparison
+Format:			complete
+CSS:        report.css
+
+# SNV Comparison Report
+
+<% loader = YouAndMe::RawDataFileLoader.new %>
+
+- Left file: <%= @left_file %>
+- Right file: <%= @right_file %>
+- SNPs sequenced in both profiles: <%= @both_rsid.length %> (<%= 100.0 * @both_rsid.length / @left.length %>% of left and <%= 100.0 * @both_rsid.length / @right.length %>% of right.)
+- Same genotype when SNV in both profiles: <%= @rsid_same.length %> (<%= "%.3f" % (100.0 * @rsid_same.length / @left.length) %>% of left and <%= "%.3f" % (100.0 * @rsid_same.length / @right.length) %>% of right.))
+- Differing genotypes when SNV in both profiles: <%= @rsid_diff.length %> (<%= "%.3f" % (100.0 * @rsid_diff.length / @left.length) %>% of left and <%= "%.3f" % (100.0 * @rsid_diff.length / @right.length) %>% of right.))
+- Generated <%= Time.now.strftime("%m/%d/%Y at %I:%M%p") %>.
+
+## Same Genotype
+
+The following <%= @rsid_same.length %> SNVs are the *same* in both profiles. Click the links in the last column for access to scientific literature.
+
+[Same Genotype]
+| rsID | Genotype | Reference Position | Links ||
+ -------- |
+<% @rsid_same.each do |n| %><%= n[0][:rsid] %> | <%= n[0][:genotype] %> | <%= n[0][:position] %> |<%= loader.markdown_links(n[0]) %>
+<% end %>
+
+
+## Different Genotype
+
+The follow <%= @rsid_diff.length %> SNVs *differ* between the profiles. Click the links in the last column for access to scientific literature.
+
+[Same Genotype]
+| rsID | Left Genotype | Right Genotype | Reference Position | Links ||
+ -------- |
+<% @rsid_diff.each do |n| %><%= n[0][:rsid] %> | <%= n[0][:genotype] %> | <%= n[1][:genotype] %> | <%= n[0][:position] %> | <%= loader.markdown_links(n[0]) %>
+<% end %>
+

data/lib/youandme/xhtml-toc.xslt

@@ -0,0 +1,134 @@
+<?xml version='1.0' encoding='utf-8'?>
+
+<!-- XHTML-to-XHTML converter by Fletcher Penney
+	specifically designed for use with MultiMarkdown created XHTML
+	
+	Adds a Table of Contents to the top of the XHTML document,
+	and adds linkbacks from h1 and h2's.
+	
+	Also, an example of the sorts of things that can be done to customize
+	the XHTML output of MultiMarkdown.
+	
+	MultiMarkdown Version 2.0.b6
+	
+	$Id: xhtml-toc.xslt 499 2008-03-23 13:03:19Z fletcher $
+
+	TODO: If a section has no children, a "<ol></ol>" is generated, which is invalid
+-->
+
+<!-- 
+# Copyright (C) 2007-2008  Fletcher T. Penney <fletcher@fletcherpenney.net>
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 2 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the
+#    Free Software Foundation, Inc.
+#    59 Temple Place, Suite 330
+#    Boston, MA 02111-1307 USA
+-->
+
+	
+<xsl:stylesheet
+	xmlns:xsl="http://www.w3.org/1999/XSL/Transform"
+	xmlns:xhtml="http://www.w3.org/1999/xhtml"
+	xmlns="http://www.w3.org/1999/xhtml"
+  	exclude-result-prefixes="xhtml xsl"
+	version="1.0">
+
+	<xsl:variable name="newline">
+<xsl:text>
+</xsl:text>
+	</xsl:variable>
+	
+	<xsl:output method='xml' version="1.0" encoding='utf-8' doctype-public="-//W3C//DTD XHTML 1.1 plus MathML 2.0//EN" doctype-system="http://www.w3.org/TR/MathML2/dtd/xhtml-math11-f.dtd" indent="no"/>
+
+	<!-- the identity template, based on http://www.xmlplease.com/xhtmlxhtml -->
+	<xsl:template match="@*|node()">
+		<xsl:copy>
+			<xsl:apply-templates select="@*|node()"/>
+		</xsl:copy>
+	</xsl:template>
+
+	<!-- adjust the body to add a ToC -->
+	<!-- TODO: Will need to move this to just before first <h1> to allow for introductory comments -->
+	<xsl:template match="xhtml:body">
+		<xsl:copy>
+			<xsl:value-of select="$newline"/>
+			<h1>Table of Contents</h1>
+			<xsl:value-of select="$newline"/>
+			<ol>
+				<xsl:apply-templates select="xhtml:h1" mode="ToC"/>
+				<xsl:value-of select="$newline"/>
+			</ol>
+			<xsl:apply-templates select="@*|node()"/>
+		</xsl:copy>
+	</xsl:template>
+	
+	
+	<!-- create ToC entry -->
+	<xsl:template match="xhtml:h1" mode="ToC">
+		<xsl:value-of select="$newline"/>
+		<xsl:variable name="link">
+			<xsl:value-of select="@id"/>
+		</xsl:variable>
+		<xsl:variable name="myId">
+			<xsl:value-of select="generate-id(.)"/>
+		</xsl:variable>
+		<li>
+			<a id="ToC-{$link}" href="#{$link}">
+				<xsl:apply-templates select="node()"/>
+			</a>
+			<xsl:if test="following::xhtml:h2[1][preceding::xhtml:h1[1]]">
+				<xsl:value-of select="$newline"/>
+				<ol>
+					<xsl:apply-templates select="following::xhtml:h2[preceding::xhtml:h1[1][generate-id() = $myId]]" mode="ToC"/>
+					<xsl:value-of select="$newline"/>
+				</ol>
+				<xsl:value-of select="$newline"/>
+			</xsl:if>
+		</li>
+	</xsl:template>
+
+	<xsl:template match="xhtml:h2" mode="ToC">
+		<xsl:value-of select="$newline"/>
+		<xsl:variable name="link">
+			<xsl:value-of select="@id"/>
+		</xsl:variable>
+		<li>
+			<a id="ToC-{$link}" href="#{$link}">
+				<xsl:apply-templates select="node()"/>
+			</a>
+		</li>
+	</xsl:template>
+	
+	<!-- h1 and h2's should point back to the ToC for easy navigation -->
+	<xsl:template match="xhtml:h1">
+		<xsl:variable name="link">
+			<xsl:value-of select="@id"/>
+		</xsl:variable>
+		<xsl:copy>
+			<xsl:apply-templates select="@*|node()"/>
+			<a href="#ToC-{$link}">&#160;&#8617;</a>
+		</xsl:copy>
+	</xsl:template>
+
+	<xsl:template match="xhtml:h2">
+		<xsl:variable name="link">
+			<xsl:value-of select="@id"/>
+		</xsl:variable>
+		<xsl:copy>
+			<xsl:apply-templates select="@*|node()"/>
+			<a href="#ToC-{$link}">&#160;&#8617;</a>
+		</xsl:copy>
+	</xsl:template>
+	
+</xsl:stylesheet>

data/test/helper.rb

@@ -0,0 +1,18 @@
+require 'rubygems'
+require 'bundler'
+begin
+  Bundler.setup(:default, :development)
+rescue Bundler::BundlerError => e
+  $stderr.puts e.message
+  $stderr.puts "Run `bundle install` to install missing gems"
+  exit e.status_code
+end
+require 'test/unit'
+require 'shoulda'
+
+$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
+$LOAD_PATH.unshift(File.dirname(__FILE__))
+require 'youandme'
+
+class Test::Unit::TestCase
+end

data/test/test_youandme.rb

@@ -0,0 +1,7 @@
+require 'helper'
+
+class TestYouandme < Test::Unit::TestCase
+  should "probably rename this file and start testing for real" do
+    flunk "hey buddy, you should probably rename this file and start testing for real"
+  end
+end

metadata

@@ -0,0 +1,146 @@
+--- !ruby/object:Gem::Specification
+name: youandme
+version: !ruby/object:Gem::Version
+  version: 0.2.0
+  prerelease: 
+platform: ruby
+authors:
+- Preston Lee
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2011-11-04 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: getopt
+  requirement: &70244552095660 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.4.1
+  type: :runtime
+  prerelease: false
+  version_requirements: *70244552095660
+- !ruby/object:Gem::Dependency
+  name: rpeg-multimarkdown
+  requirement: &70244552094940 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 0.1.1
+  type: :runtime
+  prerelease: false
+  version_requirements: *70244552094940
+- !ruby/object:Gem::Dependency
+  name: libxslt-ruby
+  requirement: &70244552094060 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.0.8
+  type: :runtime
+  prerelease: false
+  version_requirements: *70244552094060
+- !ruby/object:Gem::Dependency
+  name: shoulda
+  requirement: &70244552093220 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: *70244552093220
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: &70244552091740 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.0.0
+  type: :development
+  prerelease: false
+  version_requirements: *70244552091740
+- !ruby/object:Gem::Dependency
+  name: jeweler
+  requirement: &70244552090860 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.6.4
+  type: :development
+  prerelease: false
+  version_requirements: *70244552090860
+- !ruby/object:Gem::Dependency
+  name: rcov
+  requirement: &70244552090000 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: *70244552090000
+description: An unofficial ruby library for quickly parsing 23andme raw data files
+  into a plain Ruby structures for quick processing and analysis.
+email: conmotto@gmail.com
+executables:
+- youandme
+extensions: []
+extra_rdoc_files:
+- LICENSE.txt
+- README.md
+files:
+- .document
+- Gemfile
+- Gemfile.lock
+- LICENSE.txt
+- README.md
+- Rakefile
+- VERSION
+- bin/youandme
+- lib/.DS_Store
+- lib/youandme.rb
+- lib/youandme/data_processor.rb
+- lib/youandme/raw_data_file_loader.rb
+- lib/youandme/report.css
+- lib/youandme/report.md.erb
+- lib/youandme/xhtml-toc.xslt
+- test/helper.rb
+- test/test_youandme.rb
+homepage: http://github.com/preston/youandme
+licenses:
+- Apache 2.0
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+      segments:
+      - 0
+      hash: -3067078396370175135
+required_rubygems_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 1.8.11
+signing_key: 
+specification_version: 3
+summary: Data comparison and analysis tools for 23andme raw data files.
+test_files: []