youandme 0.2.3 → 0.2.4

data/VERSION

@@ -1 +1 @@
-0.2.3
+0.2.4

data/lib/youandme/raw_data_file_loader.rb

@@ -7,7 +7,14 @@ module YouAndMe
 
 		# 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]})"
+		  s = ""
+		  if(!(snp[:rsid][0] == 'i'))  #how to break a string across rows?
+			  s = "[dbSNP](http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=#{snp[:rsid]}) " +
+			      " [HapMap](http://hapmap.ncbi.nlm.nih.gov/cgi-perl/gbrowse/hapmap27_B36/?name=SNP%3A#{snp[:rsid]})" +
+			      " [NextBio](http://www.nextbio.com/b/search/details/#{snp[:rsid]}?type=snp&q0=#{snp[:rsid]}&t0=snp#tab=populations)" +
+			      " [Ensembl](http://uswest.ensembl.org/Homo_sapiens/Variation/Summary?v=#{snp[:rsid]};vdb=variation)"
+		  end
+		  s
 		end
 
 		# Returns true if and only if the given file exists and is readable.
@@ -35,8 +42,11 @@ module YouAndMe
 					:rsid => row[0],
 					:chromosome => row[1],
 					:position => row[2],
-					:genotype => row[3]				
-				}
+					:genotype => row[3]
+				} 
+				if snp[:genotype].match(/[A-Z]/) == nil
+				    snp[:genotype] = '-'
+			    end
 				# y snp
 				snps << snp
 			end

data/lib/youandme/report.md.erb

@@ -3,7 +3,7 @@ Subtitle:		A side-by-side comparison
 Format:			complete
 CSS:        report.css
 
-# SNV Comparison Report
+# SNV Comparison Report 
 
 <% loader = YouAndMe::RawDataFileLoader.new %>
 
@@ -14,7 +14,7 @@ CSS:        report.css
 - 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
+## 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.
 
@@ -25,11 +25,11 @@ The following <%= @rsid_same.length %> SNVs are the *same* in both profiles. Cli
 <% end %>
 
 
-## Different Genotype
+## 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]
+[Different 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]) %>

data/lib/youandme/xhtml-toc.xslt

@@ -117,7 +117,7 @@
 		</xsl:variable>
 		<xsl:copy>
 			<xsl:apply-templates select="@*|node()"/>
-			<a href="#ToC-{$link}">&#160;&#8617;</a>
+			<a href="#ToC-{$link}">[top]</a>
 		</xsl:copy>
 	</xsl:template>
 
@@ -127,7 +127,7 @@
 		</xsl:variable>
 		<xsl:copy>
 			<xsl:apply-templates select="@*|node()"/>
-			<a href="#ToC-{$link}">&#160;&#8617;</a>
+			<a href="#ToC-{$link}">[top]</a>
 		</xsl:copy>
 	</xsl:template>
 	

data/youandme.gemspec

@@ -5,7 +5,7 @@
 
 Gem::Specification.new do |s|
   s.name = "youandme"
-  s.version = "0.2.3"
+  s.version = "0.2.4"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Preston Lee"]

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: youandme
 version: !ruby/object:Gem::Version
-  version: 0.2.3
+  version: 0.2.4
   prerelease: 
 platform: ruby
 authors:
@@ -13,7 +13,7 @@ date: 2011-11-05 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: getopt
-  requirement: &70365759083120 !ruby/object:Gem::Requirement
+  requirement: &70240445149260 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -21,10 +21,10 @@ dependencies:
         version: 1.4.1
   type: :runtime
   prerelease: false
-  version_requirements: *70365759083120
+  version_requirements: *70240445149260
 - !ruby/object:Gem::Dependency
   name: rpeg-multimarkdown
-  requirement: &70365759081760 !ruby/object:Gem::Requirement
+  requirement: &70240445148220 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -32,10 +32,10 @@ dependencies:
         version: 0.1.1
   type: :runtime
   prerelease: false
-  version_requirements: *70365759081760
+  version_requirements: *70240445148220
 - !ruby/object:Gem::Dependency
   name: libxslt-ruby
-  requirement: &70365759080920 !ruby/object:Gem::Requirement
+  requirement: &70240445146820 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -43,10 +43,10 @@ dependencies:
         version: 1.0.8
   type: :runtime
   prerelease: false
-  version_requirements: *70365759080920
+  version_requirements: *70240445146820
 - !ruby/object:Gem::Dependency
   name: shoulda
-  requirement: &70365759079820 !ruby/object:Gem::Requirement
+  requirement: &70240445145980 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -54,10 +54,10 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *70365759079820
+  version_requirements: *70240445145980
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &70365759078780 !ruby/object:Gem::Requirement
+  requirement: &70240445144820 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -65,10 +65,10 @@ dependencies:
         version: 1.0.0
   type: :development
   prerelease: false
-  version_requirements: *70365759078780
+  version_requirements: *70240445144820
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &70365759077740 !ruby/object:Gem::Requirement
+  requirement: &70240445143760 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -76,10 +76,10 @@ dependencies:
         version: 1.6.4
   type: :development
   prerelease: false
-  version_requirements: *70365759077740
+  version_requirements: *70240445143760
 - !ruby/object:Gem::Dependency
   name: rcov
-  requirement: &70365759076920 !ruby/object:Gem::Requirement
+  requirement: &70240445142760 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -87,7 +87,7 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *70365759076920
+  version_requirements: *70240445142760
 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
@@ -131,7 +131,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: -2633759437025662770
+      hash: -1964140714609864698
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements: