youandme 0.2.3 → 0.2.4

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data/VERSION CHANGED
@@ -1 +1 @@
1
- 0.2.3
1
+ 0.2.4
@@ -7,7 +7,14 @@ module YouAndMe
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  # Returns Markdown-formatted URLs for the given SNP hash.
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  def markdown_links(snp)
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- "[dbSNP](http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?rs=#{snp[:rsid]}) [SNPedia](http://www.snpedia.com/index.php/#{snp[:rsid]})"
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+ s = ""
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+ if(!(snp[:rsid][0] == 'i')) #how to break a string across rows?
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+ s = "[dbSNP](http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=#{snp[:rsid]}) " +
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+ " [HapMap](http://hapmap.ncbi.nlm.nih.gov/cgi-perl/gbrowse/hapmap27_B36/?name=SNP%3A#{snp[:rsid]})" +
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+ " [NextBio](http://www.nextbio.com/b/search/details/#{snp[:rsid]}?type=snp&q0=#{snp[:rsid]}&t0=snp#tab=populations)" +
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+ " [Ensembl](http://uswest.ensembl.org/Homo_sapiens/Variation/Summary?v=#{snp[:rsid]};vdb=variation)"
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+ end
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+ s
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  end
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  # Returns true if and only if the given file exists and is readable.
@@ -35,8 +42,11 @@ module YouAndMe
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  :rsid => row[0],
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  :chromosome => row[1],
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  :position => row[2],
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- :genotype => row[3]
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- }
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+ :genotype => row[3]
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+ }
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+ if snp[:genotype].match(/[A-Z]/) == nil
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+ snp[:genotype] = '-'
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+ end
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  # y snp
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  snps << snp
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  end
@@ -3,7 +3,7 @@ Subtitle: A side-by-side comparison
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  Format: complete
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  CSS: report.css
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- # SNV Comparison Report
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+ # SNV Comparison Report
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  <% loader = YouAndMe::RawDataFileLoader.new %>
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@@ -14,7 +14,7 @@ CSS: report.css
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  - 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.))
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  - Generated <%= Time.now.strftime("%m/%d/%Y at %I:%M%p") %>.
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- ## Same Genotype
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+ ## Same Genotype
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  The following <%= @rsid_same.length %> SNVs are the *same* in both profiles. Click the links in the last column for access to scientific literature.
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@@ -25,11 +25,11 @@ The following <%= @rsid_same.length %> SNVs are the *same* in both profiles. Cli
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  <% end %>
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- ## Different Genotype
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+ ## Different Genotype
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  The follow <%= @rsid_diff.length %> SNVs *differ* between the profiles. Click the links in the last column for access to scientific literature.
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- [Same Genotype]
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+ [Different Genotype]
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  | rsID | Left Genotype | Right Genotype | Reference Position | Links ||
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  -------- |
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  <% @rsid_diff.each do |n| %><%= n[0][:rsid] %> | <%= n[0][:genotype] %> | <%= n[1][:genotype] %> | <%= n[0][:position] %> | <%= loader.markdown_links(n[0]) %>
@@ -117,7 +117,7 @@
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  </xsl:variable>
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  <xsl:copy>
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  <xsl:apply-templates select="@*|node()"/>
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- <a href="#ToC-{$link}">&#160;&#8617;</a>
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+ <a href="#ToC-{$link}">[top]</a>
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  </xsl:copy>
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  </xsl:template>
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@@ -127,7 +127,7 @@
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  </xsl:variable>
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  <xsl:copy>
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  <xsl:apply-templates select="@*|node()"/>
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- <a href="#ToC-{$link}">&#160;&#8617;</a>
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+ <a href="#ToC-{$link}">[top]</a>
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  </xsl:copy>
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  </xsl:template>
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@@ -5,7 +5,7 @@
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  Gem::Specification.new do |s|
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  s.name = "youandme"
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- s.version = "0.2.3"
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+ s.version = "0.2.4"
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  s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
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  s.authors = ["Preston Lee"]
metadata CHANGED
@@ -1,7 +1,7 @@
1
1
  --- !ruby/object:Gem::Specification
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  name: youandme
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  version: !ruby/object:Gem::Version
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- version: 0.2.3
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+ version: 0.2.4
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  prerelease:
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  platform: ruby
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  authors:
@@ -13,7 +13,7 @@ date: 2011-11-05 00:00:00.000000000 Z
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  dependencies:
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  - !ruby/object:Gem::Dependency
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  name: getopt
16
- requirement: &70365759083120 !ruby/object:Gem::Requirement
16
+ requirement: &70240445149260 !ruby/object:Gem::Requirement
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  none: false
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  requirements:
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  - - ~>
@@ -21,10 +21,10 @@ dependencies:
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  version: 1.4.1
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  type: :runtime
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  prerelease: false
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- version_requirements: *70365759083120
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+ version_requirements: *70240445149260
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  - !ruby/object:Gem::Dependency
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  name: rpeg-multimarkdown
27
- requirement: &70365759081760 !ruby/object:Gem::Requirement
27
+ requirement: &70240445148220 !ruby/object:Gem::Requirement
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  none: false
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  requirements:
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  - - ~>
@@ -32,10 +32,10 @@ dependencies:
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  version: 0.1.1
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  type: :runtime
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  prerelease: false
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- version_requirements: *70365759081760
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+ version_requirements: *70240445148220
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  - !ruby/object:Gem::Dependency
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  name: libxslt-ruby
38
- requirement: &70365759080920 !ruby/object:Gem::Requirement
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+ requirement: &70240445146820 !ruby/object:Gem::Requirement
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  none: false
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  requirements:
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  - - ~>
@@ -43,10 +43,10 @@ dependencies:
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  version: 1.0.8
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  type: :runtime
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  prerelease: false
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- version_requirements: *70365759080920
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+ version_requirements: *70240445146820
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  - !ruby/object:Gem::Dependency
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  name: shoulda
49
- requirement: &70365759079820 !ruby/object:Gem::Requirement
49
+ requirement: &70240445145980 !ruby/object:Gem::Requirement
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  none: false
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  requirements:
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  - - ! '>='
@@ -54,10 +54,10 @@ dependencies:
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  version: '0'
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  type: :development
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  prerelease: false
57
- version_requirements: *70365759079820
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+ version_requirements: *70240445145980
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  - !ruby/object:Gem::Dependency
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  name: bundler
60
- requirement: &70365759078780 !ruby/object:Gem::Requirement
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+ requirement: &70240445144820 !ruby/object:Gem::Requirement
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  none: false
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  requirements:
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  - - ~>
@@ -65,10 +65,10 @@ dependencies:
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  version: 1.0.0
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  type: :development
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  prerelease: false
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- version_requirements: *70365759078780
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+ version_requirements: *70240445144820
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  - !ruby/object:Gem::Dependency
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  name: jeweler
71
- requirement: &70365759077740 !ruby/object:Gem::Requirement
71
+ requirement: &70240445143760 !ruby/object:Gem::Requirement
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  none: false
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  requirements:
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  - - ~>
@@ -76,10 +76,10 @@ dependencies:
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  version: 1.6.4
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  type: :development
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  prerelease: false
79
- version_requirements: *70365759077740
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+ version_requirements: *70240445143760
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  - !ruby/object:Gem::Dependency
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  name: rcov
82
- requirement: &70365759076920 !ruby/object:Gem::Requirement
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+ requirement: &70240445142760 !ruby/object:Gem::Requirement
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  none: false
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  requirements:
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  - - ! '>='
@@ -87,7 +87,7 @@ dependencies:
87
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  version: '0'
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  type: :development
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  prerelease: false
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- version_requirements: *70365759076920
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+ version_requirements: *70240445142760
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91
  description: An unofficial ruby library for quickly parsing 23andme raw data files
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92
  into a plain Ruby structures for quick processing and analysis.
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93
  email: conmotto@gmail.com
@@ -131,7 +131,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
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  version: '0'
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  segments:
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  - 0
134
- hash: -2633759437025662770
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+ hash: -1964140714609864698
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  required_rubygems_version: !ruby/object:Gem::Requirement
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  none: false
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  requirements: