bio-ucsc-api 0.3.0 → 0.3.1

data/Gemfile

@@ -2,9 +2,9 @@ source "http://rubygems.org"
 # Add dependencies required to use your gem here.
 # Example:
 #   gem "activesupport", ">= 2.3.5"
-gem "activerecord",         ">= 3.0.7"
-gem "activesupport",        ">= 3.0.7"
-gem "mysql",                ">= 2.8.1"
+gem "activerecord",         "~> 3.0.7"
+gem "activesupport",        "~> 3.0.7"
+gem "mysql",                "~> 2.8.1"
 gem "bio-genomic-interval", ">= 0.1.2"
 
 # Add dependencies to develop your gem here.

data/Gemfile.lock

@@ -1,21 +1,21 @@
 GEM
   remote: http://rubygems.org/
   specs:
-    activemodel (3.0.9)
-      activesupport (= 3.0.9)
+    activemodel (3.0.10)
+      activesupport (= 3.0.10)
       builder (~> 2.1.2)
       i18n (~> 0.5.0)
-    activerecord (3.0.9)
-      activemodel (= 3.0.9)
-      activesupport (= 3.0.9)
+    activerecord (3.0.10)
+      activemodel (= 3.0.10)
+      activesupport (= 3.0.10)
       arel (~> 2.0.10)
       tzinfo (~> 0.3.23)
-    activesupport (3.0.9)
+    activesupport (3.0.10)
     arel (2.0.10)
-    bio (1.4.1)
+    bio (1.4.2)
     bio-genomic-interval (0.1.2)
     builder (2.1.2)
-    diff-lcs (1.1.2)
+    diff-lcs (1.1.3)
     git (1.2.5)
     i18n (0.5.0)
     jeweler (1.5.2)
@@ -25,7 +25,7 @@ GEM
     mysql (2.8.1)
     rake (0.9.2)
     rcov (0.9.10)
-    rdoc (3.9.1)
+    rdoc (3.9.4)
     rspec (2.5.0)
       rspec-core (~> 2.5.0)
       rspec-expectations (~> 2.5.0)
@@ -40,13 +40,13 @@ PLATFORMS
   ruby
 
 DEPENDENCIES
-  activerecord (>= 3.0.7)
-  activesupport (>= 3.0.7)
+  activerecord (~> 3.0.7)
+  activesupport (~> 3.0.7)
   bio (>= 1.4.1)
   bio-genomic-interval (>= 0.1.2)
   bundler (~> 1.0.0)
   jeweler (~> 1.5.2)
-  mysql (>= 2.8.1)
+  mysql (~> 2.8.1)
   rcov
   rdoc (>= 3.9.1)
   rspec (~> 2.5.0)

data/README.rdoc

@@ -6,6 +6,12 @@ Your comments, suggestions and requests are welcome. Documentation and
 feedback are available at the UserEcho site at
 http://rubyucscapi.userecho.com/.
 
+== Install
+
+ $ gem install bio-ucsc-api --no-ri --no-rdoc
+
+You may need to be root or use "sudo". "--no-ri" and "--no-rdoc" options are recommended because generation of ri/rdoc files takes considerable time. 
+
 == Features
 
 * Supporting all organisms in the UCSC genome database.
@@ -44,7 +50,7 @@ Supported Ruby interpreter implementations:
 
 Major dependent gems:
 
-* active_record - http://api.rubyonrails.org/classes/ActiveRecord/Base.html
+* active_record (version ~> 3.0.7. version 3.1 is not supported yet.) - http://api.rubyonrails.org/classes/ActiveRecord/Base.html
 * bioruby-genomic-interval - https://github.com/misshie/bioruby-genomic-interval
 * mysql (MySQL/Ruby MySQL API module) - http://www.tmtm.org/mysql/ruby/README.html
 
@@ -54,6 +60,9 @@ See also:
 * UCSCBin library - https://github.com/misshie/UCSCBin
  
 == Change Log
+* *BUG* (v.0.3.1): Does not work with ActiveRecord version 3.1.0. Data retrieval methods occur the error, "(Object doesn't support #inspect)". The author is working on this bug. So far, please use version 3.0 seriese. Gemfile for gem dependencies is updated. Thanks for bug reports from Diego Pereira.
+* *BUG-FIX* (v.0.3.1): "func" fields in tables did not work. The bug was fixed.
+* *BUG-FIX* (v.0.3.1): PredGene-type tables without the bin index did not work. The bug was fixed.
 * *NEW* (v.0.3.0): Now genomic interval queries are expressed using the named scope "with_interval". Table#find_(all_)by_interval is now deprecated. Sorry for an inconstant API. However, this change enable combination queries using genomic intervals and any fields. 
 * *NEW* (v.0.3.0): Bio::GenomicInterval#bin_all and Bio::GenomicInterval#bin return the bin index for the given interval.
 * *NEW* (v.0.3.0): Supporting JRuby 1.6.3 or later. Appropiate Java heap size may have to be specified to invoke JRuby, especially when you use Bio::Ucsc::Reference. Try "jruby -J-Xmx3g your_script.rb" to keep 3G byte heap.
@@ -71,12 +80,6 @@ See also:
 * *MODIFIED* (v0.0.3): For the "TABLE" class and the "column" column, TABLE.find_by_column retrieves a first record, and TABLE.find_all_by_column retrieves all the records as an Array.
 * *NEW* (v0.0.3-0.0.4): Supporting tables divided into each chromosome, such as "*_RmsK" and "*_gold". Actual names of them are like "chr1_Rmsk", "chr2_Rmsk"... They can be accessed without chromosome names; but with just like "Rmsk" and "Gold".
 
-== Install
-
- $ gem install bio-ucsc-api --no-ri --no-rdoc
-
-You may need to be root or use "sudo". "--no-ri" and "--no-rdoc" options are recommended because generation of ri/rdoc files takes considerable time. 
-
 == How to Use
 === Basics
 * A database of a genome assembly is represented as a module in the Bio::Ucsc module. For example, human hg19 database is referred by "Bio::Ucsc::Hg19".
@@ -142,6 +145,7 @@ And see also sample scripts in the samples directory.
 * symbol2summary.rb - getting summary descriptions using gene symbol
 * hg19-2bit-retrieve - outputting reference sequence in FASTA format   
 * bed2refseq - getting unique gene symbols in the genomic intervals in a BED file.
+* snp2gene - sample for retrieving fields from associated tables
 
 === Notes of Exceptions in Table Support
 * Table names starting with a number: Because Ruby class names cannot start with number, use the table class name starting with "T" (T for Table). Thus, the "2micron_est" table is supported by the "T2micron_est" class.
@@ -150,7 +154,7 @@ And see also sample scripts in the samples directory.
 * For honey bee ApiMel2 database, Group*_chainDm2 and Group*_chainDm2Link tables are accessible using find(_all)_by_interval class methods of the ChainDm2 and ChainDm2Link classes. 
 * Special field (column) names: Field names such as 'attribute', 'valid', 'validate', 'class', 'method', 'methods', and 'type' cannot be accessed using instance methods. This restriction is because of the collision of method names that are internally used by ActiveRecord. Instead, use hash to access the field like "result[:type]".
 
-=== details in "with_interval"
+=== Details in "with_interval"
 * When a table class is referred first time, the API prefetches the table to get a list of fields and dynamically defines a class using following algorithm.
 * If chrom/chromStart/chromEnd fields exist (BED table), the API uses them for interval queries.
 * When tName/tStart/tEnd fields exist (PSL table), the API uses them for interval queries.
@@ -158,6 +162,38 @@ And see also sample scripts in the samples directory.
 * When genoName/genoStart/genoEnd fields exist (RMSK table), the API uses them for interval queries.
 * If the table has the "bin" column, the API calculate bin index to build a query.
 * Otherwise, the API does not support interval queries but support only ActiveRecord's standard methods such as "find_(all_)by_[field name]".
+=== Table Associations
+See samples/snp2gene.rb. Association definition using "has_one/has_many/belongs_to" methods is shown below. class_eval is used not to replace but to add definition. 
+
+ Bio::Ucsc::Hg19::KnownGene.class_eval %!
+   has_one :knownToEnsembl, {:primary_key => :name, :foreign_key => :name}
+ !
+ Bio::Ucsc::Hg19::KnownToEnsembl.class_eval %!
+   belongs_to :knownGene
+   has_one :ensGtp, {:primary_key => :value, :foreign_key => :transcript}
+   has_one :kgXref, {:primary_key => :name, :foreign_key => :kgID}
+ !
+ Bio::Ucsc::Hg19::EnsGtp.class_eval %!
+   belongs_to :knownToEnsembl
+ !
+ Bio::Ucsc::Hg19::KgXref.class_eval %!
+   belongs_to :knownToEnsembl
+   has_one :refLink, {:primary_key => :mRNA, :foreign_key => :mrnaAcc}
+ !
+ Bio::Ucsc::Hg19::RefLink.class_eval %!
+   belongs_to :kgXref
+ !
+
+ActiveRecord::Base#find can be used with the :include option to perform "eager fetching".
+ kg = Bio::Ucsc::Hg19::KnownGene.with_interval(gi).
+        find(:first,
+             :include => [:knownToEnsembl => :ensGtp,
+                          :knownToEnsembl => {:kgXref => :refLink}])
+
+And fields can be referred like the followings: 
+ kg.knownToEnsembl.ensGtp.gene
+ kg.knownToEnsembl.kgXref.geneSymbol
+ kg.knownToEnsembl.kgXref.refLink.mrnaAcc
 
 == Copyright
 Copyright:: (c) 2011 MISHIMA, Hiroyuki (missy at be.to / hmishima at nagasaki-u.ac.jp / @mishimahryk in Twitter)

data/VERSION

@@ -1 +1 @@
-0.3.0
+0.3.1

data/bio-ucsc-api.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = %q{bio-ucsc-api}
-  s.version = "0.3.0"
+  s.version = "0.3.1"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = [%q{Hiroyuki Mishima}, %q{Jan Aerts}]
-  s.date = %q{2011-08-23}
+  s.date = %q{2011-09-06}
   s.description = %q{Ruby UCSC API: accessing the UCSC Genome Database using Ruby}
   s.email = %q{missy@be.to}
   s.extra_rdoc_files = [
@@ -524,6 +524,7 @@ Gem::Specification.new do |s|
     "samples/hg19-2bit-retrieve.rb",
     "samples/hg19-sample.rb",
     "samples/num-gene-exon.rb",
+    "samples/snp2genes.rb",
     "samples/symbol2summary.rb"
   ]
   s.homepage = %q{http://github.com/misshie/bioruby-ucsc-api}
@@ -5481,9 +5482,9 @@ Gem::Specification.new do |s|
     s.specification_version = 3
 
     if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
-      s.add_runtime_dependency(%q<activerecord>, [">= 3.0.7"])
-      s.add_runtime_dependency(%q<activesupport>, [">= 3.0.7"])
-      s.add_runtime_dependency(%q<mysql>, [">= 2.8.1"])
+      s.add_runtime_dependency(%q<activerecord>, ["~> 3.0.7"])
+      s.add_runtime_dependency(%q<activesupport>, ["~> 3.0.7"])
+      s.add_runtime_dependency(%q<mysql>, ["~> 2.8.1"])
       s.add_runtime_dependency(%q<bio-genomic-interval>, [">= 0.1.2"])
       s.add_development_dependency(%q<rspec>, ["~> 2.5.0"])
       s.add_development_dependency(%q<bundler>, ["~> 1.0.0"])
@@ -5492,9 +5493,9 @@ Gem::Specification.new do |s|
       s.add_development_dependency(%q<bio>, [">= 1.4.1"])
       s.add_development_dependency(%q<rdoc>, [">= 3.9.1"])
     else
-      s.add_dependency(%q<activerecord>, [">= 3.0.7"])
-      s.add_dependency(%q<activesupport>, [">= 3.0.7"])
-      s.add_dependency(%q<mysql>, [">= 2.8.1"])
+      s.add_dependency(%q<activerecord>, ["~> 3.0.7"])
+      s.add_dependency(%q<activesupport>, ["~> 3.0.7"])
+      s.add_dependency(%q<mysql>, ["~> 2.8.1"])
       s.add_dependency(%q<bio-genomic-interval>, [">= 0.1.2"])
       s.add_dependency(%q<rspec>, ["~> 2.5.0"])
       s.add_dependency(%q<bundler>, ["~> 1.0.0"])
@@ -5504,9 +5505,9 @@ Gem::Specification.new do |s|
       s.add_dependency(%q<rdoc>, [">= 3.9.1"])
     end
   else
-    s.add_dependency(%q<activerecord>, [">= 3.0.7"])
-    s.add_dependency(%q<activesupport>, [">= 3.0.7"])
-    s.add_dependency(%q<mysql>, [">= 2.8.1"])
+    s.add_dependency(%q<activerecord>, ["~> 3.0.7"])
+    s.add_dependency(%q<activesupport>, ["~> 3.0.7"])
+    s.add_dependency(%q<mysql>, ["~> 2.8.1"])
     s.add_dependency(%q<bio-genomic-interval>, [">= 0.1.2"])
     s.add_dependency(%q<rspec>, ["~> 2.5.0"])
     s.add_dependency(%q<bundler>, ["~> 1.0.0"])

data/lib/bio-ucsc-api.rb

@@ -6,4 +6,4 @@
 #
 # Just a alias for bio-ucsc
 
-require './bio-ucsc'
+require 'bio-ucsc'

data/lib/bio-ucsc.rb

@@ -5,12 +5,16 @@
 # License::     Ruby licence (Ryby's / GPLv2 dual)
 
 base = "#{File.dirname(__FILE__)}/bio-ucsc"
+
+require 'rubygems'
+gem 'activerecord', "~>3.0.7"
+require "active_record"
 require "#{base}/ucsc_bin"
 require "#{base}/genomic-interval-bin"
 
 module Bio
   module Ucsc
-    VERSION = "0.3.0"
+    VERSION = "0.3.1"
     base = "#{File.dirname(__FILE__)}/bio-ucsc"
     
     # mammmals #####################################

data/lib/bio-ucsc/table_class_detector.rb

@@ -10,16 +10,16 @@
 # psl :tableName, :bin => true
 # bed :tableName, :bin => true
 # genepred :tableName, :bin=> true
-# genetic :tableName
+# rmsk :tableName, :bin=> true
+# generic :tableName
 #
-# rmsk :tableName
 
 module Bio 
   module Ucsc
     module TableClassDetector
 
       RESERVED_METHODS = 
-        ['attribute', 'valid', 'validate', 'class', 'method', 'methods', 'type']
+        ['func', 'attribute', 'valid', 'validate', 'class', 'method', 'methods', 'type']
       UPPERCASED_TABLE_PREFIX = 
         ['HInv', 'NIAGene']
       COMMON_CLASS_METHODS = %!
@@ -405,31 +405,25 @@ AND  (txEnd BETWEEN :zstart AND :zend))
               #{delete_reserved_methods}
               #{COMMON_CLASS_METHODS}
 
-              def self.with_interval(gi, opt = {:partial => true})
-                if opt[:partial] == true
-                  where = <<-SQL
+              where = <<-SQL
        chrom = :chrom
 AND ((txStart BETWEEN :zstart AND :zend)
  OR   (txEnd BETWEEN :zstart AND :zend)
  OR   (txStart <= :zstart AND txEnd >= :zend))
-                  SQL
-                else
-                  where = <<-SQL
+              SQL
+              scope(:with_interval,
+                    Proc.new{|gi|{:conditions => [where, {:chrom => gi.chrom,
+                                                          :zstart => gi.zero_start,
+                                                          :zend => gi.zero_end}]}})
+              where = <<-SQL
         chrom = :chrom 
   AND ((txStart BETWEEN :zstart AND :zend)
   AND  (txEnd BETWEEN :zstart AND :zend))
-                  SQL
-                end
-                values = {
-                  :chrom => gi.chrom,
-                  :zstart => gi.zero_start,
-                  :zend => gi.zero_end,
-                }
-
-                with_scope(:find => {:conditions => [where, values]}) do
-                  yield
-                end
-              end # def self.with_interval
+              SQL
+              scope(:with_interval_excl,
+                    Proc.new{|gi|{:conditions => [where, {:chrom => gi.chrom,
+                                                          :zstart => gi.zero_start,
+                                                          :zend => gi.zero_end}]}})
 
               def self.find_first_or_all_by_interval(interval, first_all, opt)
                 zstart = interval.zero_start
@@ -455,7 +449,7 @@ AND ((txStart BETWEEN :zstart AND :zend)
                 }
                 self.find(first_all,
                           { :select => "*",
-                            :conditions => [where, cond], })
+                            :conditions => [where, cond], })-u
               end
             end
           !

data/samples/snp2genes.rb

@@ -0,0 +1,111 @@
+#!/usr/local/bin/ruby-1.9
+#
+# Usage:: snp2genes.rb rs_id (default is "rs100")
+#
+# This example is an answer of a question at BioStar
+# http://biostar.stackexchange.com/questions/9737/mapping-snps-to-genes-and-pathways-go-etc
+#
+# Copyright::
+#   Copyright (C) 2011 MISHIMA, Hiroyuki
+#                      <missy at be.to / hmishima at ngit agasaki-u.ac.jp>
+# License::     The Ruby licence (Ryby's / GPLv2 dual)
+#
+
+PADDING = 60_000
+
+# require 'bio-ucsc'
+require File.dirname(__FILE__) + '/../lib/bio-ucsc'
+
+# require 'active_record'
+# require 'logger'
+# ActiveRecord::Base.logger = Logger.new("sql.log")
+# ActiveRecord::Base.logger.level = 0
+
+include Bio
+
+class Snp2gene
+  def define_association
+    Ucsc::Hg19::KnownGene.class_eval %!
+      has_one :knownToEnsembl, {:primary_key => :name, :foreign_key => :name}
+    !
+    Ucsc::Hg19::KnownToEnsembl.class_eval %!
+      belongs_to :knownGene
+      has_one :ensGtp, {:primary_key => :value, :foreign_key => :transcript}
+      has_one :kgXref, {:primary_key => :name, :foreign_key => :kgID}
+    !
+    Ucsc::Hg19::EnsGtp.class_eval %!
+      belongs_to :knownToEnsembl
+    !
+    Ucsc::Hg19::KgXref.class_eval %!
+      belongs_to :knownToEnsembl
+      has_one :refLink, {:primary_key => :mRNA, :foreign_key => :mrnaAcc}
+    !
+    Ucsc::Hg19::RefLink.class_eval %!
+      belongs_to :kgXref
+    !
+  end
+
+  def run(rs_id)
+    Ucsc::Hg19::DBConnection.connect
+    define_association
+
+    snps = Ucsc::Hg19::Snp132.
+      select([:name, :avHet, :chrom, :chromStart, :chromEnd, :func]).
+      find_all_by_name(rs_id)
+ 
+    snps.each do |snp|
+      puts "====="
+      gi = GenomicInterval.new("chr1",
+                               snp.chromStart - PADDING,
+                               snp.chromEnd + PADDING)
+      snp_pos = GenomicInterval.zero_based(snp.chrom, snp.chromStart, snp.chromEnd)
+
+      knowngenes =
+        Ucsc::Hg19::KnownGene.
+        with_interval(gi).
+        find(:all,
+             :include => [:knownToEnsembl => :ensGtp,
+                          :knownToEnsembl => {:kgXref => :refLink}])
+
+      if knowngenes.empty?
+        puts "proteinID: NO HIT"
+        puts "name: #{snp.name}"
+        puts "avHet: #{snp.avHet}"
+        puts "chrom: #{snp.chrom}"
+        puts "chromStart: #{snp_pos.chr_start}"
+        puts "func: #{snp.func}"
+        puts
+        next
+      end
+
+      knowngenes.each do |kg|
+        puts "proteinID: #{kg.proteinID}"
+        k2e_gtp = kg.knownToEnsembl.ensGtp
+        puts "ensGtp: gene=#{k2e_gtp.gene}, transcript=#{k2e_gtp.transcript}, protein=#{k2e_gtp.protein}"
+        puts "name: #{snp.name}"
+        puts "avHet: #{snp.avHet}"
+        puts "chrom: #{snp.chrom}"
+        puts "chromStart: #{snp_pos.chr_start}"
+        puts "func: #{snp.func}"
+        puts "txStart: #{kg.txStart}"
+        puts "txEnd: #{kg.txEnd}"
+        puts "kgXref-geneSymbol: #{kg.knownToEnsembl.kgXref.geneSymbol}"
+        puts "kgXref-description: #{kg.knownToEnsembl.kgXref.description}"
+        reflink = kg.knownToEnsembl.kgXref.refLink
+        if reflink
+          mrnaacc = reflink.mrnaAcc
+        else
+          mrnaacc = "NO HIT"
+        end
+        puts "refLink-mrnaAcc: #{mrnaacc}"
+        puts
+      end
+    end
+  end
+end
+
+if $0 == __FILE__
+  rs_id = ARGV[0]
+  rs_id ||= "rs100"
+  Snp2gene.new.run(rs_id)
+end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bio-ucsc-api
 version: !ruby/object:Gem::Version
-  version: 0.3.0
+  version: 0.3.1
   prerelease: 
 platform: ruby
 authors:
@@ -10,44 +10,44 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2011-08-23 00:00:00.000000000Z
+date: 2011-09-06 00:00:00.000000000Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: activerecord
-  requirement: &174367420 !ruby/object:Gem::Requirement
+  requirement: &156765300 !ruby/object:Gem::Requirement
     none: false
     requirements:
-    - - ! '>='
+    - - ~>
       - !ruby/object:Gem::Version
         version: 3.0.7
   type: :runtime
   prerelease: false
-  version_requirements: *174367420
+  version_requirements: *156765300
 - !ruby/object:Gem::Dependency
   name: activesupport
-  requirement: &174366940 !ruby/object:Gem::Requirement
+  requirement: &156764820 !ruby/object:Gem::Requirement
     none: false
     requirements:
-    - - ! '>='
+    - - ~>
       - !ruby/object:Gem::Version
         version: 3.0.7
   type: :runtime
   prerelease: false
-  version_requirements: *174366940
+  version_requirements: *156764820
 - !ruby/object:Gem::Dependency
   name: mysql
-  requirement: &174366460 !ruby/object:Gem::Requirement
+  requirement: &156764340 !ruby/object:Gem::Requirement
     none: false
     requirements:
-    - - ! '>='
+    - - ~>
       - !ruby/object:Gem::Version
         version: 2.8.1
   type: :runtime
   prerelease: false
-  version_requirements: *174366460
+  version_requirements: *156764340
 - !ruby/object:Gem::Dependency
   name: bio-genomic-interval
-  requirement: &174365980 !ruby/object:Gem::Requirement
+  requirement: &156763840 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -55,10 +55,10 @@ dependencies:
         version: 0.1.2
   type: :runtime
   prerelease: false
-  version_requirements: *174365980
+  version_requirements: *156763840
 - !ruby/object:Gem::Dependency
   name: rspec
-  requirement: &174365500 !ruby/object:Gem::Requirement
+  requirement: &156763360 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -66,10 +66,10 @@ dependencies:
         version: 2.5.0
   type: :development
   prerelease: false
-  version_requirements: *174365500
+  version_requirements: *156763360
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &174365020 !ruby/object:Gem::Requirement
+  requirement: &156762880 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -77,10 +77,10 @@ dependencies:
         version: 1.0.0
   type: :development
   prerelease: false
-  version_requirements: *174365020
+  version_requirements: *156762880
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &174327460 !ruby/object:Gem::Requirement
+  requirement: &156762400 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -88,10 +88,10 @@ dependencies:
         version: 1.5.2
   type: :development
   prerelease: false
-  version_requirements: *174327460
+  version_requirements: *156762400
 - !ruby/object:Gem::Dependency
   name: rcov
-  requirement: &174326840 !ruby/object:Gem::Requirement
+  requirement: &156761920 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -99,10 +99,10 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *174326840
+  version_requirements: *156761920
 - !ruby/object:Gem::Dependency
   name: bio
-  requirement: &174326240 !ruby/object:Gem::Requirement
+  requirement: &156761440 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -110,10 +110,10 @@ dependencies:
         version: 1.4.1
   type: :development
   prerelease: false
-  version_requirements: *174326240
+  version_requirements: *156761440
 - !ruby/object:Gem::Dependency
   name: rdoc
-  requirement: &174325620 !ruby/object:Gem::Requirement
+  requirement: &156760960 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -121,7 +121,7 @@ dependencies:
         version: 3.9.1
   type: :development
   prerelease: false
-  version_requirements: *174325620
+  version_requirements: *156760960
 description: ! 'Ruby UCSC API: accessing the UCSC Genome Database using Ruby'
 email: missy@be.to
 executables: []
@@ -637,6 +637,7 @@ files:
 - samples/hg19-2bit-retrieve.rb
 - samples/hg19-sample.rb
 - samples/num-gene-exon.rb
+- samples/snp2genes.rb
 - samples/symbol2summary.rb
 - spec/ailmel1_spec.rb
 - spec/anocar2_spec.rb
@@ -5596,7 +5597,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: 2327058743331415747
+      hash: 1643967241848508000
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements: