bio-locus 0.0.2 → 0.0.6

checksums.yaml

@@ -1,7 +1,7 @@
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data/Gemfile

@@ -1,14 +1,14 @@
 source "http://rubygems.org"
-# Add dependencies required to use your gem here.
-# Example:
-#   gem "activesupport", ">= 2.3.5"
-
-# Add dependencies to develop your gem here.
-# Include everything needed to run rake, tests, features, etc.
 group :development do
   gem "cucumber"
   gem "jeweler" 
   gem "bundler"
+  gem "rspec"
+  gem "tokyocabinet"
+  gem "localmemcache"
+  gem "moneta"
 end
-gem "localmemcache"
-gem "moneta"
+# The following are optional (Ruby serialize is the default)
+# gem "tokyocabinet"
+# gem "localmemcache"
+# gem "moneta"

data/README.md

@@ -6,8 +6,22 @@ Bio-locus is a tool for fast querying of genome locations. Many file
 formats in bioinformatics contain records that start with a chromosome
 name and a position for a SNP, or a start-end position for indels.
 
-This tool essentially allows your to store this information in a Hash
-or database:
+This tool essentially allows your to store this chr+pos or chr+pos+alt
+information in a fast database.
+
+Why would you use bio-locus?
+
+1. Fast comparison of VCF files and other formats that use chr+pos
+2. Fast comparison of VCF files and other formats that use chr+pos+alt
+3. See what positions match an EVS or GoNL database
+4. Compare locations from databases such as the TCGA and COSMIC
+5. Comparison of overlap or difference
+
+In principle any of the Moneta supported backends can be used,
+including LocalMemCache, RubySerialize and TokyoCabinet. The default
+is RubySerialize because it works out of the box.
+
+Usage: 
 
 ```sh
   bio-locus --store < one.vcf 
@@ -19,7 +33,7 @@ listed alt alleles. To find positions in another dataset which match
 those in the database:
 
 ```sh
-  bio-locus --match < two.vcf
+  bio-locus --match < two.vcf > matched.vcf
 ```
 
 The point is that this is a two-step process, first create the
@@ -29,40 +43,46 @@ with the --delete switch.
 To match with alt use
 
 ```sh
-  bio-locus --match --include-alt < two.vcf
+  bio-locus --match --alt only < two.vcf > matched.vcf
 ```
 
-Why would you use bio-locus?
+So, with bio-locus you can
 
-* To reduce the size of large SNP databases before storage/querying
-* To gain performance
-* To filter on chr+pos (default)
-* To filter on chr+pos+field (where field can be a VCF ALT)
+* reduce the size of large SNP databases before storage/querying
+* gain performance
+* filter on chr+pos (default)
+* filter on chr+pos+field (where field can be a VCF ALT)
 
 Use cases are 
 
-* To filter for annotated variants
+* To filter for annotated variants (including INDELS)
 * To remove common variants from a set
 
 In short a more targeted approach allowing you to work with less data. This
-tool is decently fast. For example, looking for 130 positions in 20 million SNPs
-in GoNL takes 0.11s to store and 1.5 minutes to match on my laptop:
+tool is decently fast. For example, looking for 130 positions in 20 million
+SNPs in GoNL takes 0.11s to store and 1.5 minutes to match on my laptop (using
+localmemcache):
 
 ```sh
-cat my_130_variants.vcf | ./bin/bio-locus --store
+cat my_130_variants.vcf | ./bin/bio-locus --store --storage :localmemcache
   Stored 130 positions out of 130 in locus.db
   real    0m0.119s
   user    0m0.108s
   sys     0m0.012s
 
-cat gonl.*.vcf |./bin/bio-locus --match
+cat gonl.*.vcf |./bin/bio-locus --match --storage :localmemcache
   Matched 3 out of 20736323 lines in locus.db!
   real    1m34.577s
   user    1m33.602s
   sys     0m1.868s
 ```
 
-Note: for the storage the [moneta](https://github.com/minad/moneta) gem is used, currently with localmemcache.
+Note: for the storage here the
+[moneta](https://github.com/minad/moneta) gem is used, currently with
+localmemcache. The default mode for bio-locus is Ruby serialization,
+and :tokyocabinet is also supported. The larger your data becomes, the
+more likely it is that you need :tokyocabinet because the others are
+more RAM oriented.
 
 Note: the ALT field is split into components for matching, so A,C
 becomes two chr+pos records, one for A and one for C.
@@ -82,18 +102,25 @@ of options available through
 bio-locus --help
 ```
 
+The most important one is the handling of ALT. Both with --store and
+--match ALT (chr+pos+alt) can be matched in conjuction with POS
+(chr+pos). When using --alt only, only ALT is matched. When using
+--alt include, both ALT and POS are matched. When using --alt exclude,
+only POS is matched. 
+
+
 ### Deleting keys
 
-To delete entries use 
+To delete entries from the database use 
 
 ```sh
   bio-locus --delete < two.vcf
 ```
 
-To match with alt use
+To delete those that match with alt use
 
 ```sh
-  bio-locus --delete --include-alt < two.vcf
+  bio-locus --delete --alt only < two.vcf
 ```
 
 You may need to run both with and without alt, depending on your needs!
@@ -113,29 +140,64 @@ can be done with
 bio-locus --store --eval-alt 'field[2].split(/\//)[1]'
 ```
 
+Actually, if the --in-format is 'snv', this is exactly what is used.
+
 ### COSMIC
 
 COSMIC is pretty large, so it can be useful to cut the database down to the
 variants that you have. The locus information is combined
 in the before last column as chr:start-end, e.g.,
-19:58861911-58861911. This will work:
+19:58861911-58861911. This may work for COSMICv68
 
 ```sh
 bio-locus -i --match --eval-chr='field[13] =~ /^([^:]+)/ ; $1' --eval-pos='field[13] =~ /:(\d+)-/ ; $1 ' < CosmicMutantExportIncFus_v68.tsv
 ```
 
+You may also use the --in-format cosmic switch for supported COSMIC
+versions.
+
 Note the -i switch is needed to skip records that lack position
-information.
+information or are non-SNV.
+
+## GoNL INDEL example
 
-## Usage
+Here an example of filtering out all INDELs that also exist in a
+different dataste, in this case
+[GoNL](http://www.genoomvannederland.nl/) which provides a database of
+population INDELs in VCF format. First we use
+[bio-vcf](https://github.com/pjotrp/bioruby-vcf) to create a
+subset of common INDELS:
 
-```ruby
-require 'bio-locus'
+```sh
+cat gonl.*.snps_indels.r5.vcf |bio-vcf --filter 'r.info.set=="INDEL" and r.info.af>0.05' > gonl_indel0.05.vcf
+```
+
+Create a locus database from this VCF
+
+```sh
+bio-locus --store --db gonl_indel0.05.db --alt only < gonl_indel0.05.vcf 
+  Stored 480639 positions out of 480639 in gonl_indel0.05.db (0 duplicate hits)
+```
+
+Next, we take our datafile and filter for INDELs that are
+in the population set
+
+```sh
+ bio-locus --match -v --db gonl_indel0.05.db --alt only < varscan2_indel_nfreq30_tfreq30.vcf > /dev/null
+  Matched 635 (unique 75) lines out of 1005 (header 18, unique 174) in gonl_indel0.05.db!
+```
+Which says that 75 INDELs were population matches. We have 635 hits
+because there are multiple samples in this VCF.
+
+This is not what we want in our file, so now we take our datafile and
+filter for INDELs that are *not* in the population set
+
+```sh
+bio-locus --match -v --db gonl_indel0.05.db --alt only < varscan2_indel_nfreq30_tfreq30.vcf > unique_indels.vcf
+  Matched 370 (unique 99) lines out of 1005 (header 18, unique 174) in gonl_indel0.05.db!
 ```
+So now we have 99 INDELs for this dataset which are not common INDELs.
 
-The API doc is online. For more code examples see the test files in
-the source tree.
-        
 ## Project home page
 
 Information on the source tree, documentation, examples, issues and

data/Rakefile

@@ -25,21 +25,27 @@ Jeweler::Tasks.new do |gem|
 end
 Jeweler::RubygemsDotOrgTasks.new
 
-# require 'rspec/core'
-# require 'rspec/core/rake_task'
-# RSpec::Core::RakeTask.new(:spec) do |spec|
-#   spec.pattern = FileList['spec/**/*_spec.rb']
-# end
+require 'rspec/core'
+require 'rspec/core/rake_task'
+RSpec::Core::RakeTask.new(:spec) do |spec|
+  spec.pattern = FileList['spec/**/*_spec.rb']
+end
 
 # RSpec::Core::RakeTask.new(:rcov) do |spec|
 # spec.pattern = 'spec/**/*_spec.rb'
 # spec.rcov = true
 # end
 
-require 'cucumber/rake/task'
-Cucumber::Rake::Task.new(:features)
+# require 'cucumber/rake/task'
+# Cucumber::Rake::Task.new(:features)
 
 task :default => :spec
+task :test => [:spec]
+
+RSpec::Core::RakeTask.new(:rcov) do |spec|
+  spec.pattern = 'spec/**/*_spec.rb'
+  spec.rcov = true
+end
 
 require 'rdoc/task'
 Rake::RDocTask.new do |rdoc|

data/VERSION

@@ -1 +1 @@
-0.0.2
+0.0.6

data/bin/bio-locus

@@ -16,13 +16,16 @@ end
 require 'bio-locus'
 require 'optparse'
 
-options = {task: nil, db: 'locus.db', show_help: false, header: 1}
+options = {task: nil, db: 'locus.db', show_help: false, header: 1, in_format: :vcf, alt: :include, storage: :serialize}
 opts = OptionParser.new do |o|
   o.banner = "Usage: #{File.basename($0)} [options] filename\ne.g. #{File.basename($0)} test.txt"
 
   o.on("--store", 'Create or add to a cache file') do
     options[:task] = :store
-    options[:include_alt] = true  # always include alt
+  end
+
+  o.on("--storage [:serialize,:tokyocabinet,:localmemcache]", [:serialize,:tokyocabinet,:localmemcache], 'Persistent cache type (default :serialize)') do |t|
+    options[:storage] = t
   end
 
   o.on("--delete", 'Remove matches from a cache file') do
@@ -33,40 +36,60 @@ opts = OptionParser.new do |o|
     options[:task] = :match
   end
 
-  o.on("--include-alt", 'Include chr+pos+ALT VCF field to filter') do
-    options[:include_alt] = true
-  end
+  # o.on("--include-alt", 'Include chr+pos+ALT VCF field to filter') do
+  #   options[:include_alt] = true
+  # end
 
-  o.on("--exclude-alt", 'Override adding chr+pos+ALT field to store') do
-    options[:exclude_alt] = true
+  o.on('--alt [include,exclude,only]', [:include,:exclude,:only],
+  'Include, exclude, only ALT (default include)') do |par|
+    options[:alt] = par.to_sym
   end
 
+  # o.on("--only-alt", 'Only look for chr+pos+ALT field in filter') do
+  #   options[:only_alt] = true
+  # end
+
+  # o.on("--exclude-alt", 'Override adding chr+pos+ALT field to store') do
+  #   options[:exclude_alt] = true
+  # end
 
   o.on("--db filename",String,"Use db file") do | fn |
     options[:db] = fn
   end
 
-  o.on("--eval-chr expr",String,"Evaluate record to retrieve chr name") do | expr |
+  o.on('--in-format [vcf,tab,cosmic,snv]', [:vcf,:tab,:cosmic,:snv], 'Input format (default vcf)') do |par|
+    options[:in_format] = par.to_sym
+  end
+
+  o.on("--eval-chr expr",String,"Evaluate record to retrieve chr name (default field[0])") do | expr |
     options[:eval_chr] = expr
   end
 
-  o.on("--eval-pos expr",String,"Evaluate record to retrieve position") do | expr |
+  o.on("--eval-pos expr",String,"Evaluate record to retrieve position (default field[1])") do | expr |
     options[:eval_pos] = expr
   end
 
-  o.on("--eval-alt expr",String,"Evaluate record to retrieve alt list") do | expr |
+  o.on("--eval-alt expr",String,"Evaluate record to retrieve alt list (default field[4])") do | expr |
     options[:eval_alt] = expr
   end
-  
+
   o.on("--header num", "Header lines (default 1)") do |l|
     options[:header] = l.to_i
   end
+
+  o.on("-v", "--invert-match", "Invert the sense of matching, to select non-matching lines") do 
+    options[:invert_match] = true
+  end
    
+  o.on("--header num", "Header lines (default 1)") do |l|
+    options[:header] = l.to_i
+  end
+
   o.on("-q", "--quiet", "Run quietly") do |q|
     options[:quiet] = true
   end
    
-  o.on("-v", "--verbose", "Run verbosely") do |v|
+  o.on("--verbose", "Run verbosely") do |v|
     options[:verbose] = true
   end
    
@@ -78,6 +101,10 @@ opts = OptionParser.new do |o|
     options[:ignore_errors] = true
   end
 
+  o.on("--once", "Only one copy stored/matched") do |q|
+    options[:once] = true
+  end
+   
 
   o.separator ""
   o.on_tail('-h', '--help', 'display this help and exit') do
@@ -107,7 +134,6 @@ end
 case options[:task] 
   when :store then
     require 'bio-locus/store'
-    options[:include_alt]=false if options[:exclude_alt]
     BioLocus::Store.run(options)
   when :match ,:delete then
     require 'bio-locus/match'

data/lib/bio-locus.rb

@@ -8,5 +8,6 @@
 #
 # In this file only require other files. Avoid other source code.
 
+require 'bio-locus/dbmapper'
 require 'bio-locus/locus.rb'
 

data/lib/bio-locus/dbmapper.rb

@@ -0,0 +1,106 @@
+module BioLocus
+
+  class SerializeMapper 
+    def initialize dbname
+      @dbname = dbname
+      @h = {}
+      if File.exist?(@dbname)
+        @h = Marshal.load(File.read(@dbname))
+      end
+    end
+
+    def [] key
+      @h[key]
+    end
+
+    def []= key, value
+      @h[key] = value
+    end
+
+    def close
+      File.open(@dbname, 'w') {|f| f.write(Marshal.dump(@h)) }
+    end
+  end
+
+  class MonetaMapper 
+    def initialize storage, dbname
+      begin
+        require 'moneta'
+      rescue LoadError
+        $stderr.print "Error: Missing moneta. Install with command 'gem install moneta'\n"
+        exit 1
+      end
+      @store = Moneta.new(storage, file: dbname)
+    end
+
+    def [] key
+      @store[key]
+    end
+
+    def []= key, value
+      @store[key] = value
+    end
+
+    def close
+      @store.close
+    end
+  end
+
+  class TokyoCabinetMapper 
+    def initialize dbname
+      begin
+        require 'tokyocabinet'
+      rescue LoadError
+        $stderr.print "Error: Missing tokyocabinet. Install with command 'gem install tokyocabinet'\n"
+        exit 1
+      end
+      @hdb = TokyoCabinet::HDB::new
+      if File.exist?(dbname)
+        if !@hdb.open(dbname, TokyoCabinet::HDB::OREADER)
+          ecode = @hdb.ecode
+          raise sprintf("open error: %s\n", @hdb.errmsg(ecode))
+        end
+      else
+        if !@hdb.open(dbname, TokyoCabinet::HDB::OWRITER | TokyoCabinet::HDB::OCREAT)
+          ecode = @hdb.ecode
+          raise sprintf("open error: %s\n", @hdb.errmsg(ecode))
+        end
+      end
+    end
+
+    def [] key
+      @hdb.get(key)
+    end
+
+    def []= key, value
+      if !@hdb.put(key,value) 
+        ecode = @hdb.ecode
+        raise sprintf("put error: %s\n", @hdb.errmsg(ecode))
+      end
+    end
+
+    def close
+      if !@hdb.close
+        ecode = @hdb.ecode
+        raise sprintf("close error: %s\n", @hdb.errmsg(ecode))
+      end
+    end
+  end
+
+  module DbMapper 
+    def DbMapper::factory options
+      dbname = options[:db]
+      if File.exist?(dbname)
+        $stderr.print "Database #{dbname} exists!\n"
+      end
+      case options[:storage]
+        when :tokyocabinet
+          TokyoCabinetMapper.new(dbname)
+        when :localmemcache
+          MonetaMapper.new(:LocalMemCache,dbname)
+        else
+          SerializeMapper.new(dbname)
+      end
+    end
+  end
+end

data/lib/bio-locus/locus.rb

@@ -1,41 +1,70 @@
 
 module BioLocus
   module Keys
+    @@in_list = {}
+
     def Keys::each_key(line,options)
+      use_alt = (options[:alt] == :include or options[:alt] == :only)
+      use_pos = (options[:alt] == :include or options[:alt] == :exclude)
+
       if line =~ /^[[:alnum:]]+/
         fields = nil
-        # The default layout (VCF) may or may not work
+        # The default layout (VCF) may or may not work. Critically
+        # chr,pos and alt are expected in positions 0,1,4 respectively.
         chr,pos,id,no_use,alt,rest = line.split(/\t/,6)[0..-1]
-        # Override parsing with
-        if options[:eval_chr]
-          fields ||= line.split(/\t/)
-          field = fields
-          chr = eval(options[:eval_chr])
-        end
-        if options[:eval_pos] 
-          fields ||= line.split(/\t/)
-          field = fields
-          pos = eval(options[:eval_pos])
-        end
-        if options[:eval_alt] 
-          fields ||= line.split(/\t/)
+        if options[:in_format] or options[:eval_chr] or options[:eval_pos] or options[:eval_alt]
+          fields = line.split(/\t/)
           field = fields
-          alt = eval(options[:eval_alt])
+          case options[:in_format]
+            when :tab then
+              # chr,pos,ref,alt
+              alt = field[3].strip.split(/,/)[0] if field[3]
+            when :snv then
+              alt = field[2].split(/\//)[1] if field[2]
+            when :cosmic then
+              # COSMIC tsv files, either in field 17 (COSMICv70)
+              locus_field = field[17]
+              locus_field = field[13] if locus_field !~ /:/
+              if field[15] !~ /delet/i and locus_field =~ /:/
+                chr = /^([^:]+)/.match(locus_field)[1]
+                a = /:(\d+)-(\d+)/.match(locus_field)
+                pos = a[1] if a[1]==a[2]
+              end
+          end
+          # Override parsing with
+          if options[:eval_chr]
+            chr = eval(options[:eval_chr])
+          end
+          if options[:eval_pos] 
+            pos = eval(options[:eval_pos])
+          end
+          if options[:eval_alt] 
+            alt = eval(options[:eval_alt])
+          end
         end
-        p [chr,pos] if options[:debug]
+        # p [:debug,chr,pos,alt] if options[:debug]
 
         # If we have a position emit it
         if pos =~ /^\d+$/ and chr and chr != ''
-          alts = ['']  # position only
-          alts += alt.split(/,/) if options[:include_alt]
+          alts = if use_pos
+                   ['']  
+                 else
+                   []
+                 end
+          alts += alt.split(/,/) if use_alt and alt
           alts.each do | nuc |
             key = chr+"\t"+pos
             key += "\t"+nuc if nuc != ''
+            if options[:once]
+              # check we haven't already sent this out in this run
+              return if @@in_list[key]
+              @@in_list[key] = true
+            end
             yield key
           end
         else
           if options[:ignore_errors]
-            $stderr.print "WARNING, skipping: ",line if not options[:quiet]
+            $stderr.print "WARNING, <#{chr}:#{pos}> skipping: ",line if not options[:quiet]
           else
             p line
             p fields

data/lib/bio-locus/match.rb

@@ -1,42 +1,58 @@
 module BioLocus
-
-  require 'moneta'
-
   module Match
     def Match.run(options)
       do_delete = (options[:task] == :delete)
-      store = Moneta.new(:LocalMemCache, file: options[:db])
+      invert_match = options[:invert_match]
+      store = DbMapper.factory(options)
       lines = 0 
+      header_lines = 0
       count = 0
       in_header = true
-      uniq = {}
+      uniq_match = {}
+      uniq_no_match = {}
       STDIN.each_line do | line |
         if in_header and line =~ /^#/
           # Retain comments in header (for VCF)
           print line
+          header_lines += 1
           next
         else
           in_header = false
         end
-        lines += 1
+        if line =~ /^#/
+          header_lines += 1
+        else
+          lines += 1
+        end
         $stderr.print '.' if (lines % 1_000_000) == 0 if not options[:quiet]
         Keys::each_key(line,options) do | key |
-          if store[key]
+          has_match = lambda { 
+                               if invert_match
+                                 not store[key]
+                               else
+                                 store[key]
+                               end
+                             }
+          if has_match.call
+            # We have a match
+            $stderr.print "Matched <#{key}>\n" if options[:debug]
             count += 1
             if do_delete
               store.delete(key)
             else
               print line
-              uniq[key] ||= true
+              uniq_match[key] ||= true
             end
+          else
+            uniq_no_match[key] ||= true
           end
         end
       end
       store.close
       if do_delete
-        $stderr.print "\nDeleted #{count} keys representing #{lines} in #{options[:db]}!\n" if not options[:quiet]
+        $stderr.print "\nDeleted #{count} keys in #{options[:db]} reading #{lines} lines !\n" if not options[:quiet]
       else
-        $stderr.print "\nMatched #{count} (unique #{uniq.keys.size}) lines out of #{lines} in #{options[:db]}!\n" if not options[:quiet]
+        $stderr.print "\nMatched #{count} (unique #{uniq_match.keys.size}) lines out of #{lines} (header #{header_lines}, unique #{uniq_no_match.keys.size+uniq_match.keys.size}) in #{options[:db]}!\n" if not options[:quiet]
       end
     end
   end

data/lib/bio-locus/store.rb

@@ -1,14 +1,20 @@
 module BioLocus
 
-  require 'moneta'
-
   module Store
     def Store.run(options)
-      store = Moneta.new(:LocalMemCache, file: options[:db])
+      invert_match = options[:invert_match]
+      store = DbMapper.factory(options)
       count = count_new = count_dup = 0
       STDIN.each_line do | line |
         Keys::each_key(line,options) do | key |
-          if not store[key]
+          has_match = lambda { 
+                               if invert_match
+                                 not store[key]
+                               else
+                                 store[key]
+                               end
+                             }
+          if not has_match.call
             count_new += 1 
             store[key] = true
           else
@@ -23,7 +29,7 @@ module BioLocus
         end
       end
       store.close
-      $stderr.print "Stored #{count_new} positions out of #{count} in #{options[:db]} (#{count_dup} hits)\n" if !options[:quiet]
+      $stderr.print "Stored #{count_new} positions out of #{count} in #{options[:db]} (#{count_dup} duplicate hits)\n" if !options[:quiet]
     end
   end
 end

data/spec/bio-locus_spec.rb

@@ -1,7 +1,37 @@
 require File.expand_path(File.dirname(__FILE__) + '/spec_helper')
 
-describe "BioLocus" do
-  it "fails" do
-    fail "hey buddy, you should probably rename this file and start specing for real"
-  end
+describe "BioLocus with Serialize" do
+  fn = 'biolocus_serialize.db'
+  store = BioLocus::DbMapper.factory({storage: :serialize, db: fn})
+  store['test'] = 'yes'
+  store['test2'] = 'no'
+  a = store['test']
+  store['test'].should == 'yes'
+  store['test2'].should  == 'no'
+  store.close
+  File.unlink(fn)
+end
+
+describe "BioLocus with Moneta" do
+  fn = 'biolocus_moneta_localmemcache.db'
+  store = BioLocus::MonetaMapper.new(:LocalMemCache,fn)
+  store['test'] = 'yes'
+  store['test2'] = 'no'
+  a = store['test']
+  store['test'].should == 'yes'
+  store['test2'].should  == 'no'
+  store.close
+  File.unlink(fn)
+end
+
+describe "BioLocus with TokyoCabinet" do
+  fn = 'biolocus_tokyocabinet.db'
+  store = BioLocus::TokyoCabinetMapper.new(fn)
+  store['test'] = 'yes'
+  store['test2'] = 'no'
+  a = store['test']
+  store['test'].should == 'yes'
+  store['test2'].should  == 'no'
+  store.close
+  File.unlink(fn)
 end

metadata

@@ -1,23 +1,23 @@
 --- !ruby/object:Gem::Specification
 name: bio-locus
 version: !ruby/object:Gem::Version
-  version: 0.0.2
+  version: 0.0.6
 platform: ruby
 authors:
 - Pjotr Prins
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-06-05 00:00:00.000000000 Z
+date: 2014-10-10 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
-  name: localmemcache
+  name: cucumber
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - ">="
       - !ruby/object:Gem::Version
         version: '0'
-  type: :runtime
+  type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
@@ -25,13 +25,13 @@ dependencies:
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
-  name: moneta
+  name: jeweler
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - ">="
       - !ruby/object:Gem::Version
         version: '0'
-  type: :runtime
+  type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
@@ -39,7 +39,7 @@ dependencies:
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
-  name: cucumber
+  name: bundler
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - ">="
@@ -53,7 +53,7 @@ dependencies:
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
-  name: jeweler
+  name: rspec
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - ">="
@@ -67,7 +67,35 @@ dependencies:
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
-  name: bundler
+  name: tokyocabinet
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: localmemcache
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: moneta
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - ">="
@@ -103,6 +131,7 @@ files:
 - features/step_definitions/bio-locus_steps.rb
 - features/support/env.rb
 - lib/bio-locus.rb
+- lib/bio-locus/dbmapper.rb
 - lib/bio-locus/locus.rb
 - lib/bio-locus/match.rb
 - lib/bio-locus/store.rb