bio-ucsc-api 0.5.2 → 0.5.3

data/lib/bio-ucsc/{galgal3/chainfr2link.rb → rn5/chainpantro2.rb}

@@ -9,16 +9,13 @@
 
 module Bio
   module Ucsc
-    module GalGal3
+    module Rn4
 
-      class ChainFr2Link
-        include DBConnector
-        DBConnection.database "galGal3"
+      class ChainPanTro2
+        KLASS = "ChainPanTro2"
+        KLASS_S = "chainPanTro2"
 
-        KLASS = "ChainFr2Link"
-        KLASS_S = KLASS[0..0].downcase + KLASS[1..-1]
-
-        Bio::Ucsc::GalGal3::CHROMS.each do |chr|
+        Bio::Ucsc::Rn4::CHROMS.each do |chr|
           class_eval %!
             class #{chr[0..0].upcase + chr[1..-1]}_#{KLASS} < DBConnection
               self.table_name = "#{chr[0..0].downcase + chr[1..-1]}_#{KLASS_S}"

data/lib/bio-ucsc/{galgal3/chainrn4.rb → rn5/chainpantro2link.rb}

@@ -9,16 +9,13 @@
 
 module Bio
   module Ucsc
-    module GalGal3
+    module Rn4
 
-      class ChainRn4
-        include DBConnector
-        DBConnection.database "galGal3"
+      class ChainPanTro2Link
+        KLASS = "ChainPanTro2Link"
+        KLASS_S = "chainPanTro2Link"
 
-        KLASS = "ChainRn4"
-        KLASS_S = KLASS[0..0].downcase + KLASS[1..-1]
-
-        Bio::Ucsc::GalGal3::CHROMS.each do |chr|
+        Bio::Ucsc::Rn4::CHROMS.each do |chr|
           class_eval %!
             class #{chr[0..0].upcase + chr[1..-1]}_#{KLASS} < DBConnection
               self.table_name = "#{chr[0..0].downcase + chr[1..-1]}_#{KLASS_S}"
@@ -74,6 +71,7 @@ AND  (tEnd BETWEEN :zstart AND :zend))
 
         def self.find_all_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
           chrom = interval.chrom[0..0].upcase + interval.chrom[1..-1]
+
           chr_klass = self.const_get("#{chrom}_#{KLASS}")
           chr_klass.__send__(:find_all_by_interval, interval, opt)
         end

data/lib/bio-ucsc/rn5/chainrhemac2.rb

@@ -0,0 +1,81 @@
+# Copyright::
+#  Copyright (C) 2011 MISHIMA, Hiroyuki <missy at be.to / hmishima at nagasaki-u.ac.jp> 
+# License::     The Ruby licence (Ryby's / GPLv2 dual)
+#
+# In the hg18 database, this table is actually separated
+# into "chr1_*", "chr2_*", etc. This class dynamically
+# define *::Chr1_*, *::Chr2_*, etc. The
+# Rmsk.find_by_interval calls an appropreate class automatically.
+
+module Bio
+  module Ucsc
+    module Rn4
+
+      class ChainRheMac2
+        KLASS = "ChainRheMac2"
+        KLASS_S = "chainRheMac2"
+
+        Bio::Ucsc::Rn4::CHROMS.each do |chr|
+          class_eval %!
+            class #{chr[0..0].upcase + chr[1..-1]}_#{KLASS} < DBConnection
+              self.table_name = "#{chr[0..0].downcase + chr[1..-1]}_#{KLASS_S}"
+              self.primary_key = nil
+              self.inheritance_column = nil
+
+              def self.find_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
+                find_first_or_all_by_interval(interval, :first, opt)
+              end
+        
+              def self.find_all_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
+                find_first_or_all_by_interval(interval, :all, opt)
+              end
+
+              def self.find_first_or_all_by_interval(interval, first_all, opt); interval =  Bio::Ucsc::Gi.wrap(interval)
+                zstart = interval.zero_start
+                zend   = interval.zero_end
+                if opt[:partial] == true
+                  where = <<-SQL
+      tName = :chrom
+AND   bin in (:bins)
+AND ((tStart BETWEEN :zstart AND :zend)
+ OR  (tEnd BETWEEN :zstart AND :zend)
+ OR  (tStart <= :zstart AND tEnd >= :zend))
+                  SQL
+                else
+                  where = <<-SQL
+      tName = :chrom
+AND   bin in (:bins)
+AND ((tStart BETWEEN :zstart AND :zend)
+AND  (tEnd BETWEEN :zstart AND :zend))
+                  SQL
+                end
+                cond = {
+                  :chrom  => interval.chrom,
+                  :bins   => Bio::Ucsc::UcscBin.bin_all(zstart, zend),
+                  :zstart => zstart,
+                  :zend   => zend,
+                }
+                self.find(first_all,
+                          { :select => "*",
+                            :conditions => [where, cond], })
+              end
+            end
+          !
+        end # each chromosome
+
+        def self.find_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
+          chrom = interval.chrom[0..0].upcase + interval.chrom[1..-1]
+          chr_klass = self.const_get("#{chrom}_#{KLASS}")
+          chr_klass.__send__(:find_by_interval, interval, opt)
+        end
+
+        def self.find_all_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
+          chrom = interval.chrom[0..0].upcase + interval.chrom[1..-1]
+          chr_klass = self.const_get("#{chrom}_#{KLASS}")
+          chr_klass.__send__(:find_all_by_interval, interval, opt)
+        end
+      end # class
+
+    end # module Hg18 
+  end # module Ucsc
+end # module Bio

data/lib/bio-ucsc/rn5/chainrhemac2link.rb

@@ -0,0 +1,81 @@
+# Copyright::
+#  Copyright (C) 2011 MISHIMA, Hiroyuki <missy at be.to / hmishima at nagasaki-u.ac.jp> 
+# License::     The Ruby licence (Ryby's / GPLv2 dual)
+#
+# In the hg18 database, this table is actually separated
+# into "chr1_*", "chr2_*", etc. This class dynamically
+# define *::Chr1_*, *::Chr2_*, etc. The
+# Rmsk.find_by_interval calls an appropreate class automatically.
+
+module Bio
+  module Ucsc
+    module Rn4
+
+      class ChainRheMac2Link
+        KLASS = "ChainRheMac2Link"
+        KLASS_S = "chainRheMac2Link"
+
+        Bio::Ucsc::Rn4::CHROMS.each do |chr|
+          class_eval %!
+            class #{chr[0..0].upcase + chr[1..-1]}_#{KLASS} < DBConnection
+              self.table_name = "#{chr[0..0].downcase + chr[1..-1]}_#{KLASS_S}"
+              self.primary_key = nil
+              self.inheritance_column = nil
+
+              def self.find_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
+                find_first_or_all_by_interval(interval, :first, opt)
+              end
+        
+              def self.find_all_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
+                find_first_or_all_by_interval(interval, :all, opt)
+              end
+
+              def self.find_first_or_all_by_interval(interval, first_all, opt); interval =  Bio::Ucsc::Gi.wrap(interval)
+                zstart = interval.zero_start
+                zend   = interval.zero_end
+                if opt[:partial] == true
+                  where = <<-SQL
+      tName = :chrom
+AND   bin in (:bins)
+AND ((tStart BETWEEN :zstart AND :zend)
+ OR  (tEnd BETWEEN :zstart AND :zend)
+ OR  (tStart <= :zstart AND tEnd >= :zend))
+                  SQL
+                else
+                  where = <<-SQL
+      tName = :chrom
+AND   bin in (:bins)
+AND ((tStart BETWEEN :zstart AND :zend)
+AND  (tEnd BETWEEN :zstart AND :zend))
+                  SQL
+                end
+                cond = {
+                  :chrom  => interval.chrom,
+                  :bins   => Bio::Ucsc::UcscBin.bin_all(zstart, zend),
+                  :zstart => zstart,
+                  :zend   => zend,
+                }
+                self.find(first_all,
+                          { :select => "*",
+                            :conditions => [where, cond], })
+              end
+            end
+          !
+        end # each chromosome
+
+        def self.find_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
+          chrom = interval.chrom[0..0].upcase + interval.chrom[1..-1]
+          chr_klass = self.const_get("#{chrom}_#{KLASS}")
+          chr_klass.__send__(:find_by_interval, interval, opt)
+        end
+
+        def self.find_all_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
+          chrom = interval.chrom[0..0].upcase + interval.chrom[1..-1]
+          chr_klass = self.const_get("#{chrom}_#{KLASS}")
+          chr_klass.__send__(:find_all_by_interval, interval, opt)
+        end
+      end # class
+
+    end # module Hg18 
+  end # module Ucsc
+end # module Bio

data/lib/bio-ucsc/{galgal3 → rn5}/est.rb

@@ -9,16 +9,13 @@
 
 module Bio
   module Ucsc
-    module GalGal3
+    module Rn4
 
       class Est
-        include DBConnector
-        DBConnection.database "galGal3"
-
         KLASS = "Est"
         KLASS_S = "est"
 
-        Bio::Ucsc::GalGal3::CHROMS.each do |chr|
+        Bio::Ucsc::Rn4::CHROMS.each do |chr|
           class_eval %!
             class #{chr[0..0].upcase + chr[1..-1]}_#{KLASS} < DBConnection
               self.table_name = "#{chr[0..0].downcase + chr[1..-1]}_#{KLASS_S}"

data/lib/bio-ucsc/{galgal3 → rn5}/gap.rb

@@ -9,16 +9,13 @@
 
 module Bio
   module Ucsc
-    module GalGal3
+    module Rn4
 
       class Gap
-        include DBConnector
-        DBConnection.database "galGal3"
-
         KLASS = "Gap"
         KLASS_S = "gap"
 
-        Bio::Ucsc::GalGal3::CHROMS.each do |chr|
+        Bio::Ucsc::Rn4::CHROMS.each do |chr|
           class_eval %!
             class #{chr[0..0].upcase + chr[1..-1]}_#{KLASS} < DBConnection
               self.table_name = "#{chr[0..0].downcase + chr[1..-1]}_#{KLASS_S}"

data/lib/bio-ucsc/{galgal3 → rn5}/gold.rb

@@ -9,16 +9,13 @@
 
 module Bio
   module Ucsc
-    module GalGal3
+    module Rn4
 
       class Gold
-        include DBConnector
-        DBConnection.database "galGal3"
-
         KLASS = "Gold"
         KLASS_S = "gold"
 
-        Bio::Ucsc::GalGal3::CHROMS.each do |chr|
+        Bio::Ucsc::Rn4::CHROMS.each do |chr|
           class_eval %!
             class #{chr[0..0].upcase + chr[1..-1]}_#{KLASS} < DBConnection
               self.table_name = "#{chr[0..0].downcase + chr[1..-1]}_#{KLASS_S}"

data/lib/bio-ucsc/{galgal3 → rn5}/intronest.rb

@@ -9,16 +9,13 @@
 
 module Bio
   module Ucsc
-    module GalGal3
+    module Rn4
 
       class IntronEst
-        include DBConnector
-        DBConnection.database "galGal3"
-
         KLASS = "IntronEst"
         KLASS_S = "intronEst"
 
-        Bio::Ucsc::GalGal3::CHROMS.each do |chr|
+        Bio::Ucsc::Rn4::CHROMS.each do |chr|
           class_eval %!
             class #{chr[0..0].upcase + chr[1..-1]}_#{KLASS} < DBConnection
               self.table_name = "#{chr[0..0].downcase + chr[1..-1]}_#{KLASS_S}"

data/lib/bio-ucsc/{galgal3 → rn5}/mrna.rb

@@ -9,16 +9,13 @@
 
 module Bio
   module Ucsc
-    module GalGal3
+    module Rn4
 
       class Mrna
-        include DBConnector
-        DBConnection.database "galGal3"
-
         KLASS = "Mrna"
         KLASS_S = "mrna"
 
-        Bio::Ucsc::GalGal3::CHROMS.each do |chr|
+        Bio::Ucsc::Rn4::CHROMS.each do |chr|
           class_eval %!
             class #{chr[0..0].upcase + chr[1..-1]}_#{KLASS} < DBConnection
               self.table_name = "#{chr[0..0].downcase + chr[1..-1]}_#{KLASS_S}"

data/lib/bio-ucsc/{galgal3 → rn5}/rmsk.rb

@@ -10,13 +10,10 @@
 
 module Bio
   module Ucsc
-    module GalGal3
+    module Rn4
 
       class Rmsk
-        include DBConnector
-        DBConnection.database "galGal3"
-
-        Bio::Ucsc::GalGal3::CHROMS.each do |chr|
+        Bio::Ucsc::Rn4::CHROMS.each do |chr|
           class_eval %!
             class #{chr[0..0].upcase + chr[1..-1]}_Rmsk < DBConnection
               self.table_name = "#{chr[0..0].downcase + chr[1..-1]}_rmsk"

data/lib/bio-ucsc/taegut1/chaingalgal3.rb

@@ -13,7 +13,7 @@ module Bio
         KLASS = "ChainGalGal3"
         KLASS_S = KLASS[0..0].downcase + KLASS[1..-1]
 
-        Bio::Ucsc::GalGal3::CHROMS.each do |chr|
+        Bio::Ucsc::TaeGut1::CHROMS.each do |chr|
           class_eval %!
             class #{chr[0..0].upcase + chr[1..-1]}_#{KLASS} < DBConnection
               self.table_name = "#{chr[0..0].downcase + chr[1..-1]}_#{KLASS_S}"

data/lib/bio-ucsc/taegut1/chaingalgal3link.rb

@@ -15,7 +15,7 @@ module Bio
         KLASS = "ChainGalGal3Link"
         KLASS_S = KLASS[0..0].downcase + KLASS[1..-1]
 
-        Bio::Ucsc::GalGal3::CHROMS.each do |chr|
+        Bio::Ucsc::TaeGut1::CHROMS.each do |chr|
           class_eval %!
             class #{chr[0..0].upcase + chr[1..-1]}_#{KLASS} < DBConnection
               self.table_name = "#{chr[0..0].downcase + chr[1..-1]}_#{KLASS_S}"

data/lib/bio-ucsc/visigene.rb

@@ -6,7 +6,6 @@
 # License::     The Ruby licence (Ryby's / GPLv2 dual)
 #
 
-require "#{::File.dirname(__FILE__)}/db_connector"
 require "#{::File.dirname(__FILE__)}/table_class_detector"
 
 module Bio

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bio-ucsc-api
 version: !ruby/object:Gem::Version
-  version: 0.5.2
+  version: 0.5.3
   prerelease: 
 platform: ruby
 authors:
@@ -10,33 +10,33 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-12-20 00:00:00.000000000 Z
+date: 2013-08-27 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: activerecord
-  requirement: &254854620 !ruby/object:Gem::Requirement
+  requirement: &258436740 !ruby/object:Gem::Requirement
     none: false
     requirements:
-    - - ! '>='
+    - - ~>
       - !ruby/object:Gem::Version
         version: 3.0.7
   type: :runtime
   prerelease: false
-  version_requirements: *254854620
+  version_requirements: *258436740
 - !ruby/object:Gem::Dependency
   name: activesupport
-  requirement: &254853820 !ruby/object:Gem::Requirement
+  requirement: &258436120 !ruby/object:Gem::Requirement
     none: false
     requirements:
-    - - ! '>='
+    - - ~>
       - !ruby/object:Gem::Version
         version: 3.0.7
   type: :runtime
   prerelease: false
-  version_requirements: *254853820
+  version_requirements: *258436120
 - !ruby/object:Gem::Dependency
   name: mysql
-  requirement: &254853120 !ruby/object:Gem::Requirement
+  requirement: &258435560 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -44,10 +44,10 @@ dependencies:
         version: 2.8.1
   type: :runtime
   prerelease: false
-  version_requirements: *254853120
+  version_requirements: *258435560
 - !ruby/object:Gem::Dependency
   name: bio-genomic-interval
-  requirement: &254868560 !ruby/object:Gem::Requirement
+  requirement: &258451220 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -55,10 +55,10 @@ dependencies:
         version: 0.1.2
   type: :runtime
   prerelease: false
-  version_requirements: *254868560
+  version_requirements: *258451220
 - !ruby/object:Gem::Dependency
   name: safe_attributes
-  requirement: &254867560 !ruby/object:Gem::Requirement
+  requirement: &258450100 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -66,21 +66,21 @@ dependencies:
         version: 1.0.8
   type: :runtime
   prerelease: false
-  version_requirements: *254867560
+  version_requirements: *258450100
 - !ruby/object:Gem::Dependency
   name: rake
-  requirement: &254866900 !ruby/object:Gem::Requirement
+  requirement: &258449180 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: 0.9.2.2
+        version: 10.1.0
   type: :development
   prerelease: false
-  version_requirements: *254866900
+  version_requirements: *258449180
 - !ruby/object:Gem::Dependency
   name: rspec
-  requirement: &254866200 !ruby/object:Gem::Requirement
+  requirement: &258448320 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -88,21 +88,21 @@ dependencies:
         version: 2.9.0
   type: :development
   prerelease: false
-  version_requirements: *254866200
+  version_requirements: *258448320
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &254865620 !ruby/object:Gem::Requirement
+  requirement: &258447480 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: 1.1.0
+        version: 1.3.5
   type: :development
   prerelease: false
-  version_requirements: *254865620
+  version_requirements: *258447480
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &254864760 !ruby/object:Gem::Requirement
+  requirement: &258446680 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -110,10 +110,10 @@ dependencies:
         version: 1.8.3
   type: :development
   prerelease: false
-  version_requirements: *254864760
+  version_requirements: *258446680
 - !ruby/object:Gem::Dependency
   name: bio
-  requirement: &254864120 !ruby/object:Gem::Requirement
+  requirement: &258445800 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -121,10 +121,10 @@ dependencies:
         version: 1.4.1
   type: :development
   prerelease: false
-  version_requirements: *254864120
+  version_requirements: *258445800
 - !ruby/object:Gem::Dependency
   name: rdoc
-  requirement: &254863240 !ruby/object:Gem::Requirement
+  requirement: &258444980 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -132,7 +132,7 @@ dependencies:
         version: 3.9.1
   type: :development
   prerelease: false
-  version_requirements: *254863240
+  version_requirements: *258444980
 description: ! 'Ruby UCSC API: accessing the UCSC Genome Database using Ruby'
 email: missy@be.to
 executables: []
@@ -333,37 +333,7 @@ files:
 - lib/bio-ucsc/fr2/intronest.rb
 - lib/bio-ucsc/fr2/mrna.rb
 - lib/bio-ucsc/fr2/rmsk.rb
-- lib/bio-ucsc/galgal3.rb
-- lib/bio-ucsc/galgal3/chainanocar1.rb
-- lib/bio-ucsc/galgal3/chainanocar1link.rb
-- lib/bio-ucsc/galgal3/chainbraflo1.rb
-- lib/bio-ucsc/galgal3/chainbraflo1link.rb
-- lib/bio-ucsc/galgal3/chaincavpor3.rb
-- lib/bio-ucsc/galgal3/chaincavpor3link.rb
-- lib/bio-ucsc/galgal3/chaindanrer4.rb
-- lib/bio-ucsc/galgal3/chaindanrer4link.rb
-- lib/bio-ucsc/galgal3/chainfr2.rb
-- lib/bio-ucsc/galgal3/chainfr2link.rb
-- lib/bio-ucsc/galgal3/chaingasacu1.rb
-- lib/bio-ucsc/galgal3/chaingasacu1link.rb
-- lib/bio-ucsc/galgal3/chainmm9.rb
-- lib/bio-ucsc/galgal3/chainmm9link.rb
-- lib/bio-ucsc/galgal3/chainornana1.rb
-- lib/bio-ucsc/galgal3/chainornana1link.rb
-- lib/bio-ucsc/galgal3/chainpetmar1.rb
-- lib/bio-ucsc/galgal3/chainpetmar1link.rb
-- lib/bio-ucsc/galgal3/chainrn4.rb
-- lib/bio-ucsc/galgal3/chainrn4link.rb
-- lib/bio-ucsc/galgal3/chaintaegut1.rb
-- lib/bio-ucsc/galgal3/chaintaegut1link.rb
-- lib/bio-ucsc/galgal3/chainxentro2.rb
-- lib/bio-ucsc/galgal3/chainxentro2link.rb
-- lib/bio-ucsc/galgal3/est.rb
-- lib/bio-ucsc/galgal3/gap.rb
-- lib/bio-ucsc/galgal3/gold.rb
-- lib/bio-ucsc/galgal3/intronest.rb
-- lib/bio-ucsc/galgal3/mrna.rb
-- lib/bio-ucsc/galgal3/rmsk.rb
+- lib/bio-ucsc/galgal4.rb
 - lib/bio-ucsc/gasacu1.rb
 - lib/bio-ucsc/gasacu1/chainanocar1.rb
 - lib/bio-ucsc/gasacu1/chainanocar1link.rb
@@ -521,6 +491,31 @@ files:
 - lib/bio-ucsc/rn4/intronest.rb
 - lib/bio-ucsc/rn4/mrna.rb
 - lib/bio-ucsc/rn4/rmsk.rb
+- lib/bio-ucsc/rn5.rb
+- lib/bio-ucsc/rn5/chaincanfam2.rb
+- lib/bio-ucsc/rn5/chaincanfam2link.rb
+- lib/bio-ucsc/rn5/chaincavpor3.rb
+- lib/bio-ucsc/rn5/chaincavpor3link.rb
+- lib/bio-ucsc/rn5/chaindanrer4.rb
+- lib/bio-ucsc/rn5/chaindanrer4link.rb
+- lib/bio-ucsc/rn5/chainequcab1.rb
+- lib/bio-ucsc/rn5/chainequcab1link.rb
+- lib/bio-ucsc/rn5/chaingalgal3.rb
+- lib/bio-ucsc/rn5/chaingalgal3link.rb
+- lib/bio-ucsc/rn5/chainmm9.rb
+- lib/bio-ucsc/rn5/chainmm9link.rb
+- lib/bio-ucsc/rn5/chainmondom4.rb
+- lib/bio-ucsc/rn5/chainmondom4link.rb
+- lib/bio-ucsc/rn5/chainpantro2.rb
+- lib/bio-ucsc/rn5/chainpantro2link.rb
+- lib/bio-ucsc/rn5/chainrhemac2.rb
+- lib/bio-ucsc/rn5/chainrhemac2link.rb
+- lib/bio-ucsc/rn5/est.rb
+- lib/bio-ucsc/rn5/gap.rb
+- lib/bio-ucsc/rn5/gold.rb
+- lib/bio-ucsc/rn5/intronest.rb
+- lib/bio-ucsc/rn5/mrna.rb
+- lib/bio-ucsc/rn5/rmsk.rb
 - lib/bio-ucsc/saccer2.rb
 - lib/bio-ucsc/saccer2/est.rb
 - lib/bio-ucsc/saccer2/gap.rb
@@ -575,7 +570,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: 3725389478649005497
+      hash: 4260927560665571568
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements: