bio-ucsc-api 0.2.0 → 0.2.1

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bio-ucsc-api
 version: !ruby/object:Gem::Version
-  version: 0.2.0
+  version: 0.2.1
   prerelease: 
 platform: ruby
 authors:
@@ -10,11 +10,11 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2011-08-08 00:00:00.000000000Z
+date: 2011-08-14 00:00:00.000000000Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: activerecord
-  requirement: &178761500 !ruby/object:Gem::Requirement
+  requirement: &130996320 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -22,10 +22,10 @@ dependencies:
         version: 3.0.7
   type: :runtime
   prerelease: false
-  version_requirements: *178761500
+  version_requirements: *130996320
 - !ruby/object:Gem::Dependency
   name: activesupport
-  requirement: &178761020 !ruby/object:Gem::Requirement
+  requirement: &130995840 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -33,10 +33,10 @@ dependencies:
         version: 3.0.7
   type: :runtime
   prerelease: false
-  version_requirements: *178761020
+  version_requirements: *130995840
 - !ruby/object:Gem::Dependency
   name: mysql
-  requirement: &178760540 !ruby/object:Gem::Requirement
+  requirement: &130995360 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -44,10 +44,10 @@ dependencies:
         version: 2.8.1
   type: :runtime
   prerelease: false
-  version_requirements: *178760540
+  version_requirements: *130995360
 - !ruby/object:Gem::Dependency
   name: bio-genomic-interval
-  requirement: &178760060 !ruby/object:Gem::Requirement
+  requirement: &130994840 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -55,10 +55,10 @@ dependencies:
         version: 0.1.2
   type: :runtime
   prerelease: false
-  version_requirements: *178760060
+  version_requirements: *130994840
 - !ruby/object:Gem::Dependency
   name: rspec
-  requirement: &178759580 !ruby/object:Gem::Requirement
+  requirement: &130994360 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -66,10 +66,10 @@ dependencies:
         version: 2.5.0
   type: :development
   prerelease: false
-  version_requirements: *178759580
+  version_requirements: *130994360
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &178759100 !ruby/object:Gem::Requirement
+  requirement: &130993880 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -77,10 +77,10 @@ dependencies:
         version: 1.0.0
   type: :development
   prerelease: false
-  version_requirements: *178759100
+  version_requirements: *130993880
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &178758620 !ruby/object:Gem::Requirement
+  requirement: &130993400 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -88,10 +88,10 @@ dependencies:
         version: 1.5.2
   type: :development
   prerelease: false
-  version_requirements: *178758620
+  version_requirements: *130993400
 - !ruby/object:Gem::Dependency
   name: rcov
-  requirement: &178758140 !ruby/object:Gem::Requirement
+  requirement: &130992920 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -99,10 +99,10 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *178758140
+  version_requirements: *130992920
 - !ruby/object:Gem::Dependency
   name: bio
-  requirement: &178757660 !ruby/object:Gem::Requirement
+  requirement: &130992440 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -110,10 +110,10 @@ dependencies:
         version: 1.4.1
   type: :development
   prerelease: false
-  version_requirements: *178757660
+  version_requirements: *130992440
 - !ruby/object:Gem::Dependency
   name: rdoc
-  requirement: &178757180 !ruby/object:Gem::Requirement
+  requirement: &130991960 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -121,7 +121,7 @@ dependencies:
         version: 3.9.1
   type: :development
   prerelease: false
-  version_requirements: *178757180
+  version_requirements: *130991960
 description: ! 'Ruby UCSC API: accessing the UCSC Genome Database using Ruby'
 email: missy@be.to
 executables: []
@@ -139,6 +139,105 @@ files:
 - bio-ucsc-api.gemspec
 - lib/bio-ucsc-api.rb
 - lib/bio-ucsc.rb
+- lib/bio-ucsc/ailmel1.rb
+- lib/bio-ucsc/ailmel1/db_connection.rb
+- lib/bio-ucsc/anocar2.rb
+- lib/bio-ucsc/anocar2/db_connection.rb
+- lib/bio-ucsc/anogam1.rb
+- lib/bio-ucsc/anogam1/chaindm3.rb
+- lib/bio-ucsc/anogam1/chaindm3link.rb
+- lib/bio-ucsc/anogam1/db_connection.rb
+- lib/bio-ucsc/anogam1/est.rb
+- lib/bio-ucsc/anogam1/gap.rb
+- lib/bio-ucsc/anogam1/gold.rb
+- lib/bio-ucsc/anogam1/intronest.rb
+- lib/bio-ucsc/anogam1/mrna.rb
+- lib/bio-ucsc/anogam1/rmsk.rb
+- lib/bio-ucsc/apimel2.rb
+- lib/bio-ucsc/apimel2/chaindm2.rb
+- lib/bio-ucsc/apimel2/chaindm2link.rb
+- lib/bio-ucsc/apimel2/db_connection.rb
+- lib/bio-ucsc/aplcal1.rb
+- lib/bio-ucsc/aplcal1/chaincaepb1.rb
+- lib/bio-ucsc/aplcal1/chaincaepb1link.rb
+- lib/bio-ucsc/aplcal1/chaincaerem2.rb
+- lib/bio-ucsc/aplcal1/chaincaerem2link.rb
+- lib/bio-ucsc/aplcal1/chaincb3.rb
+- lib/bio-ucsc/aplcal1/chaincb3link.rb
+- lib/bio-ucsc/aplcal1/chaince6.rb
+- lib/bio-ucsc/aplcal1/chaince6link.rb
+- lib/bio-ucsc/aplcal1/db_connection.rb
+- lib/bio-ucsc/aplcal1/gap.rb
+- lib/bio-ucsc/aplcal1/gold.rb
+- lib/bio-ucsc/aplcal1/rmsk.rb
+- lib/bio-ucsc/bostau4.rb
+- lib/bio-ucsc/bostau4/db_connection.rb
+- lib/bio-ucsc/braflo1.rb
+- lib/bio-ucsc/braflo1/chaingalgal3.rb
+- lib/bio-ucsc/braflo1/chaingalgal3link.rb
+- lib/bio-ucsc/braflo1/chainhg18.rb
+- lib/bio-ucsc/braflo1/chainhg18link.rb
+- lib/bio-ucsc/braflo1/chainmm9.rb
+- lib/bio-ucsc/braflo1/chainmm9link.rb
+- lib/bio-ucsc/braflo1/chainpetmar1.rb
+- lib/bio-ucsc/braflo1/chainpetmar1link.rb
+- lib/bio-ucsc/braflo1/db_connection.rb
+- lib/bio-ucsc/braflo1/gap.rb
+- lib/bio-ucsc/braflo1/gold.rb
+- lib/bio-ucsc/caejap1.rb
+- lib/bio-ucsc/caejap1/chaince6.rb
+- lib/bio-ucsc/caejap1/chaince6link.rb
+- lib/bio-ucsc/caejap1/db_connection.rb
+- lib/bio-ucsc/caejap1/gap.rb
+- lib/bio-ucsc/caejap1/gold.rb
+- lib/bio-ucsc/caepb2.rb
+- lib/bio-ucsc/caepb2/chaince6.rb
+- lib/bio-ucsc/caepb2/chaince6link.rb
+- lib/bio-ucsc/caepb2/db_connection.rb
+- lib/bio-ucsc/caepb2/gap.rb
+- lib/bio-ucsc/caepb2/gold.rb
+- lib/bio-ucsc/caerem3.rb
+- lib/bio-ucsc/caerem3/chaince6.rb
+- lib/bio-ucsc/caerem3/chaince6link.rb
+- lib/bio-ucsc/caerem3/db_connection.rb
+- lib/bio-ucsc/caerem3/gap.rb
+- lib/bio-ucsc/caerem3/gold.rb
+- lib/bio-ucsc/caljac3.rb
+- lib/bio-ucsc/caljac3/db_connection.rb
+- lib/bio-ucsc/canfam2.rb
+- lib/bio-ucsc/canfam2/chainbostau4.rb
+- lib/bio-ucsc/canfam2/chainbostau4link.rb
+- lib/bio-ucsc/canfam2/chainmm9.rb
+- lib/bio-ucsc/canfam2/chainmm9link.rb
+- lib/bio-ucsc/canfam2/chainrn4.rb
+- lib/bio-ucsc/canfam2/chainrn4link.rb
+- lib/bio-ucsc/canfam2/chainself.rb
+- lib/bio-ucsc/canfam2/chainselflink.rb
+- lib/bio-ucsc/canfam2/db_connection.rb
+- lib/bio-ucsc/canfam2/est.rb
+- lib/bio-ucsc/canfam2/gap.rb
+- lib/bio-ucsc/canfam2/gold.rb
+- lib/bio-ucsc/canfam2/intronest.rb
+- lib/bio-ucsc/canfam2/mrna.rb
+- lib/bio-ucsc/canfam2/rmsk.rb
+- lib/bio-ucsc/cavpor3.rb
+- lib/bio-ucsc/cavpor3/db_connection.rb
+- lib/bio-ucsc/cb3.rb
+- lib/bio-ucsc/cb3/chaincaepb1.rb
+- lib/bio-ucsc/cb3/chaincaepb1link.rb
+- lib/bio-ucsc/cb3/chaincaerem2.rb
+- lib/bio-ucsc/cb3/chaincaerem2link.rb
+- lib/bio-ucsc/cb3/chaince6.rb
+- lib/bio-ucsc/cb3/chaince6link.rb
+- lib/bio-ucsc/cb3/chainpripac1.rb
+- lib/bio-ucsc/cb3/chainpripac1link.rb
+- lib/bio-ucsc/cb3/db_connection.rb
+- lib/bio-ucsc/cb3/est.rb
+- lib/bio-ucsc/cb3/gap.rb
+- lib/bio-ucsc/cb3/gold.rb
+- lib/bio-ucsc/cb3/intronest.rb
+- lib/bio-ucsc/cb3/mrna.rb
+- lib/bio-ucsc/cb3/rmsk.rb
 - lib/bio-ucsc/ce6.rb
 - lib/bio-ucsc/ce6/chaincaejap1.rb
 - lib/bio-ucsc/ce6/chaincaejap1link.rb
@@ -160,6 +259,10 @@ files:
 - lib/bio-ucsc/ce6/mrna.rb
 - lib/bio-ucsc/ce6/rmsk.rb
 - lib/bio-ucsc/ce6/t25mersrepeats.rb
+- lib/bio-ucsc/ci2.rb
+- lib/bio-ucsc/ci2/db_connection.rb
+- lib/bio-ucsc/danrer7.rb
+- lib/bio-ucsc/danrer7/db_connection.rb
 - lib/bio-ucsc/dm3.rb
 - lib/bio-ucsc/dm3/chainanogam1.rb
 - lib/bio-ucsc/dm3/chainanogam1link.rb
@@ -186,6 +289,124 @@ files:
 - lib/bio-ucsc/dm3/intronest.rb
 - lib/bio-ucsc/dm3/mrna.rb
 - lib/bio-ucsc/dm3/rmsk.rb
+- lib/bio-ucsc/dp3.rb
+- lib/bio-ucsc/dp3/chaindm3.rb
+- lib/bio-ucsc/dp3/chaindm3link.rb
+- lib/bio-ucsc/dp3/db_connection.rb
+- lib/bio-ucsc/dp3/est.rb
+- lib/bio-ucsc/dp3/gap.rb
+- lib/bio-ucsc/dp3/gold.rb
+- lib/bio-ucsc/dp3/intronest.rb
+- lib/bio-ucsc/dp3/mrna.rb
+- lib/bio-ucsc/dp3/rmsk.rb
+- lib/bio-ucsc/droana2.rb
+- lib/bio-ucsc/droana2/db_connection.rb
+- lib/bio-ucsc/droere1.rb
+- lib/bio-ucsc/droere1/db_connection.rb
+- lib/bio-ucsc/drogri1.rb
+- lib/bio-ucsc/drogri1/db_connection.rb
+- lib/bio-ucsc/dromoj2.rb
+- lib/bio-ucsc/dromoj2/db_connection.rb
+- lib/bio-ucsc/droper1.rb
+- lib/bio-ucsc/droper1/db_connection.rb
+- lib/bio-ucsc/drosec1.rb
+- lib/bio-ucsc/drosec1/db_connection.rb
+- lib/bio-ucsc/drosim1.rb
+- lib/bio-ucsc/drosim1/chaindm3.rb
+- lib/bio-ucsc/drosim1/chaindm3link.rb
+- lib/bio-ucsc/drosim1/db_connection.rb
+- lib/bio-ucsc/drosim1/est.rb
+- lib/bio-ucsc/drosim1/gap.rb
+- lib/bio-ucsc/drosim1/gold.rb
+- lib/bio-ucsc/drosim1/intronest.rb
+- lib/bio-ucsc/drosim1/mrna.rb
+- lib/bio-ucsc/drosim1/rmsk.rb
+- lib/bio-ucsc/drovir2.rb
+- lib/bio-ucsc/drovir2/db_connection.rb
+- lib/bio-ucsc/droyak2.rb
+- lib/bio-ucsc/droyak2/chaindm3.rb
+- lib/bio-ucsc/droyak2/chaindm3link.rb
+- lib/bio-ucsc/droyak2/db_connection.rb
+- lib/bio-ucsc/droyak2/est.rb
+- lib/bio-ucsc/droyak2/gap.rb
+- lib/bio-ucsc/droyak2/gold.rb
+- lib/bio-ucsc/droyak2/intronest.rb
+- lib/bio-ucsc/droyak2/mrna.rb
+- lib/bio-ucsc/droyak2/rmsk.rb
+- lib/bio-ucsc/equcab2.rb
+- lib/bio-ucsc/equcab2/db_connection.rb
+- lib/bio-ucsc/equcab2/est.rb
+- lib/bio-ucsc/equcab2/gap.rb
+- lib/bio-ucsc/equcab2/gold.rb
+- lib/bio-ucsc/equcab2/intronest.rb
+- lib/bio-ucsc/equcab2/mrna.rb
+- lib/bio-ucsc/equcab2/rmsk.rb
+- lib/bio-ucsc/felcat4.rb
+- lib/bio-ucsc/felcat4/db_connection.rb
+- lib/bio-ucsc/fr2.rb
+- lib/bio-ucsc/fr2/chaingalgal3.rb
+- lib/bio-ucsc/fr2/chaingalgal3link.rb
+- lib/bio-ucsc/fr2/chaingasacu1.rb
+- lib/bio-ucsc/fr2/chaingasacu1link.rb
+- lib/bio-ucsc/fr2/chainmm9.rb
+- lib/bio-ucsc/fr2/chainmm9link.rb
+- lib/bio-ucsc/fr2/chainorylat2.rb
+- lib/bio-ucsc/fr2/chainorylat2link.rb
+- lib/bio-ucsc/fr2/db_connection.rb
+- lib/bio-ucsc/fr2/est.rb
+- lib/bio-ucsc/fr2/gap.rb
+- lib/bio-ucsc/fr2/gold.rb
+- 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/db_connection.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/gasacu1.rb
+- lib/bio-ucsc/gasacu1/chainanocar1.rb
+- lib/bio-ucsc/gasacu1/chainanocar1link.rb
+- lib/bio-ucsc/gasacu1/chainfr2.rb
+- lib/bio-ucsc/gasacu1/chainfr2link.rb
+- lib/bio-ucsc/gasacu1/chaingalgal3.rb
+- lib/bio-ucsc/gasacu1/chaingalgal3link.rb
+- lib/bio-ucsc/gasacu1/chainmm9.rb
+- lib/bio-ucsc/gasacu1/chainmm9link.rb
+- lib/bio-ucsc/gasacu1/chainorylat2.rb
+- lib/bio-ucsc/gasacu1/chainorylat2link.rb
+- lib/bio-ucsc/gasacu1/db_connection.rb
+- lib/bio-ucsc/gasacu1/est.rb
+- lib/bio-ucsc/gasacu1/intronest.rb
+- lib/bio-ucsc/gasacu1/mrna.rb
+- lib/bio-ucsc/gasacu1/rmsk.rb
 - lib/bio-ucsc/go.rb
 - lib/bio-ucsc/go/db_connection.rb
 - lib/bio-ucsc/hg18.rb
@@ -227,6 +448,8 @@ files:
 - lib/bio-ucsc/hg19/gbcdnainfo.rb
 - lib/bio-ucsc/hgfixed.rb
 - lib/bio-ucsc/hgfixed/db_connection.rb
+- lib/bio-ucsc/loxafr3.rb
+- lib/bio-ucsc/loxafr3/db_connection.rb
 - lib/bio-ucsc/mm9.rb
 - lib/bio-ucsc/mm9/chainanocar1.rb
 - lib/bio-ucsc/mm9/chainanocar1link.rb
@@ -267,22 +490,186 @@ files:
 - lib/bio-ucsc/mm9/intronest.rb
 - lib/bio-ucsc/mm9/mrna.rb
 - lib/bio-ucsc/mm9/rmsk.rb
+- lib/bio-ucsc/mondom5.rb
+- lib/bio-ucsc/mondom5/db_connection.rb
+- lib/bio-ucsc/ornana1.rb
+- lib/bio-ucsc/ornana1/db_connection.rb
+- lib/bio-ucsc/orycun2.rb
+- lib/bio-ucsc/orycun2/db_connection.rb
+- lib/bio-ucsc/orylat2.rb
+- lib/bio-ucsc/orylat2/db_connection.rb
+- lib/bio-ucsc/oviari1.rb
+- lib/bio-ucsc/oviari1/db_connection.rb
+- lib/bio-ucsc/pantro3.rb
+- lib/bio-ucsc/pantro3/db_connection.rb
+- lib/bio-ucsc/petmar1.rb
+- lib/bio-ucsc/petmar1/db_connection.rb
+- lib/bio-ucsc/ponabe2.rb
+- lib/bio-ucsc/ponabe2/chainmm9.rb
+- lib/bio-ucsc/ponabe2/chainmm9link.rb
+- lib/bio-ucsc/ponabe2/chainornana1.rb
+- lib/bio-ucsc/ponabe2/chainornana1link.rb
+- lib/bio-ucsc/ponabe2/chainrhemac2.rb
+- lib/bio-ucsc/ponabe2/chainrhemac2link.rb
+- lib/bio-ucsc/ponabe2/db_connection.rb
+- lib/bio-ucsc/ponabe2/est.rb
+- lib/bio-ucsc/ponabe2/gap.rb
+- lib/bio-ucsc/ponabe2/gold.rb
+- lib/bio-ucsc/ponabe2/intronest.rb
+- lib/bio-ucsc/ponabe2/mrna.rb
+- lib/bio-ucsc/ponabe2/rmsk.rb
+- lib/bio-ucsc/pripac1.rb
+- lib/bio-ucsc/pripac1/chaincaepb1.rb
+- lib/bio-ucsc/pripac1/chaincaepb1link.rb
+- lib/bio-ucsc/pripac1/chaincaerem2.rb
+- lib/bio-ucsc/pripac1/chaincaerem2link.rb
+- lib/bio-ucsc/pripac1/chaincb3.rb
+- lib/bio-ucsc/pripac1/chaincb3link.rb
+- lib/bio-ucsc/pripac1/chaince6.rb
+- lib/bio-ucsc/pripac1/chaince6link.rb
+- lib/bio-ucsc/pripac1/db_connection.rb
+- lib/bio-ucsc/pripac1/gap.rb
+- lib/bio-ucsc/pripac1/gold.rb
+- lib/bio-ucsc/pripac1/rmsk.rb
 - lib/bio-ucsc/proteome.rb
 - lib/bio-ucsc/proteome/db_connection.rb
 - lib/bio-ucsc/reference.rb
+- lib/bio-ucsc/rhemac2.rb
+- lib/bio-ucsc/rhemac2/chainmm9.rb
+- lib/bio-ucsc/rhemac2/chainmm9link.rb
+- lib/bio-ucsc/rhemac2/chainpantro2.rb
+- lib/bio-ucsc/rhemac2/chainpantro2link.rb
+- lib/bio-ucsc/rhemac2/chainponabe2.rb
+- lib/bio-ucsc/rhemac2/chainponabe2link.rb
+- lib/bio-ucsc/rhemac2/chainrn4.rb
+- lib/bio-ucsc/rhemac2/chainrn4link.rb
+- lib/bio-ucsc/rhemac2/db_connection.rb
+- lib/bio-ucsc/rn4.rb
+- lib/bio-ucsc/rn4/chainbostau3.rb
+- lib/bio-ucsc/rn4/chainbostau3link.rb
+- lib/bio-ucsc/rn4/chaincanfam2.rb
+- lib/bio-ucsc/rn4/chaincanfam2link.rb
+- lib/bio-ucsc/rn4/chaincavpor3.rb
+- lib/bio-ucsc/rn4/chaincavpor3link.rb
+- lib/bio-ucsc/rn4/chaindanrer4.rb
+- lib/bio-ucsc/rn4/chaindanrer4link.rb
+- lib/bio-ucsc/rn4/chainequcab1.rb
+- lib/bio-ucsc/rn4/chainequcab1link.rb
+- lib/bio-ucsc/rn4/chaingalgal3.rb
+- lib/bio-ucsc/rn4/chaingalgal3link.rb
+- lib/bio-ucsc/rn4/chainmm9.rb
+- lib/bio-ucsc/rn4/chainmm9link.rb
+- lib/bio-ucsc/rn4/chainmondom4.rb
+- lib/bio-ucsc/rn4/chainmondom4link.rb
+- lib/bio-ucsc/rn4/chainpantro2.rb
+- lib/bio-ucsc/rn4/chainpantro2link.rb
+- lib/bio-ucsc/rn4/chainrhemac2.rb
+- lib/bio-ucsc/rn4/chainrhemac2link.rb
+- lib/bio-ucsc/rn4/chainxentro2.rb
+- lib/bio-ucsc/rn4/chainxentro2link.rb
+- lib/bio-ucsc/rn4/db_connection.rb
+- lib/bio-ucsc/rn4/est.rb
+- lib/bio-ucsc/rn4/gap.rb
+- lib/bio-ucsc/rn4/gold.rb
+- lib/bio-ucsc/rn4/intronest.rb
+- lib/bio-ucsc/rn4/mrna.rb
+- lib/bio-ucsc/rn4/rmsk.rb
+- lib/bio-ucsc/saccer2.rb
+- lib/bio-ucsc/saccer2/db_connection.rb
+- lib/bio-ucsc/saccer2/est.rb
+- lib/bio-ucsc/saccer2/gap.rb
+- lib/bio-ucsc/saccer2/gold.rb
+- lib/bio-ucsc/saccer2/intronest.rb
+- lib/bio-ucsc/saccer2/mrna.rb
+- lib/bio-ucsc/saccer2/t2micron_est.rb
+- lib/bio-ucsc/saccer2/t2micron_gap.rb
+- lib/bio-ucsc/saccer2/t2micron_gold.rb
+- lib/bio-ucsc/saccer2/t2micron_intronEst.rb
+- lib/bio-ucsc/saccer2/t2micron_mrna.rb
+- lib/bio-ucsc/strpur2.rb
+- lib/bio-ucsc/strpur2/chaingalgal3.rb
+- lib/bio-ucsc/strpur2/chaingalgal3link.rb
+- lib/bio-ucsc/strpur2/chainhg18.rb
+- lib/bio-ucsc/strpur2/chainhg18link.rb
+- lib/bio-ucsc/strpur2/chainmm9.rb
+- lib/bio-ucsc/strpur2/chainmm9link.rb
+- lib/bio-ucsc/strpur2/chainpetmar1.rb
+- lib/bio-ucsc/strpur2/chainpetmar1link.rb
+- lib/bio-ucsc/strpur2/db_connection.rb
+- lib/bio-ucsc/strpur2/gap.rb
+- lib/bio-ucsc/strpur2/gold.rb
+- lib/bio-ucsc/susscr2.rb
+- lib/bio-ucsc/susscr2/db_connection.rb
+- lib/bio-ucsc/susscr2/est.rb
+- lib/bio-ucsc/susscr2/intronest.rb
+- lib/bio-ucsc/susscr2/mrna.rb
 - lib/bio-ucsc/table_class_detector.rb
+- lib/bio-ucsc/taegut1.rb
+- lib/bio-ucsc/taegut1/chaingalgal3.rb
+- lib/bio-ucsc/taegut1/chaingalgal3link.rb
+- lib/bio-ucsc/taegut1/db_connection.rb
+- lib/bio-ucsc/taegut1/est.rb
+- lib/bio-ucsc/taegut1/gap.rb
+- lib/bio-ucsc/taegut1/gold.rb
+- lib/bio-ucsc/taegut1/intronest.rb
+- lib/bio-ucsc/taegut1/mrna.rb
+- lib/bio-ucsc/taegut1/rmsk.rb
+- lib/bio-ucsc/tetnig2.rb
+- lib/bio-ucsc/tetnig2/db_connection.rb
+- lib/bio-ucsc/tetnig2/mrna.rb
 - lib/bio-ucsc/ucsc_bin.rb
 - lib/bio-ucsc/uniprot.rb
 - lib/bio-ucsc/uniprot/db_connection.rb
 - lib/bio-ucsc/visigene.rb
 - lib/bio-ucsc/visigene/db_connection.rb
+- lib/bio-ucsc/xentro2.rb
+- lib/bio-ucsc/xentro2/chaingalgal3.rb
+- lib/bio-ucsc/xentro2/chaingalgal3link.rb
+- lib/bio-ucsc/xentro2/db_connection.rb
+- lib/bio-ucsc/xentro2/est.rb
+- lib/bio-ucsc/xentro2/gap.rb
+- lib/bio-ucsc/xentro2/gold.rb
+- lib/bio-ucsc/xentro2/intronest.rb
+- lib/bio-ucsc/xentro2/mrna.rb
+- lib/bio-ucsc/xentro2/rmsk.rb
 - samples/bed2refseq.rb
 - samples/hg19-2bit-retrieve.rb
 - samples/hg19-sample.rb
 - samples/num-gene-exon.rb
 - samples/symbol2summary.rb
+- spec/ailmel1_spec.rb
+- spec/anocar2_spec.rb
+- spec/anogam1_spec.rb
+- spec/apimel2_spec.rb
+- spec/aplcal1_spec.rb
+- spec/bostau4_spec.rb
+- spec/braflo1_spec.rb
+- spec/caejap1_spec.rb
+- spec/caepb2_spec.rb
+- spec/caerem3_spec.rb
+- spec/caljac3_spec.rb
+- spec/canfam2_spec.rb
+- spec/cavpor3_spec.rb
+- spec/cb3_spec.rb
 - spec/ce6_spec.rb
+- spec/ci2_spec.rb
+- spec/danrer7_spec.rb
 - spec/dm3_spec.rb
+- spec/dp3_spec.rb
+- spec/droana2_spec.rb
+- spec/droere1_spec.rb
+- spec/drogri1_spec.rb
+- spec/dromoj2_spec.rb
+- spec/droper1_spec.rb
+- spec/drosec1_spec.rb
+- spec/drosim1_spec.rb
+- spec/drovir2_spec.rb
+- spec/droyak2_spec.rb
+- spec/equcab2_spec.rb
+- spec/felcat4_spec.rb
+- spec/fr2_spec.rb
+- spec/galgal3_spec.rb
+- spec/gasacu1_spec.rb
 - spec/go_spec.rb
 - spec/hg18/acembly_spec.rb
 - spec/hg18/acemblyclass_spec.rb
@@ -5165,12 +5552,30 @@ files:
 - spec/hgFixed/hgfixed_transmapsrcsplicedest_spec.rb
 - spec/hgFixed/hgfixed_transmapsrcucscgenes_spec.rb
 - spec/hgfixed_spec.rb
+- spec/loxafr3_spec.rb
 - spec/mm9_spec.rb
+- spec/mondom5_spec.rb
+- spec/ornana1_spec.rb
+- spec/orycun2_spec.rb
+- spec/orylat2_spec.rb
+- spec/oviari1_spec.rb
+- spec/pantro3_spec.rb
+- spec/petmar1_spec.rb
+- spec/ponabe2_spec.rb
+- spec/pripac1_spec.rb
 - spec/proteome_spec.rb
 - spec/reference_spec.rb
+- spec/rhemac2_spec.rb
+- spec/rn4_spec.rb
+- spec/saccer2_spec.rb
 - spec/spec_helper.rb
+- spec/strpur2_spec.rb
+- spec/susscr2_spec.rb
+- spec/taegut1_spec.rb
+- spec/tetnig2_spec.rb
 - spec/uniprot_spec.rb
 - spec/visigene_spec.rb
+- spec/xentro2_spec.rb
 homepage: http://github.com/misshie/bioruby-ucsc-api
 licenses:
 - Ruby (Ruby's/GPLv2 dual)
@@ -5186,7 +5591,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: 1880418701711437715
+      hash: 3670200921648831687
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements:
@@ -5200,8 +5605,39 @@ signing_key:
 specification_version: 3
 summary: ! 'The Ruby UCSC API: accessing the UCSC Genome Database using Ruby'
 test_files:
+- spec/ailmel1_spec.rb
+- spec/anocar2_spec.rb
+- spec/anogam1_spec.rb
+- spec/apimel2_spec.rb
+- spec/aplcal1_spec.rb
+- spec/bostau4_spec.rb
+- spec/braflo1_spec.rb
+- spec/caejap1_spec.rb
+- spec/caepb2_spec.rb
+- spec/caerem3_spec.rb
+- spec/caljac3_spec.rb
+- spec/canfam2_spec.rb
+- spec/cavpor3_spec.rb
+- spec/cb3_spec.rb
 - spec/ce6_spec.rb
+- spec/ci2_spec.rb
+- spec/danrer7_spec.rb
 - spec/dm3_spec.rb
+- spec/dp3_spec.rb
+- spec/droana2_spec.rb
+- spec/droere1_spec.rb
+- spec/drogri1_spec.rb
+- spec/dromoj2_spec.rb
+- spec/droper1_spec.rb
+- spec/drosec1_spec.rb
+- spec/drosim1_spec.rb
+- spec/drovir2_spec.rb
+- spec/droyak2_spec.rb
+- spec/equcab2_spec.rb
+- spec/felcat4_spec.rb
+- spec/fr2_spec.rb
+- spec/galgal3_spec.rb
+- spec/gasacu1_spec.rb
 - spec/go_spec.rb
 - spec/hg18/acembly_spec.rb
 - spec/hg18/acemblyclass_spec.rb
@@ -10084,9 +10520,27 @@ test_files:
 - spec/hgFixed/hgfixed_transmapsrcsplicedest_spec.rb
 - spec/hgFixed/hgfixed_transmapsrcucscgenes_spec.rb
 - spec/hgfixed_spec.rb
+- spec/loxafr3_spec.rb
 - spec/mm9_spec.rb
+- spec/mondom5_spec.rb
+- spec/ornana1_spec.rb
+- spec/orycun2_spec.rb
+- spec/orylat2_spec.rb
+- spec/oviari1_spec.rb
+- spec/pantro3_spec.rb
+- spec/petmar1_spec.rb
+- spec/ponabe2_spec.rb
+- spec/pripac1_spec.rb
 - spec/proteome_spec.rb
 - spec/reference_spec.rb
+- spec/rhemac2_spec.rb
+- spec/rn4_spec.rb
+- spec/saccer2_spec.rb
 - spec/spec_helper.rb
+- spec/strpur2_spec.rb
+- spec/susscr2_spec.rb
+- spec/taegut1_spec.rb
+- spec/tetnig2_spec.rb
 - spec/uniprot_spec.rb
 - spec/visigene_spec.rb
+- spec/xentro2_spec.rb