bio-ucsc-api 0.2.0 → 0.2.1

data/README.rdoc

@@ -2,54 +2,68 @@
 
 The Ruby UCSC API: accessing the UCSC Genome Database using Ruby.
 
+Your comments, suggestions and requests are welcome. Documentation and
+feedback are available at the UserEcho site at
+http://rubyucscapi.userecho.com/.
+
+== Features
+
+* Supporting all organisms in the UCSC genome database.
+* Using ActiveRecord as an O/R mapping framework. Basically, each tables can access using ActiveRecord methods.
+* Using the Bin index system to improve query performance. This is one of the reason why you use Ruby UCSC API instead of submitting SQL queries directly.
+* Supporting genomic sequence query using locally downloaded "2bit" files. Genomic sequences are not stored in UCSC's official MySQL database. 
+* Automatic conversion of "1-based full-closed intervals" to internal "0-based left-closed right-open intervals" (see also bioruby-genomic-interval)
+* Supporting non-official MySql hosts (e.g. local servers)
+* Using Rspec for the testing framework
+* Designed as a BioRuby plugin
+* Current version does not support tables linking to bigWIG or bigBED files.
+
+== Supported databases (genome assemblies)
+[human] Hg19, Hg18
+[mammals] chimp (PanTro3), orangutan (PonAbe2), rhesus (RheMac2), marmoset (CalJac3), mouse (Mm9), rat (Rn4), guinea pig (CavPor3), rabbit (OryCun2), cat (FelCat4), panda (AilMel1), dog (CanFam2), horse (EquCab2), pig (SusScr2), sheep (OviAri1), cow (BosTau4), elephant (LoxAfr3), opossum (MonDom5), platypus (OrnAna1)
+[vertebrates] chicken (GalGal3), zebra finch (TaeGut1), lizard (AnoCar2), X. tropicalis (XenTro2), zebrafish (DanRer7), tetraodon (TetNig2), fugu (Fr2), stickleback (GasAcu1), medaka (OryLat2), lamprey (PetMar1)
+[deuterostomes] lancelet (BraFlo1), sea squirt (Ci2), sea urchin (StrPur2)
+[insects] D.melanogaster (Dm3), D.simulans (DroSim1), D.sechellia (DroSec1), D.yakuba (DroYak2), D.erecta (DroEre1), D.ananassae (DroAna2), D.pseudoobscura (Dp3), D.persimilis (DroPer1), D.virilis (DroVir2), D.mojavensis (DroMoj2), D.grimshawi (DroGri1), Anopheles mosquito (AnoGam1), honey bee (ApiMel2)
+[nematodes] C.elegans (Ce6), C.brenneri (CaePb3), C.briggsae (Cb3), C.remanei (CaeRem3), C.japonica (CarJap1), P.pacificus (PriPac1)
+[others] sea hare (AplCal1), yeast (SacCer2)
+[genome assembly independent] Go, HgFixed, Proteome, UniProt, VisiGene
+
+== Implementation
 This package is based on the followings:
+
 * original ruby-ucsc-api: https://github.com/jandot/ruby-ucsc-api
 * ruby-ensembl-api: https://github.com/jandot/ruby-ensembl-api
 
 Major dependent gems:
+
 * active_record http://api.rubyonrails.org/classes/ActiveRecord/Base.html
 * bioruby-genomic-interval https://github.com/misshie/bioruby-genomic-interval
 
 Requirement:
+
 * Ruby version 1.9.2 or later
-* (To Do: supporting Ruby version 1.8.7)
+* Ruby version 1.8.7 or later
+* (To-Do: JRuby support)
 
-See also a paper:
+See also:
 
-Strozzi F, Aerts J: A Ruby API to query the Ensembl database for genomic features.
+* Strozzi F, Aerts J: A Ruby API to query the Ensembl database for genomic features.
 Bioinformatics 2011, 27:1013-1014.
-
-Your comments, suggestions and requests are welcome. Documentation and
-feedback are available at the UserEcho site at
-http://rubyucscapi.userecho.com/.
-
-== Features
-
-* Designed as a BioRuby plugin
-* Using ActiveRecord as an O/R mapping framework
-* Using the Bin index system to improve query performance (see https://github.com/misshie/UCSCBin )
-* Automatic conversion of "1-based full-closed intervals" to internal "0-based left-closed right-open intervals" (see also bioruby-genomic-interval)
-* Supporting non-official MySql hosts (e.g. local servers)
-* Using Rspec for the testing framework
-* Support hg19 and hg18 databases. Current version does not support tables containing only single records of the fileName columns linking to bigWIG or bigBED files.
-
-== Supporting Databases
-[human] Hg19, Hg18
-[mouse] Mm9
-[fruitfly] Dm3
-[C.Elegans] Ce6
-[genome assembly independent] Go, HgFixed, Proteome, UniProt, VisiGene,
-
+* UCSCBin library - https://github.com/misshie/UCSCBin
+ 
 == Change Log
-* *UPDATE* (v0.2.0): Now table structures are automatically detected and dynamically defined as classes.
-* *UPDATE* (v0.2.0): Bio::Ucsc::Reference changed to more object-oriented.
+* *NEW* (v.0.2.1): New genome assemblies are supported: [chimp] PanTro3, [orangutan] PonAbe2, [rhesus] RheMac2, [marmoset] CalJac3, [rat] Rn4, [guinea pig] CavPor3, [rabbit] OryCun2, [cat] FelCat4, [panda] AilMel1, [Dog] CanFam2, [horse] EquCab2, [pig] SusScr2, [sheep] OviAri1, [cow] BosTau4, [elephant] LoxAfr3, [opossum] MonDom5, [platypus] OrnAna1, [chicken] GalGal3, [zebra finch] TaeGut1, [lizard] AnoCar2, [X. tropicalis] XenTro2, [zebrafish] DanRer7, [tetraodon] TetNig2, [fugu] Fr2, [stickleback] GasAcu1, [medaka] OryLat2, [lamprey] PerMar1, [lancelet] BraFlo1, [sea squirt] Ci2, [sea urchin] StrPur2, [D.simulans] DroSim1, [D.sechellia] DroSec1, [D.yakuba] DroYak2, [D.electa] DroEre1, [D.ananassae] DroAna2, [D.pseudoobscura] Dp3, [D.persimilis] DroPer1, [D. virilis] DroVir2, [D.mojavensis] DroMoj2, [D.grimshawi] DroGri1, [Anopheles mosquito] AnoGam1, [honey bee] ApiMel2,  [C.brenneri] CaePb3, [C.briggsae] Cb3, [C.remanei] CaeRem3, [P.pacificus] PriPac1, [sea hare] AplCal1, [yeast] SacCer2
+* *NEW* (v.0.2.1): Supporting Ruby 1.8.7 or later
+* *NEW* Adding to human Hg19 and Hg18, the following genome assemblies are supported: [mouse] Mm9, [fruitfly] Dm3, [C. elegans] Ce6, [genome assembly independent] Go, HgFixed, Proteome, UniProt, VisiGene
+* *UPDATE* (v0.2.0): Internal table class mapping algorithm are changed. Now table types are automatically detected and dynamically defined as classes. Previous versions used static class definition for all tables.
+* *MODIFIED* (v0.2.0):  Bio::Ucsc::[Hg18|Hg19]::ReferenceSequence are removed. Use Bio::Ucsc::Reference instead. This class is more object-oriented.
 * *MODIFIED* (v0.1.0): The name of this library is now "Ruby UCSC API". The RubyGem name and the GitHub account and the library name are not changed.
 *  *MODIFIED* (v0.1.0): Bio::Ucsc::[Hg18|Hg19]::Reference is replaced by Bio::Ucsc::[Hg18|Hg19]::ReferenceSequence.
 * *UPDATE* (v0.0.5): Almost all hg18 tables are supported.
 * *UPDATE* (v0.0.5): find_by_interval and find_all_by_interval class methods accept the "partial" option. Default is true. When "partial: false" is opted, return value will be only fully-included (non-partially-included) records.  
 * *UPDATE* (v0.0.4): Almost all hg19 tables are supported. "filename" tables in ENCODE dataset are omitted. Each of them contains only single record of a path to the raw data file. Definitions of table relations are incomplete. 
-* *NEW* (v0.0.3): Supporting locally-stored '2bit' files, which can be downloaded from the UCSC site, to retrieve referencial sequence. Now supporting unknown "N" nucleotide blocks, however, "mask-blocks", which are shown in lower-case in UCSC's DNA function, are not supported yet.
-* *MODIFIED* (v0.0.3): For the "TABLE" class and the "column" column, TABLE.find_by_column retrives a first record, and TABLE.find_all_by_column retrieves all the records as an Array.
+* *NEW* (v0.0.3): Supporting locally-stored '2bit' files, which can be downloaded from the UCSC site, to retrieve referential sequence. Now supporting unknown "N" nucleotide blocks, however, "mask-blocks", which are shown in lower-case in UCSC's DNA function, are not supported yet.
+* *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
@@ -59,27 +73,35 @@ http://rubyucscapi.userecho.com/.
 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".
+* Before using a database, establish a connection to the database. For example, "Bio::Ucsc::Hg19::DBConnection.connect". 
+* A table in a database is represented as a class in the database module. For example, the snp132 table in the hg19 database is referred by "Bio::Ucsc::Hg19::Snp132".
+* Queries to a field (column) in a table are represented by class methods of the table class. For example, finding the first record (row) of the snp132 table in the hg19 database is "Bio::Ucsc::Hg19::Snp132.first". 
+* Queries using genomic intervals are supported by .find_by_intervals (returns the first hit record) and .find_all_by (returns all the hit records) class methods. Each method accepts a Bio::GenomicInterval object containing a genomic interval such as "chr1:1233-5678". If a table to query has the "bin"column, the bin index system is automatically used to speed-up the query.
+* Fields in a retrieved record can be acccessed by using instance methods of a record object. For example, the name field of a table record stored in the "result" variable is "result.name".  
+
+=== Sample Codes
  require 'bio-ucsc'
 
  include Bio::Ucsc::Hg19 
  DBConnection.connect
 
  # When using a table-class first time, refer the class using full-path.
- # If not, the API will fail to prefetch the table and define the appropreate class.
+ # If not, the API will fail to prefetch the table and define the appropriate class.
  # After that, you can refer the table class with a short name enabled by
- # top level "include" funtion 
+ # top level "include" function 
  Bio::Ucsc::Hg19::Snp131 # This line just refer the table class
 
- itv =  Bio::GenomicInterval.parse("chr1:1-11,000")
- Snp131.find_all_by_interval(itv).each do |e|
+ gi =  Bio::GenomicInterval.parse("chr1:1-11,000")
+ Snp131.find_all_by_interval(gi).each do |e|
    i = Bio::GenomicInterval.zero_based(e.chrom, e.chromStart, e.chromEnd)
    puts "#{i.chrom}\t#{i.chr_start}\t#{e.name}\t#{e[:class]}"
  end
 
- itv =  Bio::GenomicInterval.parse("chr17:7,579,614-7,579,700")
- p Snp131.find_all_by_interval(itv)
- p Snp131.find_all_by_interval(itv, partial:false)
+ gi =  Bio::GenomicInterval.parse("chr17:7,579,614-7,579,700")
+ p Snp131.find_all_by_interval(gi)
+ p Snp131.find_all_by_interval(gi, partial:false)
 
  p Snp131.find_by_name("rs56289060")
 
@@ -93,14 +115,9 @@ You may need to be root or use "sudo". "--no-ri" and "--no-rdoc" options are rec
  p Snp131.find_by_sql(sql)
 
  # retrieve reference sequence from a locally-stored 2bit file
-
- # Obsolete
- # ReferenceSequence.load("hg19.2bit")
- # itv = Bio::GenomicInterval.parse("chr1:9,500-10,999")
- # p ReferenceSequence.find_by_interval(itv)
- hg19ref = Bio::Ucsc:Reference.load("hg19.2bit")
- itv = Bio::GenomicInterval.parse("chr1:9,500-10,999")
- hg19ref.find_by_interval(itv)
+ hg19ref = Bio::Ucsc::Reference.load("hg19.2bit")
+ gi = Bio::GenomicInterval.parse("chr1:9,500-10,999")
+ hg19ref.find_by_interval(gi)
 
  # Connetcting to non-official or local mirror MySQL servers
  DBConnection.db_host = 'foo.example.edu'
@@ -111,9 +128,24 @@ You may need to be root or use "sudo". "--no-ri" and "--no-rdoc" options are rec
  DBConnection.default # reset to connect UCSC's public MySQL sever
  DBConnection.connect
 
+=== 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.
+* Table names starting with uppercase character: Classes for "HInv" and "NIAGene" tables are "HInv" and "NIAGene", respectively
+* Tables separated into each chromosome, like 'chr1_rmsk', 'chr2_rmsk'... are supported by a representative class ('Rmsk'). When using the find(_all)_by_interval class method, the API invoke required separated tables automatically.
+* 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 "find_(all_)by_intervals"
+* 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.
+* When chrom/txStart/txEnd fields exist (genePred table), the API uses them for interval queries.
+* 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]".
+
 == Copyright
 Copyright:: (c) 2011 MISHIMA, Hiroyuki (missy at be.to / hmishima at nagasaki-u.ac.jp / @mishimahryk in Twitter)
 Copyright:: (c) 2010 Jan Aerts
 
-License:: Ruby license (Ruby's / GPLv2 dual). See COPYING and COPYING.ja for further details.
-
+License:: Ruby license (Ruby's / GPLv2 dual). See COPYING and COPYING.ja for further details.

data/Rakefile

@@ -47,8 +47,10 @@ end
 
 task :default => :spec
 
-require 'rake/rdoctask'
-Rake::RDocTask.new do |rdoc|
+# require 'rake/rdoctask'
+require 'rdoc/task'
+# Rake::RDocTask.new do |rdoc|
+RDoc::Task.new do |rdoc|
   version = File.exist?('VERSION') ? File.read('VERSION') : ""
 
   rdoc.rdoc_dir = 'rdoc'

data/VERSION

@@ -1 +1 @@
-0.2.0
+0.2.1

data/bio-ucsc-api.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = %q{bio-ucsc-api}
-  s.version = "0.2.0"
+  s.version = "0.2.1"
 
   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{2011-08-08}
+  s.date = %q{2011-08-14}
   s.description = %q{Ruby UCSC API: accessing the UCSC Genome Database using Ruby}
   s.email = %q{missy@be.to}
   s.extra_rdoc_files = [
@@ -26,6 +26,105 @@ Gem::Specification.new do |s|
     "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",
@@ -47,6 +146,10 @@ Gem::Specification.new do |s|
     "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",
@@ -73,6 +176,124 @@ Gem::Specification.new do |s|
     "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",
@@ -114,6 +335,8 @@ Gem::Specification.new do |s|
     "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",
@@ -154,15 +377,148 @@ Gem::Specification.new do |s|
     "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",
@@ -175,8 +531,39 @@ Gem::Specification.new do |s|
   s.rubygems_version = %q{1.8.6}
   s.summary = %q{The Ruby UCSC API: accessing the UCSC Genome Database using Ruby}
   s.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",
@@ -5059,12 +5446,30 @@ Gem::Specification.new do |s|
     "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/visigene_spec.rb",
+    "spec/xentro2_spec.rb"
   ]
 
   if s.respond_to? :specification_version then