bio-ucsc-api 0.2.1 → 0.3.0

data/COPYING.ja

@@ -1,3 +1,5 @@
+# -*- coding: iso-2022-jp -*-
+
 $BK\%W%m%0%i%`$O%U%j!<%=%U%H%&%'%"$G$9!%(BGPL (the GNU General
 Public License)$B%P!<%8%g%s(B2$B$^$?$O0J2<$K<($9>r7o$GK\%W%m%0%i%`(B
 $B$r:FG[I[$G$-$^$9!%(BGPL$B$K$D$$$F$O(BGPL$B%U%!%$%k$r;2>H$7$F2<$5$$!%(B

data/README.rdoc

@@ -9,22 +9,24 @@ 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 ActiveRecord as an O/R mapping framework. Basically, each tables can access using ActiveRecord method convention.
 * 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)
+* Supporting non-official full/partial mirror MySql hosts (e.g. local servers)
 * Using Rspec for the testing framework
+* Written in pure Ruby and supporting multiple Ruby interpreter implementations including Ruby1.8, Ruby1.9, and JRuby1.6
 * Designed as a BioRuby plugin
-* Current version does not support tables linking to bigWIG or bigBED files.
+* Current version does not support table-linked bigWIG/bigBED/BAM 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)
+[nematodes] C.elegans (Ce6), C.brenneri (CaePb3), C.briggsae (Cb3), C.remanei (CaeRem3), C.japonica (CaeJap1), P.pacificus (PriPac1)
 [others] sea hare (AplCal1), yeast (SacCer2)
 [genome assembly independent] Go, HgFixed, Proteome, UniProt, VisiGene
 
@@ -34,24 +36,27 @@ 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:
+Supported Ruby interpreter implementations:
 
 * Ruby version 1.9.2 or later
 * Ruby version 1.8.7 or later
-* (To-Do: JRuby support)
+* JRuby version 1.6.3 or later - Appropiate Java heap size may have to be specified to invoke JRuby, especially when you use Bio::Ucsc::Reference. Try "jruby -J-Xmx3g your_script.rb" to keep 3G byte heap.
+
+Major dependent gems:
+
+* active_record - http://api.rubyonrails.org/classes/ActiveRecord/Base.html
+* bioruby-genomic-interval - https://github.com/misshie/bioruby-genomic-interval
+* mysql (MySQL/Ruby MySQL API module) - http://www.tmtm.org/mysql/ruby/README.html
 
 See also:
 
-* Strozzi F, Aerts J: A Ruby API to query the Ensembl database for genomic features.
-Bioinformatics 2011, 27:1013-1014.
+* Strozzi F, Aerts J: A Ruby API to query the Ensembl database for genomic features. Bioinformatics 2011, 27:1013-1014.
 * UCSCBin library - https://github.com/misshie/UCSCBin
  
 == Change Log
+* *NEW* (v.0.3.0): Now genomic interval queries are expressed using the named scope "with_interval". Table#find_(all_)by_interval is now deprecated. Sorry for an inconstant API. However, this change enable combination queries using genomic intervals and any fields. 
+* *NEW* (v.0.3.0): Bio::GenomicInterval#bin_all and Bio::GenomicInterval#bin return the bin index for the given interval.
+* *NEW* (v.0.3.0): Supporting JRuby 1.6.3 or later. Appropiate Java heap size may have to be specified to invoke JRuby, especially when you use Bio::Ucsc::Reference. Try "jruby -J-Xmx3g your_script.rb" to keep 3G byte heap.
 * *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
@@ -78,64 +83,74 @@ You may need to be root or use "sudo". "--no-ri" and "--no-rdoc" options are rec
 * 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.
+* Queries using genomic intervals are supported by the named scope ".with_intervals" and ".with_intervals_excl (omitting pertially included annotations)" method of the table class. The 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
+At first, you have to declare the API and establish the connection to a database. 
  require 'bio-ucsc'
 
- include Bio::Ucsc::Hg19 
- DBConnection.connect
+ include Bio # To short-cut the class path
+ 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 appropriate class.
- # After that, you can refer the table class with a short name enabled by
- # top level "include" function 
- Bio::Ucsc::Hg19::Snp131 # This line just refer the table class
+In the first reference of a table class, the followings does not work: 
+ include Bio::Ucsc::Hg19
+ Snp131.first # The Ruby interpreter searchs Snp131 at the top-level
+But the following line works because the API will fail to prefetch the table and define the appropriate class dynamically.  "include Bio" or "include Bio::Ucsc" will work.
+ Ucsc::Hg19::Snp131 # This line works
 
- 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]}"
+Table search using genomic intervals:
+ gi =  GenomicInterval.parse("chr1:1-11,000")
+ Ucsc::Hg19::Snp131.with_interval(gi).find(:all).each do |e|
+   i = GenomicInterval.zero_based(e.chrom, e.chromStart, e.chromEnd)
+   puts "#{i.chrom}\t#{i.chr_start}\t#{e.name}\t#{e[:class]}" # "e.class" does not work
  end
 
- 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)
+ gi = GenomicInterval.parse("chr17:7,579,614-7,579,700")
+ Ucsc::Hg19::Snp131.with_interval(gi).find(:all)
+
+ Ucsc::Hg19::Snp131.with_interval_excl(gi).find(:all)
 
- p Snp131.find_by_name("rs56289060")
+ Ucsc::Hg19::Snp132.with_interval(gi).select(:name).find_all_by_class_and_strand("in-del", "+")
 
- # Sometimes, queries using raw SQL provide elegant solutions.
- # 
+ Ucsc::Hg19::Snp131.find_by_name("rs56289060")
+
+Sometimes, queries using raw SQLs provide elegant solutions.
  sql << 'SQL'
  SELECT name,chrom,chromStart,chromEnd,observed
  FROM snp131 
  WHERE name="rs56289060"
  SQL
- p Snp131.find_by_sql(sql)
+ p Ucsc::Hg19::Snp131.find_by_sql(sql)
 
- # retrieve reference sequence from a locally-stored 2bit file
- hg19ref = Bio::Ucsc::Reference.load("hg19.2bit")
- gi = Bio::GenomicInterval.parse("chr1:9,500-10,999")
+retrieve reference sequence from a locally-stored 2bit file. The "hg19.2bit" file can be downloaded from http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/hg19.2bit
+ hg19ref = Ucsc::Reference.load("hg19.2bit")
+ gi = 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'
- DBConnection.db_username = 'genome'
- DBConnection.db_password = ''
- DBConnection.connect
+Connetcting to non-official or local full/partial mirror MySQL servers
+ Ucsc::Hg18::DBConnection.db_host = 'localhost'
+ Ucsc::Hg18::DBConnection.db_username = 'genome'
+ Ucsc::Hg18::DBConnection.db_password = ''
+ Ucsc::Hg18::DBConnection.connect
+
+ Ucsc::Hg18::DBConnection.default # reset to connect UCSC's public MySQL sever
+ Ucsc::Hg18::DBConnection.connect
 
- DBConnection.default # reset to connect UCSC's public MySQL sever
- DBConnection.connect
+And see also sample scripts in the samples directory.
+* num-gene-exon.rb - calculation of total number of genes and exons using genomic interval
+* symbol2summary.rb - getting summary descriptions using gene symbol
+* hg19-2bit-retrieve - outputting reference sequence in FASTA format   
+* bed2refseq - getting unique gene symbols in the genomic intervals in a BED file.
 
 === 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.
+* Accessing chromosome-specific tables: For example, the 'rmsk' table in hg18 is actually separated into 'chr1_rmsk', 'chr2_rmsk'... There is two way to access to them. (1) Accessing separated tables directly. There is no difference from other regular tables. However, you have to manage each separated tables. (2) Use abstract table classes (e.g., 'Rmsk') and their class methods ".find_by_interval' or '.find_all_by_interval'. These methods look for correspondent separated tables automatically. However, you cannot combine with other 'find_by_[field]' methods. Moreover, if you have to perform single- or multi-chromosomal search, you have to access separated tables individually and integrate results by yourself. Fortunately, recent databases, including hg19, seem not to use chromosome-specific tables.
 * 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"
+=== details in "with_interval"
 * When a table class is referred first time, the API prefetches the table to get a list of fields and dynamically defines a class using following algorithm.
 * If chrom/chromStart/chromEnd fields exist (BED table), the API uses them for interval queries.
 * When tName/tStart/tEnd fields exist (PSL table), the API uses them for interval queries.

data/VERSION

@@ -1 +1 @@
-0.2.1
+0.3.0

data/bio-ucsc-api.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = %q{bio-ucsc-api}
-  s.version = "0.2.1"
+  s.version = "0.3.0"
 
   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{2011-08-14}
+  s.date = %q{2011-08-23}
   s.description = %q{Ruby UCSC API: accessing the UCSC Genome Database using Ruby}
   s.email = %q{missy@be.to}
   s.extra_rdoc_files = [
@@ -294,6 +294,7 @@ Gem::Specification.new do |s|
     "lib/bio-ucsc/gasacu1/intronest.rb",
     "lib/bio-ucsc/gasacu1/mrna.rb",
     "lib/bio-ucsc/gasacu1/rmsk.rb",
+    "lib/bio-ucsc/genomic-interval-bin.rb",
     "lib/bio-ucsc/go.rb",
     "lib/bio-ucsc/go/db_connection.rb",
     "lib/bio-ucsc/hg18.rb",
@@ -546,6 +547,7 @@ Gem::Specification.new do |s|
     "spec/cavpor3_spec.rb",
     "spec/cb3_spec.rb",
     "spec/ce6_spec.rb",
+    "spec/chromosome_specific_tables_spec.rb",
     "spec/ci2_spec.rb",
     "spec/danrer7_spec.rb",
     "spec/dm3_spec.rb",
@@ -561,9 +563,11 @@ Gem::Specification.new do |s|
     "spec/droyak2_spec.rb",
     "spec/equcab2_spec.rb",
     "spec/felcat4_spec.rb",
+    "spec/find_by_and_spec.rb",
     "spec/fr2_spec.rb",
     "spec/galgal3_spec.rb",
     "spec/gasacu1_spec.rb",
+    "spec/genomic-interval-bin_spec.rb",
     "spec/go_spec.rb",
     "spec/hg18/acembly_spec.rb",
     "spec/hg18/acemblyclass_spec.rb",
@@ -5449,6 +5453,7 @@ Gem::Specification.new do |s|
     "spec/loxafr3_spec.rb",
     "spec/mm9_spec.rb",
     "spec/mondom5_spec.rb",
+    "spec/named_scope_spec.rb",
     "spec/ornana1_spec.rb",
     "spec/orycun2_spec.rb",
     "spec/orylat2_spec.rb",

data/lib/bio-ucsc.rb

@@ -4,13 +4,13 @@
 #               MISHIMA, Hiroyuki <missy at be.to / hmishima at nagasaki-u.ac.jp> 
 # License::     Ruby licence (Ryby's / GPLv2 dual)
 
-base = File.dirname(__FILE__)
-require "#{base}/bio-ucsc/ucsc_bin"
-require "bio-genomic-interval"
+base = "#{File.dirname(__FILE__)}/bio-ucsc"
+require "#{base}/ucsc_bin"
+require "#{base}/genomic-interval-bin"
 
 module Bio
   module Ucsc
-    VERSION = "0.2.1"
+    VERSION = "0.3.0"
     base = "#{File.dirname(__FILE__)}/bio-ucsc"
     
     # mammmals #####################################

data/lib/bio-ucsc/genomic-interval-bin.rb

@@ -0,0 +1,13 @@
+require "bio-genomic-interval"
+
+module Bio
+  class GenomicInterval
+    def bin
+      Bio::Ucsc::UcscBin.bin(self.zero_start, self.zero_end)
+    end
+
+    def bin_all
+      Bio::Ucsc::UcscBin.bin_all(self.zero_start, self.zero_end)
+    end
+  end
+end

data/lib/bio-ucsc/table_class_detector.rb

@@ -22,6 +22,15 @@ module Bio
         ['attribute', 'valid', 'validate', 'class', 'method', 'methods', 'type']
       UPPERCASED_TABLE_PREFIX = 
         ['HInv', 'NIAGene']
+      COMMON_CLASS_METHODS = %!
+        def self.find_by_interval(interval, opt = {:partial => true})
+          find_first_or_all_by_interval(interval, :first, opt)
+        end
+        
+        def self.find_all_by_interval(interval, opt = {:partial => true})
+          find_first_or_all_by_interval(interval, :all, opt)
+        end
+      !
 
       def const_missing(sym)
         module_eval generic(sym)
@@ -81,13 +90,31 @@ module Bio
             class #{uphead(sym)} < DBConnection
               set_table_name "#{downhead(sym)}"
               #{delete_reserved_methods}
-              def self.find_by_interval(interval, opt = {:partial => true})
-                find_first_or_all_by_interval(interval, :first, opt)
-              end
-        
-              def self.find_all_by_interval(interval, opt = {:partial => true})
-                find_first_or_all_by_interval(interval, :all, opt)
-              end
+              #{COMMON_CLASS_METHODS}
+
+              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
+              scope(:with_interval,
+                    Proc.new{|gi|{:conditions => [where, {:chrom => gi.chrom,
+                                                          :bins => gi.bin_all,
+                                                          :zstart => gi.zero_start,
+                                                          :zend => gi.zero_end,}]}})
+              where = <<-SQL
+     tName = :chrom
+AND bin in (:bins)
+AND ((tStart BETWEEN :zstart AND :zend)
+AND  (tEnd BETWEEN :zstart AND :zend))
+                SQL
+              scope(:with_interval_excl,
+                    Proc.new{|gi|{:conditions => [where,{:chrom => gi.chrom,
+                                                         :bins => gi.bin_all,
+                                                         :zstart => gi.zero_start,
+                                                         :zend => gi.zero_end,}]}})
 
               def self.find_first_or_all_by_interval(interval, first_all, opt)
                 zstart = interval.zero_start
@@ -100,13 +127,14 @@ AND bin in (:bins)
 AND ((tStart BETWEEN :zstart AND :zend)
  OR (tEnd BETWEEN :zstart AND :zend)
  OR (tStart <= :zstart AND tEnd >= :zend))
-                SQL
+                  SQL
                 else
-            where = <<-SQL
+                  where = <<-SQL
     tName = :chrom 
+AND bin in (:bins)
 AND ((tStart BETWEEN :zstart AND :zend)
 AND  (tEnd BETWEEN :zstart AND :zend))
-                SQL
+                  SQL
                 end
                 cond = {
                 :chrom => interval.chrom,
@@ -125,15 +153,28 @@ AND  (tEnd BETWEEN :zstart AND :zend))
             class #{uphead(sym)} < DBConnection
               set_table_name "#{downhead(sym)}"
               #{delete_reserved_methods}
-              
-              def self.find_by_interval(interval, opt = {:partial => true})
-                find_first_or_all_by_interval(interval, :first, opt)
-              end
-              
-              def self.find_all_by_interval(interval, opt = {:partial => true})
-                find_first_or_all_by_interval(interval, :all, opt)
-              end
+              #{COMMON_CLASS_METHODS}
 
+              where = <<-SQL
+         tName = :chrom
+  AND ((tStart BETWEEN :zstart AND :zend)
+  OR   (tEnd BETWEEN :zstart AND :zend)
+  OR   (tStart <= :zstart AND tEnd >= :zend))
+                  SQL
+              scope(:with_interval,
+                    Proc.new{|gi|{:conditions => [where, {:chrom => gi.chrom,
+                                                          :zstart => gi.zero_start,
+                                                          :zend => gi.zero_end,}]}})
+              where = <<-SQL
+        tName = :chrom
+  AND ((tStart BETWEEN :zstart AND :zend)
+  AND  (tEnd BETWEEN :zstart AND :zend))
+                  SQL
+               scope(:with_interval_excl,
+                     Proc.new{|gi|{:conditions => [where,{:chrom => gi.chrom,
+                                                          :zstart => gi.zero_start,
+                                                          :zend => gi.zero_end,}]}})
+             
               def self.find_first_or_all_by_interval(interval, first_all, opt)
                 zstart = interval.zero_start
                 zend   = interval.zero_end
@@ -174,15 +215,32 @@ AND  (tEnd BETWEEN :zstart AND :zend))
             class #{uphead(sym)} < DBConnection
               set_table_name "#{downhead(sym)}"
               #{delete_reserved_methods}
+              #{COMMON_CLASS_METHODS}
  
-              def self.find_by_interval(interval, opt = {:partial => true})
-                find_first_or_all_by_interval(interval, :first, opt)
-              end
-        
-              def self.find_all_by_interval(interval, opt = {:partial => true})
-                find_first_or_all_by_interval(interval, :all, opt)
-              end
-            
+              where = <<-SQL
+    chrom = :chrom
+ AND bin in (:bins)
+ AND ((chromStart BETWEEN :zstart AND :zend)
+  OR (chromEnd BETWEEN :zstart AND :zend)
+  OR (chromStart <= :zstart AND chromEnd >= :zend))
+                SQL
+              scope(:with_interval,
+                    Proc.new{|gi|{:conditions => [where, {:chrom => gi.chrom,
+                                                          :bins => gi.bin_all,
+                                                          :zstart => gi.zero_start,
+                                                          :zend => gi.zero_end,}]}})
+              where = <<-SQL
+     chrom = :chrom 
+ AND bin in (:bins)
+ AND ((chromStart BETWEEN :zstart AND :zend)
+ AND  (chromEnd BETWEEN :zstart AND :zend))
+                SQL
+              scope(:with_interval_excl,
+                    Proc.new{|gi|{:conditions => [where,{:chrom => gi.chrom,
+                                                         :bins => gi.bin_all,
+                                                         :zstart => gi.zero_start,
+                                                         :zend => gi.zero_end,}]}})
+
               def self.find_first_or_all_by_interval(interval, first_all, opt)
                 zstart = interval.zero_start
                 zend   = interval.zero_end
@@ -220,14 +278,27 @@ AND  (chromEnd BETWEEN :zstart AND :zend))
             class #{uphead(sym)} < DBConnection
               set_table_name "#{downhead(sym)}"
               #{delete_reserved_methods}
-              
-              def self.find_by_interval(interval, opt = {:partial => true})
-                find_first_or_all_by_interval(interval, :first, opt)
-              end
-              
-              def self.find_all_by_interval(interval, opt = {:partial => true})
-                find_first_or_all_by_interval(interval, :all, opt)
-              end
+              #{COMMON_CLASS_METHODS}
+
+              where = <<-SQL
+         chrom = :chrom
+  AND ((chromStart BETWEEN :zstart AND :zend)
+  OR   (chromEnd BETWEEN :zstart AND :zend)
+  OR   (chromStart <= :zstart AND chromEnd >= :zend))
+                SQL
+                scope(:with_interval,
+                      Proc.new{|gi|{:conditions => [where, {:chrom => gi.chrom,
+                                                            :zstart => gi.zero_start,
+                                                            :zend => gi.zero_end,}]}})
+              where = <<-SQL
+        chrom = :chrom 
+  AND ((chromStart BETWEEN :zstart AND :zend)
+  AND  (chromEnd BETWEEN :zstart AND :zend))
+                SQL
+              scope(:with_interval_excl,
+                    Proc.new{|gi|{:conditions => [where,{:chrom => gi.chrom,
+                                                         :zstart => gi.zero_start,
+                                                         :zend => gi.zero_end,}]}})
 
               def self.find_first_or_all_by_interval(interval, first_all, opt)
                 zstart = interval.zero_start
@@ -269,14 +340,32 @@ AND  (chromEnd BETWEEN :zstart AND :zend))
             class #{uphead(sym)} < DBConnection
               set_table_name "#{downhead(sym)}"
               #{delete_reserved_methods}
- 
-              def self.find_by_interval(interval, opt = {:partial => true})
-                find_first_or_all_by_interval(interval, :first, opt)
-              end
-        
-              def self.find_all_by_interval(interval, opt = {:partial => true})
-                find_first_or_all_by_interval(interval, :all, opt)
-              end
+              #{COMMON_CLASS_METHODS} 
+
+              where = <<-SQL
+      chrom = :chrom
+AND   bin in (:bins)
+AND ((txStart BETWEEN :zstart AND :zend)
+ OR  (txEnd BETWEEN :zstart AND :zend)
+ OR  (txStart <= :zstart AND txEnd >= :zend))
+                SQL
+              scope(:with_interval,
+                    Proc.new{|gi|{:conditions => [where, {:chrom => gi.chrom,
+                                                          :bins => gi.bin_all,
+                                                          :zstart => gi.zero_start,
+                                                          :zend => gi.zero_end,}]}})
+
+               where = <<-SQL
+      chrom = :chrom 
+AND   bin in (:bins)
+AND ((txStart BETWEEN :zstart AND :zend)
+AND  (txEnd BETWEEN :zstart AND :zend))
+                  SQL
+              scope(:with_interval_excl,
+                    Proc.new{|gi|{:conditions => [where,{:chrom => gi.chrom,
+                                                         :bins => gi.bin_all,
+                                                         :zstart => gi.zero_start,
+                                                         :zend => gi.zero_end,}]}})
 
               def self.find_first_or_all_by_interval(interval, first_all, opt)
                 zstart = interval.zero_start
@@ -314,14 +403,33 @@ AND  (txEnd BETWEEN :zstart AND :zend))
             class #{uphead(sym)} < DBConnection
               set_table_name "#{downhead(sym)}"
               #{delete_reserved_methods}
- 
-              def self.find_by_interval(interval, opt = {:partial => true})
-                find_first_or_all_by_interval(interval, :first, opt)
-              end
-        
-              def self.find_all_by_interval(interval, opt = {:partial => true})
-                find_first_or_all_by_interval(interval, :all, opt)
-              end
+              #{COMMON_CLASS_METHODS}
+
+              def self.with_interval(gi, opt = {:partial => true})
+                if opt[:partial] == true
+                  where = <<-SQL
+       chrom = :chrom
+AND ((txStart BETWEEN :zstart AND :zend)
+ OR   (txEnd BETWEEN :zstart AND :zend)
+ OR   (txStart <= :zstart AND txEnd >= :zend))
+                  SQL
+                else
+                  where = <<-SQL
+        chrom = :chrom 
+  AND ((txStart BETWEEN :zstart AND :zend)
+  AND  (txEnd BETWEEN :zstart AND :zend))
+                  SQL
+                end
+                values = {
+                  :chrom => gi.chrom,
+                  :zstart => gi.zero_start,
+                  :zend => gi.zero_end,
+                }
+
+                with_scope(:find => {:conditions => [where, values]}) do
+                  yield
+                end
+              end # def self.with_interval
 
               def self.find_first_or_all_by_interval(interval, first_all, opt)
                 zstart = interval.zero_start
@@ -363,14 +471,31 @@ AND ((txStart BETWEEN :zstart AND :zend)
             class #{uphead(sym)} < DBConnection
               set_table_name "#{downhead(sym)}"
               #{delete_reserved_methods}
+              #{COMMON_CLASS_METHODS}
  
-              def self.find_by_interval(interval, opt = {:partial => true})
-                find_first_or_all_by_interval(interval, :first, opt)
-              end
-        
-              def self.find_all_by_interval(interval, opt = {:partial => true})
-                find_first_or_all_by_interval(interval, :all, opt)
-              end
+              where = <<-SQL
+      genoName = :chrom
+AND   bin in (:bins)
+AND ((genoStart BETWEEN :zstart AND :zend)
+ OR  (genoEnd BETWEEN :zstart AND :zend)
+ OR  (genoStart <= :zstart AND genoEnd >= :zend))
+                SQL
+              scope(:with_interval,
+                    Proc.new{|gi|{:conditions => [where, {:chrom => gi.chrom,
+                                                          :bins => gi.bin_all,
+                                                          :zstart => gi.zero_start,
+                                                          :zend => gi.zero_end,}]}})
+              where = <<-SQL
+      genoName = :chrom
+AND   bin in (:bins)
+AND ((genoStart BETWEEN :zstart AND :zend)
+AND  (genoEnd BETWEEN :zstart AND :zend))
+                  SQL
+              scope(:with_interval_excl,
+                    Proc.new{|gi|{:conditions => [where,{:chrom => gi.chrom,
+                                                         :bins => gi.bin_all,
+                                                         :zstart => gi.zero_start,
+                                                         :zend => gi.zero_end,}]}})
 
               def self.find_first_or_all_by_interval(interval, first_all, opt)
                 zstart = interval.zero_start
@@ -382,14 +507,14 @@ AND   bin in (:bins)
 AND ((genoStart BETWEEN :zstart AND :zend)
  OR  (genoEnd BETWEEN :zstart AND :zend)
  OR  (genoStart <= :zstart AND genoEnd >= :zend))
-                SQL
+                  SQL
                 else
                 where = <<-SQL
       genoName = :chrom
 AND   bin in (:bins)
 AND ((genoStart BETWEEN :zstart AND :zend)
 AND  (genoEnd BETWEEN :zstart AND :zend))
-                SQL
+                  SQL
                 end
                 cond = {
                 :chrom  => interval.chrom,
@@ -408,14 +533,28 @@ AND  (genoEnd BETWEEN :zstart AND :zend))
             class #{uphead(sym)} < DBConnection
               set_table_name "#{downhead(sym)}"
               #{delete_reserved_methods}
- 
-              def self.find_by_interval(interval, opt = {:partial => true})
-                find_first_or_all_by_interval(interval, :first, opt)
-              end
-        
-              def self.find_all_by_interval(interval, opt = {:partial => true})
-                find_first_or_all_by_interval(interval, :all, opt)
-              end
+              #{COMMON_CLASS_METHODS} 
+
+              where = <<-SQL
+       genoName = :chrom
+AND ((genoStart BETWEEN :zstart AND :zend)
+ OR   (genoEnd BETWEEN :zstart AND :zend)
+ OR   (genoStart <= :zstart AND genoEnd >= :zend))
+                SQL
+              scope(:with_interval,
+                    Proc.new{|gi|{:conditions => [where, {:chrom => gi.chrom,
+                                                          :bins => gi.bin_all,
+                                                          :zstart => gi.zero_start,
+                                                          :zend => gi.zero_end,}]}})
+              where = <<-SQL
+       genoName = :chrom
+  AND ((genoStart BETWEEN :zstart AND :zend)
+  AND  (genoEnd BETWEEN :zstart AND :zend))
+                SQL
+              scope(:with_interval_excl,
+                    Proc.new{|gi|{:conditions => [where,{:chrom => gi.chrom,
+                                                         :zstart => gi.zero_start,
+                                                         :zend => gi.zero_end,}]}})
 
               def self.find_first_or_all_by_interval(interval, first_all, opt)
                 zstart = interval.zero_start

data/samples/bed2refseq.rb

@@ -1,19 +1,23 @@
 #!/usr/local/bin/ruby-1.9
 
-require 'bio-ucsc'
-include Bio::Ucsc::Hg19
+#require 'bio-ucsc'
+require '../lib/bio-ucsc'
 
-DBConnection.connect
+include Bio
+
+Ucsc::Hg19::DBConnection.connect
 
 genes = Array.new
 ARGF.each_line do |row|
   row.chomp!
   next if row.empty?
   chr, chr_start, chr_end = row.split("\t")
-  interval = Bio::GenomicInterval.zero_based(chr,
-                                             Integer(chr_start),
-                                             Integer(chr_end))
-  genes.concat(RefGene.find_all_by_interval(interval).map{|e|e.name2}) 
+  gi = GenomicInterval.zero_based(chr,
+                                  Integer(chr_start),
+                                  Integer(chr_end),)
+
+  results = Ucsc::Hg19::RefGene.with_interval(gi).select(:name2).find(:all)
+  genes.concat(results.map{|e|e.name2})
 end
 
-genes.uniq!.each{|e|puts e}
+genes.uniq.each{|e|puts e} if genes

data/samples/hg19-2bit-retrieve.rb

@@ -20,13 +20,11 @@ class Hg19Ref
 
   def run(interval)
     DBConnection.connect
-    #ReferenceSequence.load(HG19_2BIT_FILE) # v0.1
     ref = Bio::Ucsc::Reference.load(HG19_2BIT_FILE) # v0.2 and later
 
     itv = Bio::GenomicInterval.parse(interval)
 
     puts itv.to_s
-    # puts NKF.nkf("-wf50-0", ReferenceSequence.find_by_interval(itv)) # v0.1
     puts NKF.nkf("-wf50-0", ref.find_by_interval(itv)) # v0.2 and later
   end
 end

data/samples/hg19-sample.rb

@@ -11,14 +11,14 @@
 require File.dirname(__FILE__) + '/../lib/bio-ucsc'
 require 'nkf'
 
-include Bio::Ucsc
+include Bio
 
-Hg19::DBConnection.connect
+Ucsc::Hg19::DBConnection.connect
 
-itvs_a =
-  [Bio::GenomicInterval.parse("chr1:1-200,000"),
-   Bio::GenomicInterval.parse("chr2:1-200,000"),
-   Bio::GenomicInterval.parse("chr3:1-300,000"),
+gi_a =
+  [GenomicInterval.parse("chr1:1-200,000"),
+   GenomicInterval.parse("chr2:1-200,000"),
+   GenomicInterval.parse("chr3:1-300,000"),
   ]
 
 puts
@@ -26,8 +26,10 @@ puts "Queries in Slice objects using 1-based [start,end] closed intervals"
 puts "Results in 0-based [start,end) half-open intervals"
 puts
 
-::puts "test 1 (hg19/RefGene) --- Bio::Ucsc::Hg19::RefGene.find_by_interval"
-results = itvs_a.map{|i|Hg19::RefGene.find_by_interval(i)}
+puts "test 1 (hg19/RefGene) --- Bio::Ucsc::Hg19::RefGene.with_interval"
+
+results = gi_a.map{|gi| Ucsc::Hg19::RefGene.with_interval(gi).find(:all)}
+
 puts "0-based interval\t1-based interval\tGene Symbol"
 results.flatten.each do |e|
   i = Bio::GenomicInterval.zero_based(e.chrom, e.txStart, e.txEnd)
@@ -35,26 +37,27 @@ results.flatten.each do |e|
   print "#{i.chrom}:#{i.chr_start}-#{i.chr_end}\t#{e.name2}\n"
 end
 
-#
-#
+#################################################################################
 
-itvs_b =
-  [Bio::GenomicInterval.parse("chr1:1-11,000"),
-   Bio::GenomicInterval.parse("chr2:1-11,000"),
-   Bio::GenomicInterval.parse("chr3:1-12,000"),
+gi_b =
+  [GenomicInterval.parse("chr1:1-11,000"),
+   GenomicInterval.parse("chr2:1-11,000"),
+   GenomicInterval.parse("chr3:1-12,000"),
   ]
 
 puts
-puts "test 2 (hg19/Snp131) --- Bio::Ucsc::Hg19::Snp131.find_by_interval" 
+puts "test 2 (hg19/Snp131) --- Bio::Ucsc::Hg19::Snp131.with_interval" 
 puts "0-based interval\t1-based interval\tdbSNP rs ID\tClass"
-results = itvs_b.map{|i|Hg19::Snp131.find_by_interval(i)}
+
+results = gi_b.map{|gi|Ucsc::Hg19::Snp131.with_interval(gi).find(:all)}
+
 results.flatten.each do |e|
   i = Bio::GenomicInterval.zero_based(e.chrom, e.chromStart, e.chromEnd)
   print "#{e.chrom}:#{e.chromStart}-#{e.chromEnd}\t"
   print "#{i.chrom}:#{i.chr_start}-#{i.chr_end}\t#{e.name}\t#{e[:class]}\n"
 end
 
-#
+###############################################################################
 #
 
 names = %w(rs56289060 rs62636508 rs28888107)
@@ -62,26 +65,7 @@ names = %w(rs56289060 rs62636508 rs28888107)
 puts
 puts "test 3 (hg19/Snp131) ---Bio::Ucsc::Hg19::Snp131.find_by_name"
 names.each do |n|
-  r =  Hg19::Snp131.find_by_name(n)
-  i = Bio::GenomicInterval.zero_based(r.chrom, r.chromStart, r.chromEnd)
+  r = Ucsc::Hg19::Snp131.find_by_name(n)
+  i = GenomicInterval.zero_based(r.chrom, r.chromStart, r.chromEnd)
   puts "Query: #{n}\t#{i.chrom}\t#{i.chr_start}\t#{i.chr_end}\t#{r[:class]}"
 end
-
-#
-#
-
-results = GbCdnaInfo.find([1,2,3,4,5], :include => :description)
-results.each{|e| puts "#{e.acc}\t#{e.description.name}"}
-
-p GbCdnaInfo.find_by_acc("AA411542",  :include => :description)
-
-results = KgXref.find_all_by_geneSymbol("TP53")
-results.each{|e| puts "#{e.mRNA}\t#{e.description}"}
-
-#
-#
-
-puts
-puts NKF.nkf("-wF72", RefSeqSummary.find_by_mrnaAcc("NM_000546").summary)
-puts
-puts NKF.nkf("-wF72", RefSeqSummary.find_by_mrnaAcc("NR_029476").summary)

data/samples/num-gene-exon.rb

@@ -9,15 +9,14 @@
 # number of genes, and maximum number of exons.
 #
 
-require 'bio-ucsc'
-include Bio::Ucsc::Hg18
+#require 'bio-ucsc'
+require '../lib/bio-ucsc'
 
 interval = Bio::GenomicInterval.parse(ARGV[0])
 
-DBConnection.connect
+Bio::Ucsc::Hg18::DBConnection.connect
 
-genes = RefGene.find_all_by_interval(interval).map{|e|e.name2}.uniq
- 
+genes = Bio::Ucsc::Hg18::RefGene.with_interval(interval).find(:all).map{|e|e.name2}.uniq
 puts "Included  genes:"
 puts genes
 puts "Number of genes:"
@@ -25,7 +24,12 @@ puts genes.size
 
 total_exons = 0
 genes.each do |gene|
-  total_exons += RefGene.find_all_by_name2(gene).map{|e|e.exonCount}.max
+  total_exons +=
+    Bio::Ucsc::Hg18::RefGene.
+    with_interval(interval).
+    find_all_by_name2(gene).
+    map{|e|e.exonCount}.
+    max
 end
 
 puts "Number of exons (maximum):"

data/samples/symbol2summary.rb

@@ -12,13 +12,12 @@ require File.dirname(__FILE__) + '/../lib/bio-ucsc'
 require 'nkf'
 
 class Sym2Sum
-  include Bio::Ucsc::Hg19
 
   def run(genesym)
-    DBConnection.connect
-    known_gene = KgXref.find_by_geneSymbol(genesym)
-    ref_gene = RefGene.find_by_name2(genesym)
-    summary  = RefSeqSummary.find_by_mrnaAcc(ref_gene.name).summary
+    Bio::Ucsc::Hg19::DBConnection.connect
+    known_gene = Bio::Ucsc::Hg19::KgXref.find_by_geneSymbol(genesym)
+    ref_gene = Bio::Ucsc::Hg19::RefGene.find_by_name2(genesym)
+    summary  = Bio::Ucsc::Hg19::RefSeqSummary.find_by_mrnaAcc(ref_gene.name).summary
 
     puts "---"
     puts "Gene symbol: #{genesym}" if known_gene

data/spec/chromosome_specific_tables_spec.rb

@@ -0,0 +1,36 @@
+require "bio-ucsc"
+require "pp"
+
+describe "Bio::Ucsc::Hg18" do
+
+  before(:all) do
+    Bio::Ucsc::Hg18::DBConnection.connect
+  end
+
+  describe "Rmsk (separated Rmsk table)" do 
+    describe ".find_by_interval" do
+      context "given 'chr1:10,000-20,000'" do
+        it 'returns a first hit record' do
+          gi = Bio::GenomicInterval.parse("chr1:10,000-20,000")
+          results = Bio::Ucsc::Hg18::Rmsk.find_by_interval(gi)
+          pp results
+          results.should be_true
+        end
+      end
+    end
+  end
+
+  describe "Chr1_rmsk (separated Rmsk table)" do 
+    describe ".with_interval" do
+      context "given 'chr1:10,000-20,000'" do
+        it 'returns a first hit record' do
+          gi = Bio::GenomicInterval.parse("chr1:10,000-20,000")
+          results = Bio::Ucsc::Hg18::Chr1_rmsk.with_interval(gi).find(:first)
+          pp results
+          results.should be_true
+        end
+      end
+    end
+  end
+
+end

data/spec/find_by_and_spec.rb

@@ -0,0 +1,18 @@
+require "bio-ucsc"
+
+describe "Bio::Ucsc::Hg19::Snp132" do
+
+  describe ".find_all_by_bin_and_strand" do
+    context "given 'chr17:7,579,614-7,579,700' and '+'" do
+      it 'returns records' do
+        Bio::Ucsc::Hg19::DBConnection.connect
+        gi = Bio::GenomicInterval.parse("chr17:7,579,614-7,579,700")
+        results = 
+          Bio::Ucsc::Hg19::Snp132.find_all_by_chrom_and_bin_and_class("chr17",
+                                                                      gi.bin_all,
+                                                                      "in-del")
+        results.should be_kind_of(Array)
+      end
+    end
+  end 
+end

data/spec/genomic-interval-bin_spec.rb

@@ -0,0 +1,23 @@
+require "bio-ucsc"
+
+describe "Bio::GenomicInterval" do
+
+  describe ".bin_all" do
+    context "given 'chr17:7,579,614-7,579,700'" do
+      it 'returns all bins to search ([642, 80, 9, 1, 0])' do
+        gi = Bio::GenomicInterval.parse("chr17:7,579,614-7,579,700")
+        gi.bin_all.should == [642, 80, 9, 1, 0]
+      end
+    end
+  end 
+
+  describe ".bin" do
+    context "given 'chr17:7,579,614-7,579,700'" do
+      it 'returns the smallest bin to search (642)' do
+        gi = Bio::GenomicInterval.parse("chr17:7,579,614-7,579,700")
+        gi.bin.should == 642
+      end
+    end
+  end 
+
+end

data/spec/named_scope_spec.rb

@@ -0,0 +1,81 @@
+require "bio-ucsc"
+require "pp"
+
+describe "Bio::Ucsc::Hg19" do
+
+  before(:all) do
+    Bio::Ucsc::Hg19::DBConnection.connect
+  end
+
+  describe "Snp132 (BED table)" do
+    describe ".with_interval" do
+      context "given 'chr17:7,579,614-7,579,700' and class='in-del'" do
+        it 'returns records' do
+          gi = Bio::GenomicInterval.parse("chr17:7,579,614-7,579,700")
+          results = Bio::Ucsc::Hg19::Snp132.
+            with_interval(gi).
+            find_all_by_class("in-del")
+          pp results
+          results.should be_kind_of(Array)
+        end
+      end
+
+      context "given 'chr17:7,579,614-7,579,700'/non-partial and class='in-del'" do
+        it 'returns records' do
+          gi = Bio::GenomicInterval.parse("chr17:7,579,614-7,579,700")
+          results = Bio::Ucsc::Hg19::Snp132.
+            with_interval_excl(gi).
+            find_all_by_class("in-del")
+          pp results
+          results.should be_kind_of(Array)
+        end
+      end
+    end 
+  end # describe "Snp132"
+
+  describe "Rmsk (Rmsk table)" do 
+    describe ".with_interval" do
+      context "given 'chr1:10,000-200,00' and repClass='LINE'" do
+        it 'returns hit records' do
+          gi = Bio::GenomicInterval.parse("chr1:10,000-20,000")
+          results = Bio::Ucsc::Hg19::Rmsk.
+            with_interval(gi).
+            find_all_by_repClass "LINE"
+          pp results
+          results.should be_kind_of(Array)
+        end
+      end
+    end
+  end # describe "Rmsk"
+
+  describe "RefGene (genePred table)" do
+    describe ".with_interval" do
+      context "given 'chr1:10,000-100,000' and strand='+'" do
+        it 'returns hit records' do
+          gi = Bio::GenomicInterval.parse("chr1:10,000-100,000")
+          results = Bio::Ucsc::Hg19::RefGene.
+            with_interval(gi).
+            find_all_by_strand "+"
+          pp results
+          results.should be_kind_of(Array)
+        end
+      end
+    end
+  end # describe "RefGene"
+
+  describe "ChainAilMel1 (PSL table)" do
+    describe ".with_interval" do
+      context "given 'chr1:10,000-50,000' and qStrand='+'" do
+        it 'returns hit records' do
+          gi = Bio::GenomicInterval.parse("chr1:10,000-50,000")
+          results = Bio::Ucsc::Hg19::ChainAilMel1.
+            with_interval(gi).
+            find_all_by_qStrand "+"
+          pp results
+          results.should be_kind_of(Array)
+        end
+      end
+    end
+  end # "ChainAilMel1 (PSL table)"
+
+end # describe "Bio::Ucsc::Hg19"

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bio-ucsc-api
 version: !ruby/object:Gem::Version
-  version: 0.2.1
+  version: 0.3.0
   prerelease: 
 platform: ruby
 authors:
@@ -10,11 +10,11 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2011-08-14 00:00:00.000000000Z
+date: 2011-08-23 00:00:00.000000000Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: activerecord
-  requirement: &130996320 !ruby/object:Gem::Requirement
+  requirement: &174367420 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -22,10 +22,10 @@ dependencies:
         version: 3.0.7
   type: :runtime
   prerelease: false
-  version_requirements: *130996320
+  version_requirements: *174367420
 - !ruby/object:Gem::Dependency
   name: activesupport
-  requirement: &130995840 !ruby/object:Gem::Requirement
+  requirement: &174366940 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -33,10 +33,10 @@ dependencies:
         version: 3.0.7
   type: :runtime
   prerelease: false
-  version_requirements: *130995840
+  version_requirements: *174366940
 - !ruby/object:Gem::Dependency
   name: mysql
-  requirement: &130995360 !ruby/object:Gem::Requirement
+  requirement: &174366460 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -44,10 +44,10 @@ dependencies:
         version: 2.8.1
   type: :runtime
   prerelease: false
-  version_requirements: *130995360
+  version_requirements: *174366460
 - !ruby/object:Gem::Dependency
   name: bio-genomic-interval
-  requirement: &130994840 !ruby/object:Gem::Requirement
+  requirement: &174365980 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -55,10 +55,10 @@ dependencies:
         version: 0.1.2
   type: :runtime
   prerelease: false
-  version_requirements: *130994840
+  version_requirements: *174365980
 - !ruby/object:Gem::Dependency
   name: rspec
-  requirement: &130994360 !ruby/object:Gem::Requirement
+  requirement: &174365500 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -66,10 +66,10 @@ dependencies:
         version: 2.5.0
   type: :development
   prerelease: false
-  version_requirements: *130994360
+  version_requirements: *174365500
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &130993880 !ruby/object:Gem::Requirement
+  requirement: &174365020 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -77,10 +77,10 @@ dependencies:
         version: 1.0.0
   type: :development
   prerelease: false
-  version_requirements: *130993880
+  version_requirements: *174365020
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &130993400 !ruby/object:Gem::Requirement
+  requirement: &174327460 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -88,10 +88,10 @@ dependencies:
         version: 1.5.2
   type: :development
   prerelease: false
-  version_requirements: *130993400
+  version_requirements: *174327460
 - !ruby/object:Gem::Dependency
   name: rcov
-  requirement: &130992920 !ruby/object:Gem::Requirement
+  requirement: &174326840 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -99,10 +99,10 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *130992920
+  version_requirements: *174326840
 - !ruby/object:Gem::Dependency
   name: bio
-  requirement: &130992440 !ruby/object:Gem::Requirement
+  requirement: &174326240 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -110,10 +110,10 @@ dependencies:
         version: 1.4.1
   type: :development
   prerelease: false
-  version_requirements: *130992440
+  version_requirements: *174326240
 - !ruby/object:Gem::Dependency
   name: rdoc
-  requirement: &130991960 !ruby/object:Gem::Requirement
+  requirement: &174325620 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -121,7 +121,7 @@ dependencies:
         version: 3.9.1
   type: :development
   prerelease: false
-  version_requirements: *130991960
+  version_requirements: *174325620
 description: ! 'Ruby UCSC API: accessing the UCSC Genome Database using Ruby'
 email: missy@be.to
 executables: []
@@ -407,6 +407,7 @@ files:
 - lib/bio-ucsc/gasacu1/intronest.rb
 - lib/bio-ucsc/gasacu1/mrna.rb
 - lib/bio-ucsc/gasacu1/rmsk.rb
+- lib/bio-ucsc/genomic-interval-bin.rb
 - lib/bio-ucsc/go.rb
 - lib/bio-ucsc/go/db_connection.rb
 - lib/bio-ucsc/hg18.rb
@@ -652,6 +653,7 @@ files:
 - spec/cavpor3_spec.rb
 - spec/cb3_spec.rb
 - spec/ce6_spec.rb
+- spec/chromosome_specific_tables_spec.rb
 - spec/ci2_spec.rb
 - spec/danrer7_spec.rb
 - spec/dm3_spec.rb
@@ -667,9 +669,11 @@ files:
 - spec/droyak2_spec.rb
 - spec/equcab2_spec.rb
 - spec/felcat4_spec.rb
+- spec/find_by_and_spec.rb
 - spec/fr2_spec.rb
 - spec/galgal3_spec.rb
 - spec/gasacu1_spec.rb
+- spec/genomic-interval-bin_spec.rb
 - spec/go_spec.rb
 - spec/hg18/acembly_spec.rb
 - spec/hg18/acemblyclass_spec.rb
@@ -5555,6 +5559,7 @@ files:
 - spec/loxafr3_spec.rb
 - spec/mm9_spec.rb
 - spec/mondom5_spec.rb
+- spec/named_scope_spec.rb
 - spec/ornana1_spec.rb
 - spec/orycun2_spec.rb
 - spec/orylat2_spec.rb
@@ -5591,7 +5596,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: 3670200921648831687
+      hash: 2327058743331415747
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements:
@@ -5620,6 +5625,7 @@ test_files:
 - spec/cavpor3_spec.rb
 - spec/cb3_spec.rb
 - spec/ce6_spec.rb
+- spec/chromosome_specific_tables_spec.rb
 - spec/ci2_spec.rb
 - spec/danrer7_spec.rb
 - spec/dm3_spec.rb
@@ -5635,9 +5641,11 @@ test_files:
 - spec/droyak2_spec.rb
 - spec/equcab2_spec.rb
 - spec/felcat4_spec.rb
+- spec/find_by_and_spec.rb
 - spec/fr2_spec.rb
 - spec/galgal3_spec.rb
 - spec/gasacu1_spec.rb
+- spec/genomic-interval-bin_spec.rb
 - spec/go_spec.rb
 - spec/hg18/acembly_spec.rb
 - spec/hg18/acemblyclass_spec.rb
@@ -10523,6 +10531,7 @@ test_files:
 - spec/loxafr3_spec.rb
 - spec/mm9_spec.rb
 - spec/mondom5_spec.rb
+- spec/named_scope_spec.rb
 - spec/ornana1_spec.rb
 - spec/orycun2_spec.rb
 - spec/orylat2_spec.rb