bio-ucsc-api 0.5.0 → 0.5.1

data/ChangeLog.md

@@ -0,0 +1,30 @@
+#Change Log
+ * **UPDATE** (v.0.5.1): Mouse mm10 database is supported.
+ * **BUG-FIX** (v.0.5.0): Connecting multiple databeses simultaneously now works well.
+ * **NEW** (v0.5.0): Support automatic definitions of table association using the "all.joiner" schema file.
+ * **NEW** (v0.5.0): Instances in classes of the genePred tables, which have txStart and txEnd columns, now have `#exons`, `#introns` and `#cdses` methods. These methods return arrays of `Bio::GenomicInterval` instances. The arrays are sorted using gene strands.
+ * **BUG-FIX** (v0.5.0): `Bio::Ucsc::File::TwoBit#inspect` now returns only short summary of the object instead of dumping a whole-genome sequence. This fixes hung-up in the irb environment.
+ * **UPDATE** (v0.4.0): now `<TABLE>#find_by_interval` accepts both "chr1:123-456" and Bio::GenomicInterval objects
+ * **BUG-FIX** (v0.4.0): By using the safe_attribute gem, newest version of ActiveRecord is supported.
+ * **UPDATE** (v0.4.0): `Bio::Ucsc::Reference` is moved to `Bio::Ucsc::File::Twobit` (backward compatibility is kept). `Bio::Ucsc::File::Twobit.open` and `Bio::Ucsc::File::Twobit#subseq` is are introduced.
+ * **UPDATE** (v0.4.0): `<DB_NAME>::DBConnection.connect` is simplified by the new `<DB_NAME>.connect` class method (backward compatibility is kept). Server parameters can be defined by using a hash being an argument of the method.
+ * **UPDATE** (v0.3.2): Genomic interval queries are implemented using ARel's relation objects instead of (named) scopes. Usage of the API is not changed.
+ * **BUG** (v0.3.1): Does not work with ActiveRecord version 3.1.0. Data retrieval methods occur the error, "(Object doesn't support #inspect)". The author is working on this bug. So far, please use version 3.0 seriese. Gemfile for gem dependencies is updated. Thanks for bug reports from Diego F. Pereira.
+ * **BUG-FIX** (v0.3.1): "func" fields in tables did not work. The bug was fixed.
+ * **BUG-FIX** (v0.3.1): PredGene-type tables without the bin index did not work. The bug was fixed.
+ * **NEW** (v0.3.0): 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** (v0.3.0): `Bio::GenomicInterval#bin_all` and `Bio::GenomicInterval#bin` return the bin index for the given interval.
+ * **NEW** (v0.3.0): 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** (v0.2.1): 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** (v0.2.1): 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 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".

data/README.md

@@ -1,4 +1,4 @@
-# bio-ucsc-api version 0.5.0
+# bio-ucsc-api version 0.5.1
 
 **The Ruby UCSC API**: accessing the UCSC Genome Database using Ruby.
 
@@ -6,6 +6,12 @@ Your comments, suggestions and requests are welcome. Documentation and
 feedback are available at the UserEcho site at
 http://rubyucscapi.userecho.com/.
 
+# Citation
+
+The Ruby UCSC API: accessing the UCSC genome database using Ruby: Hiroyuki Mishima, Jan Aerts, Toshiaki Katayama, Raoul JP Bonnal and Koh-ichiro Yoshiura, *BMC Bioinformatics* **13**:240 (2012).  
+doi:10.1186/1471-2105-13-240  
+http://www.biomedcentral.com/1471-2105/13/240/  
+
 # Install
 
 ```bash
@@ -26,9 +32,8 @@ $ gem install bio-ucsc-api
 * 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)
+* **mammals** chimp (PanTro3), orangutan (PonAbe2), rhesus (RheMac2), marmoset (CalJac3), mouse (Mm10, 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)
@@ -61,34 +66,7 @@ See also:
 * UCSCBin library - https://github.com/misshie/UCSCBin
  
 # Change Log
-* **BUG-FIX** (v.0.5.0): Connecting multiple databeses simultaneously now works well.
-* **NEW** (v0.5.0): Support automatic definitions of table association using the "all.joiner" schema file.
-* **NEW** (v0.5.0): Instances in classes of the genePred tables, which have txStart and txEnd columns, now have `#exons`, `#introns` and `#cdses` methods. These methods return arrays of `Bio::GenomicInterval` instances. The arrays are sorted using gene strands.   
-* **BUG-FIX** (v0.5.0): `Bio::Ucsc::File::TwoBit#inspect` now returns only short summary of the object instead of dumping whole genome sequencing. This fixes hung-up in the irb environment.
-* **UPDATE** (v0.4.0): now `<TABLE>#find_by_interval` accepts both "chr1:123-456" and Bio::GenomicInterval objects
-* **BUG-FIX** (v0.4.0): By using the safe_attribute gem, newest version of ActiveRecord is supported.
-* **UPDATE** (v0.4.0): `Bio::Ucsc::Reference` is moved to `Bio::Ucsc::File::Twobit` (backward compatibility is kept). `Bio::Ucsc::File::Twobit.open` and `Bio::Ucsc::File::Twobit#subseq` is are introduced.
-* **UPDATE** (v0.4.0): `<DB_NAME>::DBConnection.connect` is simplified by the new `<DB_NAME>.connect` class method (backward compatibility is kept). Server parameters can be defined by using a hash being an argument of the method.  
-* **UPDATE** (v0.3.2): Genomic interval queries are implemented using ARel's relation objects instead of (named) scopes. Usage of the API is not changed.
-* **BUG** (v0.3.1): Does not work with ActiveRecord version 3.1.0. Data retrieval methods occur the error, "(Object doesn't support #inspect)". The author is working on this bug. So far, please use version 3.0 seriese. Gemfile for gem dependencies is updated. Thanks for bug reports from Diego F. Pereira.
-* **BUG-FIX** (v0.3.1): "func" fields in tables did not work. The bug was fixed.
-* **BUG-FIX** (v0.3.1): PredGene-type tables without the bin index did not work. The bug was fixed.
-* **NEW** (v0.3.0): 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** (v0.3.0): `Bio::GenomicInterval#bin_all` and `Bio::GenomicInterval#bin` return the bin index for the given interval.
-* **NEW** (v0.3.0): 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** (v0.2.1): 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** (v0.2.1): 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 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".
+See 'ChangeLog.md'.
 
 # How to Use
 ## Basics
@@ -249,9 +227,9 @@ joiner.define_association(Bio::Ucsc::Hg19::Snp131)
 # "first" is required because the snp131Seq method always returns an array.
 puts Bio::Ucsc::Hg19::Snp131.find_by_name("rs242").snp131Seq.first.file_offset
 ```
-# Copyright
-**Copyright**: (c) 2011-2012 MISHIMA, Hiroyuki (hmishima at nagasaki-u.ac.jp / Twitter: @mishima_eng (in English) and @mishimahryk (in Japanese)
-
-**Copyright**: (c) 2010 Jan Aerts
 
+# Copyright
+**Copyright**: (c) 2011-2012 MISHIMA, Hiroyuki (hmishima at nagasaki-u.ac.jp / Twitter: @mishima_eng (in English) and @mishimahryk (in Japanese)  
+**Copyright**: (c) 2010 Jan Aerts  
 **License**: Ruby license (Ruby's / GPLv2 dual). See COPYING and COPYING.ja for further details..
+

data/VERSION

@@ -1 +1 @@
-0.5.0
+0.5.1

data/bio-ucsc-api.gemspec

@@ -5,19 +5,21 @@
 
 Gem::Specification.new do |s|
   s.name = "bio-ucsc-api"
-  s.version = "0.5.0"
+  s.version = "0.5.1"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Hiroyuki Mishima", "Jan Aerts"]
-  s.date = "2012-08-23"
+  s.date = "2012-09-27"
   s.description = "Ruby UCSC API: accessing the UCSC Genome Database using Ruby"
   s.email = "missy@be.to"
   s.extra_rdoc_files = [
+    "ChangeLog.md",
     "README.md"
   ]
   s.files = [
     "COPYING",
     "COPYING.ja",
+    "ChangeLog.md",
     "Gemfile",
     "Gemfile.lock",
     "README.md",
@@ -294,6 +296,10 @@ Gem::Specification.new do |s|
     "lib/bio-ucsc/hgfixed.rb",
     "lib/bio-ucsc/loxafr3.rb",
     "lib/bio-ucsc/mm10.rb",
+    "lib/bio-ucsc/mm10/est.rb",
+    "lib/bio-ucsc/mm10/gbstatus.rb",
+    "lib/bio-ucsc/mm10/intronest.rb",
+    "lib/bio-ucsc/mm10/mrna.rb",
     "lib/bio-ucsc/mm9.rb",
     "lib/bio-ucsc/mm9/chainbraflo1.rb",
     "lib/bio-ucsc/mm9/chainbraflo1link.rb",

data/lib/bio-ucsc.rb

@@ -17,7 +17,7 @@ require "#{base}/gi.rb"
 
 module Bio
   module Ucsc
-    VERSION = "0.4.0"
+    VERSION = "0.5.1"
     base = "#{::File.dirname(__FILE__)}/bio-ucsc"
     
     # mammmals #####################################

data/lib/bio-ucsc/hg19/description.rb

@@ -7,6 +7,7 @@ module Bio
     module Hg19
       class Description < DBConnection
         self.table_name = "description"
+        self.inheritance_column = nil
       end
     end
   end

data/lib/bio-ucsc/mm10.rb

@@ -30,6 +30,7 @@ ChrX ChrY)
 
       class DBConnection < ActiveRecord::Base
         include SafeAttributes
+        self.inheritance_column = 'dummy_not_to_use'
 
         @@db_adapter  ||= 'mysql'
         @@db_host     ||= 'genome-mysql.cse.ucsc.edu'
@@ -57,7 +58,10 @@ ChrX ChrY)
         end
       end # class DBConnection
       
-      # base = "#{::File.dirname(__FILE__)}/mm10"
+      base = "#{::File.dirname(__FILE__)}/mm10"
+      autoload :Est, "#{base}/est"
+      autoload :IntronEst, "#{base}/intronest"
+      autoload :Mrna, "#{base}/mrna"
     end
   end
 end

data/lib/bio-ucsc/mm10/est.rb

@@ -0,0 +1,81 @@
+# Copyright::
+#  Copyright (C) 2012 MISHIMA, Hiroyuki <missy at be.to / hmishima at nagasaki-u.ac.jp> 
+# License::     The Ruby licence (Ryby's / GPLv2 dual)
+#
+# this table is actually separated
+# into "chr1_*", "chr2_*", etc. This class dynamically
+# define *::Chr1_*, *::Chr2_*, etc. The
+# Rmsk.find_by_interval calls an appropreate class automatically.
+
+module Bio
+  module Ucsc
+    module Mm10
+
+      class Est
+        KLASS = "Est"
+        KLASS_S = "est"
+
+        Bio::Ucsc::Mm10::CHROMS.each do |chr|
+          class_eval %!
+            class #{chr[0..0].upcase + chr[1..-1]}_#{KLASS} < DBConnection
+              self.table_name = "#{chr[0..0].downcase + chr[1..-1]}_#{KLASS_S}"
+              self.primary_key = nil
+              self.inheritance_column = nil
+
+              def self.find_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
+                find_first_or_all_by_interval(interval, :first, opt)
+              end
+        
+              def self.find_all_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
+                find_first_or_all_by_interval(interval, :all, opt)
+              end
+
+              def self.find_first_or_all_by_interval(interval, first_all, opt); interval =  Bio::Ucsc::Gi.wrap(interval)
+                zstart = interval.zero_start
+                zend   = interval.zero_end
+                if opt[:partial] == true
+                  where = <<-SQL
+      tName = :chrom
+AND   bin in (:bins)
+AND ((tStart BETWEEN :zstart AND :zend)
+ OR  (tEnd BETWEEN :zstart AND :zend)
+ OR  (tStart <= :zstart AND tEnd >= :zend))
+                  SQL
+                else
+                  where = <<-SQL
+      tName = :chrom
+AND   bin in (:bins)
+AND ((tStart BETWEEN :zstart AND :zend)
+AND  (tEnd BETWEEN :zstart AND :zend))
+                  SQL
+                end
+                cond = {
+                  :chrom  => interval.chrom,
+                  :bins   => Bio::Ucsc::UcscBin.bin_all(zstart, zend),
+                  :zstart => zstart,
+                  :zend   => zend,
+                }
+                self.find(first_all,
+                          { :select => "*",
+                            :conditions => [where, cond], })
+              end
+            end
+          !
+        end # each chromosome
+
+        def self.find_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
+          chrom = interval.chrom[0..0].upcase + interval.chrom[1..-1]
+          chr_klass = self.const_get("#{chrom}_#{KLASS}")
+          chr_klass.__send__(:find_by_interval, interval, opt)
+        end
+
+        def self.find_all_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
+          chrom = interval.chrom[0..0].upcase + interval.chrom[1..-1]
+          chr_klass = self.const_get("#{chrom}_#{KLASS}")
+          chr_klass.__send__(:find_all_by_interval, interval, opt)
+        end
+      end # class
+
+    end # module Hg18 
+  end # module Ucsc
+end # module Bio

data/lib/bio-ucsc/mm10/gbstatus.rb

@@ -0,0 +1,15 @@
+#
+# the "type" colomn exists
+#
+
+module Bio
+  module Ucsc
+    module Mm10
+      class GbStatus < DBConnection
+        self.table_name = "gbStatus"
+        self.inheritance_column = nil
+      end
+    end
+  end
+end
+

data/lib/bio-ucsc/mm10/intronest.rb

@@ -0,0 +1,81 @@
+# Copyright::
+#  Copyright (C) 2012 MISHIMA, Hiroyuki <missy at be.to / hmishima at nagasaki-u.ac.jp> 
+# License::     The Ruby licence (Ryby's / GPLv2 dual)
+#
+# this table is actually separated
+# into "chr1_*", "chr2_*", etc. This class dynamically
+# define *::Chr1_*, *::Chr2_*, etc.
+
+
+module Bio
+  module Ucsc
+    module Mm10
+
+      class IntronEst
+        KLASS = "IntronEst"
+        KLASS_S = "intronEst"
+
+        Bio::Ucsc::Mm9::CHROMS.each do |chr|
+          class_eval %!
+            class #{chr[0..0].upcase + chr[1..-1]}_#{KLASS} < DBConnection
+              self.table_name = "#{chr[0..0].downcase + chr[1..-1]}_#{KLASS_S}"
+              self.primary_key = nil
+              self.inheritance_column = nil
+
+              def self.find_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
+                find_first_or_all_by_interval(interval, :first, opt)
+              end
+        
+              def self.find_all_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
+                find_first_or_all_by_interval(interval, :all, opt)
+              end
+
+              def self.find_first_or_all_by_interval(interval, first_all, opt); interval =  Bio::Ucsc::Gi.wrap(interval)
+                zstart = interval.zero_start
+                zend   = interval.zero_end
+                if opt[:partial] == true
+                  where = <<-SQL
+      tName = :chrom
+AND   bin in (:bins)
+AND ((tStart BETWEEN :zstart AND :zend)
+ OR  (tEnd BETWEEN :zstart AND :zend)
+ OR  (tStart <= :zstart AND tEnd >= :zend))
+                  SQL
+                else
+                  where = <<-SQL
+      tName = :chrom
+AND   bin in (:bins)
+AND ((tStart BETWEEN :zstart AND :zend)
+AND  (tEnd BETWEEN :zstart AND :zend))
+                  SQL
+                end
+                cond = {
+                  :chrom  => interval.chrom,
+                  :bins   => Bio::Ucsc::UcscBin.bin_all(zstart, zend),
+                  :zstart => zstart,
+                  :zend   => zend,
+                }
+                self.find(first_all,
+                          { :select => "*",
+                            :conditions => [where, cond], })
+              end
+            end
+          !
+        end # each chromosome
+
+        def self.find_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
+          chrom = interval.chrom[0..0].upcase + interval.chrom[1..-1]
+          chr_klass = self.const_get("#{chrom}_#{KLASS}")
+          chr_klass.__send__(:find_by_interval, interval, opt)
+        end
+
+        def self.find_all_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
+chrom = interval.chrom[0..0].upcase + interval.chrom[1..-1]
+          chr_klass = self.const_get("#{chrom}_#{KLASS}")
+          chr_klass.__send__(:find_all_by_interval, interval, opt)
+        end
+      end # class
+
+    end # module Mm10
+  end # module Ucsc
+end # module Bio

data/lib/bio-ucsc/mm10/mrna.rb

@@ -0,0 +1,80 @@
+# Copyright::
+#  Copyright (C) 2012 MISHIMA, Hiroyuki <missy at be.to / hmishima at nagasaki-u.ac.jp> 
+# License::     The Ruby licence (Ryby's / GPLv2 dual)
+#
+# this table is actually separated
+# into "chr1_*", "chr2_*", etc. This class dynamically
+# define *::Chr1_*, *::Chr2_*, etc.
+
+module Bio
+  module Ucsc
+    module Mm10
+
+      class Mrna
+        KLASS = "Mrna"
+        KLASS_S = "mrna"
+
+        Bio::Ucsc::Mm10::CHROMS.each do |chr|
+          class_eval %!
+            class #{chr[0..0].upcase + chr[1..-1]}_#{KLASS} < DBConnection
+              self.table_name = "#{chr[0..0].downcase + chr[1..-1]}_#{KLASS_S}"
+              self.primary_key = nil
+              self.inheritance_column = nil
+
+              def self.find_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
+                find_first_or_all_by_interval(interval, :first, opt)
+              end
+        
+              def self.find_all_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
+                find_first_or_all_by_interval(interval, :all, opt)
+              end
+
+              def self.find_first_or_all_by_interval(interval, first_all, opt); interval =  Bio::Ucsc::Gi.wrap(interval)
+                zstart = interval.zero_start
+                zend   = interval.zero_end
+                if opt[:partial] == true
+                  where = <<-SQL
+      tName = :chrom
+AND   bin in (:bins)
+AND ((tStart BETWEEN :zstart AND :zend)
+ OR  (tEnd BETWEEN :zstart AND :zend)
+ OR  (tStart <= :zstart AND tEnd >= :zend))
+                  SQL
+                else
+                  where = <<-SQL
+      tName = :chrom
+AND   bin in (:bins)
+AND ((tStart BETWEEN :zstart AND :zend)
+AND  (tEnd BETWEEN :zstart AND :zend))
+                  SQL
+                end
+                cond = {
+                  :chrom  => interval.chrom,
+                  :bins   => Bio::Ucsc::UcscBin.bin_all(zstart, zend),
+                  :zstart => zstart,
+                  :zend   => zend,
+                }
+                self.find(first_all,
+                          { :select => "*",
+                            :conditions => [where, cond], })
+              end
+            end
+          !
+        end # each chromosome
+
+        def self.find_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
+          chrom = interval.chrom[0..0].upcase + interval.chrom[1..-1]
+          chr_klass = self.const_get("#{chrom}_#{KLASS}")
+          chr_klass.__send__(:find_by_interval, interval, opt)
+        end
+
+        def self.find_all_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
+          chrom = interval.chrom[0..0].upcase + interval.chrom[1..-1]
+          chr_klass = self.const_get("#{chrom}_#{KLASS}")
+          chr_klass.__send__(:find_all_by_interval, interval, opt)
+        end
+      end # class
+
+    end # module Mm10 
+  end # module Ucsc
+end # module Bio

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bio-ucsc-api
 version: !ruby/object:Gem::Version
-  version: 0.5.0
+  version: 0.5.1
   prerelease: 
 platform: ruby
 authors:
@@ -10,11 +10,11 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-08-23 00:00:00.000000000 Z
+date: 2012-09-27 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: activerecord
-  requirement: &189972880 !ruby/object:Gem::Requirement
+  requirement: &158480880 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -22,10 +22,10 @@ dependencies:
         version: 3.0.7
   type: :runtime
   prerelease: false
-  version_requirements: *189972880
+  version_requirements: *158480880
 - !ruby/object:Gem::Dependency
   name: activesupport
-  requirement: &189972180 !ruby/object:Gem::Requirement
+  requirement: &158480020 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -33,10 +33,10 @@ dependencies:
         version: 3.0.7
   type: :runtime
   prerelease: false
-  version_requirements: *189972180
+  version_requirements: *158480020
 - !ruby/object:Gem::Dependency
   name: mysql
-  requirement: &189971280 !ruby/object:Gem::Requirement
+  requirement: &158479400 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -44,10 +44,10 @@ dependencies:
         version: 2.8.1
   type: :runtime
   prerelease: false
-  version_requirements: *189971280
+  version_requirements: *158479400
 - !ruby/object:Gem::Dependency
   name: bio-genomic-interval
-  requirement: &189970380 !ruby/object:Gem::Requirement
+  requirement: &158478820 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -55,10 +55,10 @@ dependencies:
         version: 0.1.2
   type: :runtime
   prerelease: false
-  version_requirements: *189970380
+  version_requirements: *158478820
 - !ruby/object:Gem::Dependency
   name: safe_attributes
-  requirement: &189969640 !ruby/object:Gem::Requirement
+  requirement: &158494120 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -66,10 +66,10 @@ dependencies:
         version: 1.0.8
   type: :runtime
   prerelease: false
-  version_requirements: *189969640
+  version_requirements: *158494120
 - !ruby/object:Gem::Dependency
   name: rake
-  requirement: &189968780 !ruby/object:Gem::Requirement
+  requirement: &158493200 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -77,10 +77,10 @@ dependencies:
         version: 0.9.2.2
   type: :development
   prerelease: false
-  version_requirements: *189968780
+  version_requirements: *158493200
 - !ruby/object:Gem::Dependency
   name: rspec
-  requirement: &189968000 !ruby/object:Gem::Requirement
+  requirement: &158492580 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -88,10 +88,10 @@ dependencies:
         version: 2.9.0
   type: :development
   prerelease: false
-  version_requirements: *189968000
+  version_requirements: *158492580
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &189967380 !ruby/object:Gem::Requirement
+  requirement: &158491920 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -99,10 +99,10 @@ dependencies:
         version: 1.1.0
   type: :development
   prerelease: false
-  version_requirements: *189967380
+  version_requirements: *158491920
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &189966500 !ruby/object:Gem::Requirement
+  requirement: &158491160 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -110,10 +110,10 @@ dependencies:
         version: 1.8.3
   type: :development
   prerelease: false
-  version_requirements: *189966500
+  version_requirements: *158491160
 - !ruby/object:Gem::Dependency
   name: bio
-  requirement: &189965880 !ruby/object:Gem::Requirement
+  requirement: &158490320 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -121,10 +121,10 @@ dependencies:
         version: 1.4.1
   type: :development
   prerelease: false
-  version_requirements: *189965880
+  version_requirements: *158490320
 - !ruby/object:Gem::Dependency
   name: rdoc
-  requirement: &189979540 !ruby/object:Gem::Requirement
+  requirement: &158488760 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -132,16 +132,18 @@ dependencies:
         version: 3.9.1
   type: :development
   prerelease: false
-  version_requirements: *189979540
+  version_requirements: *158488760
 description: ! 'Ruby UCSC API: accessing the UCSC Genome Database using Ruby'
 email: missy@be.to
 executables: []
 extensions: []
 extra_rdoc_files:
+- ChangeLog.md
 - README.md
 files:
 - COPYING
 - COPYING.ja
+- ChangeLog.md
 - Gemfile
 - Gemfile.lock
 - README.md
@@ -418,6 +420,10 @@ files:
 - lib/bio-ucsc/hgfixed.rb
 - lib/bio-ucsc/loxafr3.rb
 - lib/bio-ucsc/mm10.rb
+- lib/bio-ucsc/mm10/est.rb
+- lib/bio-ucsc/mm10/gbstatus.rb
+- lib/bio-ucsc/mm10/intronest.rb
+- lib/bio-ucsc/mm10/mrna.rb
 - lib/bio-ucsc/mm9.rb
 - lib/bio-ucsc/mm9/chainbraflo1.rb
 - lib/bio-ucsc/mm9/chainbraflo1link.rb
@@ -569,7 +575,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: -176600740614188306
+      hash: 4141800298986362982
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements: