bio-ucsc-api 0.0.5 → 0.1.0

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

@@ -2,7 +2,6 @@
 # = hg19/refgene.rb
 # Copyright::
 #  Copyright (C) 2011 MISHIMA, Hiroyuki <missy at be.to / hmishima at nagasaki-u.ac.jp> 
-#  Copyright (C) 2008 Jan Aerts <jan.aerts@gmail.com>
 # License::     The Ruby licence (Ryby's / GPLv2 dual)
 #
 # = Table desfription in UCSC Table Browser

data/lib/bio-ucsc/hg19/snp131.rb

@@ -2,7 +2,6 @@
 # = hg19/snp131.rb
 # Copyright::
 #  Copyright (C) 2011 MISHIMA, Hiroyuki <missy at be.to / hmishima at nagasaki-u.ac.jp> 
-#  Copyright (C) 2008 Jan Aerts <jan.aerts@gmail.com>
 # License::     The Ruby licence (Ryby's / GPLv2 dual)
 #
 # = Table desfription in UCSC Table Browser

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

@@ -2,7 +2,6 @@
 # = hg19/wbrna.rb
 # Copyright::
 #  Copyright (C) 2011 MISHIMA, Hiroyuki <missy at be.to / hmishima at nagasaki-u.ac.jp> 
-#  Copyright (C) 2008 Jan Aerts <jan.aerts@gmail.com>
 # License::     The Ruby licence (Ryby's / GPLv2 dual)
 #
 # = Table desfription in UCSC Table Browser

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

@@ -20,11 +20,11 @@ class Hg19Ref
 
   def run(interval)
     DBConnection.connect
-    Reference.load(HG19_2BIT_FILE)
+    ReferenceSequence.load(HG19_2BIT_FILE)
     itv = Bio::GenomicInterval.parse(interval)
 
     puts itv.to_s
-    puts NKF.nkf("-wf50-0", Reference.find_by_interval(itv))
+    puts NKF.nkf("-wf50-0", ReferenceSequence.find_by_interval(itv))
   end
 end
 

data/spec/hg18/{reference_spec.rb → reference_sequence_spec.rb}

@@ -1,11 +1,11 @@
 require 'bio-ucsc'
 
-describe "Bio::Ucsc::Hg18::Reference" do 
+describe "Bio::Ucsc::Hg18::ReferenceSequence" do 
   
   describe ".load" do
     context 'given "../samples/hg18.2bit"' do
       it "returns true" do
-        Bio::Ucsc::Hg18::Reference.load("samples/hg18.2bit")
+        Bio::Ucsc::Hg18::ReferenceSequence.load("samples/hg18.2bit")
       end
     end
   end
@@ -13,8 +13,8 @@ describe "Bio::Ucsc::Hg18::Reference" do
   describe ".header.signarue" do
     context 'given "../samples/hg18.2bit"' do
       it "returns 0x1A412743" do
-        Bio::Ucsc::Hg18::Reference.load("samples/hg18.2bit")
-        Bio::Ucsc::Hg18::Reference.header.signature.should == 0x1A412743
+        Bio::Ucsc::Hg18::ReferenceSequence.load("samples/hg18.2bit")
+        Bio::Ucsc::Hg18::ReferenceSequence.header.signature.should == 0x1A412743
       end
     end
   end
@@ -22,8 +22,8 @@ describe "Bio::Ucsc::Hg18::Reference" do
   describe ".header.version" do
     context 'given "../samples/hg18.2bit"' do
       it "returns 0" do
-        Bio::Ucsc::Hg18::Reference.load("samples/hg18.2bit")
-        Bio::Ucsc::Hg18::Reference.header.version.should == 0
+        Bio::Ucsc::Hg18::ReferenceSequence.load("samples/hg18.2bit")
+        Bio::Ucsc::Hg18::ReferenceSequence.header.version.should == 0
       end
     end
   end
@@ -31,8 +31,8 @@ describe "Bio::Ucsc::Hg18::Reference" do
   describe ".header.sequence_count" do
     context 'given "../samples/hg18.2bit"' do
       it "returns 0x5d" do
-        Bio::Ucsc::Hg18::Reference.load("samples/hg18.2bit")
-        Bio::Ucsc::Hg18::Reference.header.sequence_count.should == 49
+        Bio::Ucsc::Hg18::ReferenceSequence.load("samples/hg18.2bit")
+        Bio::Ucsc::Hg18::ReferenceSequence.header.sequence_count.should == 49
       end
     end
   end
@@ -40,8 +40,8 @@ describe "Bio::Ucsc::Hg18::Reference" do
   describe '.offsets["chr1"]' do
     context 'given "../samples/hg18.2bit"' do
       it "returns 0x100bbd2b" do 
-        Bio::Ucsc::Hg18::Reference.load("samples/hg18.2bit")
-        Bio::Ucsc::Hg18::Reference.offsets["chr1"].should == 0x100bbd2b
+        Bio::Ucsc::Hg18::ReferenceSequence.load("samples/hg18.2bit")
+        Bio::Ucsc::Hg18::ReferenceSequence.offsets["chr1"].should == 0x100bbd2b
       end
     end
   end
@@ -49,8 +49,8 @@ describe "Bio::Ucsc::Hg18::Reference" do
   describe ".records" do
     context 'given "chr1"' do
       it 'returns (TwoBitRecord.reserved == 0)' do
-        Bio::Ucsc::Hg18::Reference.load("samples/hg18.2bit")
-        Bio::Ucsc::Hg18::Reference.records("chr1").reserved == 0
+        Bio::Ucsc::Hg18::ReferenceSequence.load("samples/hg18.2bit")
+        Bio::Ucsc::Hg18::ReferenceSequence.records("chr1").reserved == 0
       end
     end
   end
@@ -58,8 +58,8 @@ describe "Bio::Ucsc::Hg18::Reference" do
   describe ".records" do
     context 'given "chr1"' do
       it 'returns (TwoBitRecord.dna_size == 249_250_621)' do
-        Bio::Ucsc::Hg18::Reference.load("samples/hg18.2bit")
-        Bio::Ucsc::Hg18::Reference.records("chr1").dna_size.should == 247249719
+        Bio::Ucsc::Hg18::ReferenceSequence.load("samples/hg18.2bit")
+        Bio::Ucsc::Hg18::ReferenceSequence.records("chr1").dna_size.should == 247249719
       end
     end
   end
@@ -67,7 +67,7 @@ describe "Bio::Ucsc::Hg18::Reference" do
   describe ".byte_to_nucleotides" do
     context 'given 0b00011011' do
       it 'returns "TCAG"' do
-        r = Bio::Ucsc::Hg18::Reference.byte_to_nucleotides(0b00011011)
+        r = Bio::Ucsc::Hg18::ReferenceSequence.byte_to_nucleotides(0b00011011)
         r.should == "TCAG"
       end
     end
@@ -77,7 +77,7 @@ describe "Bio::Ucsc::Hg18::Reference" do
     context 'given [0b00011011, 0b11100100]' do
       it 'returns "TCAGGACT"' do
         ary = [0b00011011, 0b11100100]
-        r = Bio::Ucsc::Hg18::Reference.bytes_to_nucleotides(ary)
+        r = Bio::Ucsc::Hg18::ReferenceSequence.bytes_to_nucleotides(ary)
         r.should == "TCAGGACT"
       end
     end
@@ -86,27 +86,27 @@ describe "Bio::Ucsc::Hg18::Reference" do
   describe ".find_by_interval_raw" do
     context "given range chr1:1,000,000-1,000,030" do
       it 'returens "TACGTGGCTGCTCTCACACATGGGCCATGTG"' do
-        Bio::Ucsc::Hg18::Reference.load("samples/hg18.2bit")
+        Bio::Ucsc::Hg18::ReferenceSequence.load("samples/hg18.2bit")
         itv = Bio::GenomicInterval.parse("chr1:1,000,000-1,000,030")
-        r = Bio::Ucsc::Hg18::Reference.find_by_interval_raw(itv)
+        r = Bio::Ucsc::Hg18::ReferenceSequence.find_by_interval_raw(itv)
         r.should == "TACGTGGCTGCTCTCACACATGGGCCATGTG"
       end
     end
 
     context "given range chr2:1,123,456-1,123,499" do
       it 'returens "TAATGGCATACATGTAGAAAATGCAACTCATGAAGAAGTGGTAA"' do
-        Bio::Ucsc::Hg18::Reference.load("samples/hg18.2bit")
+        Bio::Ucsc::Hg18::ReferenceSequence.load("samples/hg18.2bit")
         itv = Bio::GenomicInterval.parse("chr2:1,123,456-1,123,499")
-        r = Bio::Ucsc::Hg18::Reference.find_by_interval_raw(itv)
+        r = Bio::Ucsc::Hg18::ReferenceSequence.find_by_interval_raw(itv)
         r.should == "TAATGGCATACATGTAGAAAATGCAACTCATGAAGAAGTGGTAA"
       end
     end
 
     context "given range chr2:1,123,456-1,123,456" do
       it 'returens "T"' do
-        Bio::Ucsc::Hg18::Reference.load("samples/hg18.2bit")
+        Bio::Ucsc::Hg18::ReferenceSequence.load("samples/hg18.2bit")
         itv = Bio::GenomicInterval.parse("chr2:1,123,456-1,123,456")
-        r = Bio::Ucsc::Hg18::Reference.find_by_interval_raw(itv)
+        r = Bio::Ucsc::Hg18::ReferenceSequence.find_by_interval_raw(itv)
         r.should == "T"
       end
     end
@@ -116,9 +116,9 @@ describe "Bio::Ucsc::Hg18::Reference" do
     context "given range chr1:217,260-217,299" do
       it 'returns "NNNNNNNNNNNNNNNNNNNNNGATTCATGGCTGAAATCGT"' do
 
-        Bio::Ucsc::Hg18::Reference.load("samples/hg18.2bit")
+        Bio::Ucsc::Hg18::ReferenceSequence.load("samples/hg18.2bit")
         itv = Bio::GenomicInterval.parse("chr1:217,260-217,299")
-        r = Bio::Ucsc::Hg18::Reference.find_by_interval(itv)
+        r = Bio::Ucsc::Hg18::ReferenceSequence.find_by_interval(itv)
         r.should == "NNNNNNNNNNNNNNNNNNNNNGATTCATGGCTGAAATCGT"
       end
     end
@@ -126,9 +126,9 @@ describe "Bio::Ucsc::Hg18::Reference" do
     # N-block => chr1:267,720-317,719
     context "given range chr1:257,560-257,600" do
       it 'returns "CAGGCGCCCGCATCCAGCTGGATNNNNNNNNNNNNNNNNNN"' do
-        Bio::Ucsc::Hg18::Reference.load("samples/hg18.2bit")
+        Bio::Ucsc::Hg18::ReferenceSequence.load("samples/hg18.2bit")
         itv = Bio::GenomicInterval.parse("chr1:257,560-257,600")
-        r = Bio::Ucsc::Hg18::Reference.find_by_interval(itv)
+        r = Bio::Ucsc::Hg18::ReferenceSequence.find_by_interval(itv)
         r.should == "CAGGCGCCCGCATCCAGCTGGATNNNNNNNNNNNNNNNNNN"
       end
     end

data/spec/hg19/{reference_spec.rb → reference_sequence_spec.rb}

@@ -1,11 +1,11 @@
 require 'bio-ucsc'
 
-describe "Bio::Ucsc::Hg19::Reference" do 
+describe "Bio::Ucsc::Hg19::ReferenceSequence" do 
   
   describe ".load" do
     context 'given "../samples/hg19.2bit"' do
       it "returns true" do
-        Bio::Ucsc::Hg19::Reference.load("samples/hg19.2bit")
+        Bio::Ucsc::Hg19::ReferenceSequence.load("samples/hg19.2bit")
       end
     end
   end
@@ -13,8 +13,8 @@ describe "Bio::Ucsc::Hg19::Reference" do
   describe ".header.signarue" do
     context 'given "../samples/hg19.2bit"' do
       it "returns 0x1A412743" do
-        Bio::Ucsc::Hg19::Reference.load("samples/hg19.2bit")
-        Bio::Ucsc::Hg19::Reference.header.signature.should == 0x1A412743
+        Bio::Ucsc::Hg19::ReferenceSequence.load("samples/hg19.2bit")
+        Bio::Ucsc::Hg19::ReferenceSequence.header.signature.should == 0x1A412743
       end
     end
   end
@@ -22,8 +22,8 @@ describe "Bio::Ucsc::Hg19::Reference" do
   describe ".header.version" do
     context 'given "../samples/hg19.2bit"' do
       it "returns 0" do
-        Bio::Ucsc::Hg19::Reference.load("samples/hg19.2bit")
-        Bio::Ucsc::Hg19::Reference.header.version.should == 0
+        Bio::Ucsc::Hg19::ReferenceSequence.load("samples/hg19.2bit")
+        Bio::Ucsc::Hg19::ReferenceSequence.header.version.should == 0
       end
     end
   end
@@ -31,8 +31,8 @@ describe "Bio::Ucsc::Hg19::Reference" do
   describe ".header.sequence_count" do
     context 'given "../samples/hg19.2bit"' do
       it "returns 0x5d" do
-        Bio::Ucsc::Hg19::Reference.load("samples/hg19.2bit")
-        Bio::Ucsc::Hg19::Reference.header.sequence_count.should == 0x5d
+        Bio::Ucsc::Hg19::ReferenceSequence.load("samples/hg19.2bit")
+        Bio::Ucsc::Hg19::ReferenceSequence.header.sequence_count.should == 0x5d
       end
     end
   end
@@ -40,8 +40,8 @@ describe "Bio::Ucsc::Hg19::Reference" do
   describe '.offsets["chr1"]' do
     context 'given "../samples/hg19.2bit"' do
       it "returns 0x0687" do 
-        Bio::Ucsc::Hg19::Reference.load("samples/hg19.2bit")
-        Bio::Ucsc::Hg19::Reference.offsets["chr1"].should == 0x0687
+        Bio::Ucsc::Hg19::ReferenceSequence.load("samples/hg19.2bit")
+        Bio::Ucsc::Hg19::ReferenceSequence.offsets["chr1"].should == 0x0687
       end
     end
   end
@@ -49,8 +49,8 @@ describe "Bio::Ucsc::Hg19::Reference" do
   describe ".records" do
     context 'given "chr1"' do
       it 'returns (TwoBitRecord.reserved == 0)' do
-        Bio::Ucsc::Hg19::Reference.load("samples/hg19.2bit")
-        Bio::Ucsc::Hg19::Reference.records("chr1").reserved == 0
+        Bio::Ucsc::Hg19::ReferenceSequence.load("samples/hg19.2bit")
+        Bio::Ucsc::Hg19::ReferenceSequence.records("chr1").reserved == 0
       end
     end
   end
@@ -58,8 +58,8 @@ describe "Bio::Ucsc::Hg19::Reference" do
   describe ".records" do
     context 'given "chr1"' do
       it 'returns (TwoBitRecord.dna_size == 249_250_621)' do
-        Bio::Ucsc::Hg19::Reference.load("samples/hg19.2bit")
-        Bio::Ucsc::Hg19::Reference.records("chr1").dna_size.should == 249_250_621
+        Bio::Ucsc::Hg19::ReferenceSequence.load("samples/hg19.2bit")
+        Bio::Ucsc::Hg19::ReferenceSequence.records("chr1").dna_size.should == 249_250_621
       end
     end
   end
@@ -67,7 +67,7 @@ describe "Bio::Ucsc::Hg19::Reference" do
   describe ".byte_to_nucleotides" do
     context 'given 0b00011011' do
       it 'returns "TCAG"' do
-        r = Bio::Ucsc::Hg19::Reference.byte_to_nucleotides(0b00011011)
+        r = Bio::Ucsc::Hg19::ReferenceSequence.byte_to_nucleotides(0b00011011)
         r.should == "TCAG"
       end
     end
@@ -77,7 +77,7 @@ describe "Bio::Ucsc::Hg19::Reference" do
     context 'given [0b00011011, 0b11100100]' do
       it 'returns "TCAGGACT"' do
         ary = [0b00011011, 0b11100100]
-        r = Bio::Ucsc::Hg19::Reference.bytes_to_nucleotides(ary)
+        r = Bio::Ucsc::Hg19::ReferenceSequence.bytes_to_nucleotides(ary)
         r.should == "TCAGGACT"
       end
     end
@@ -86,27 +86,27 @@ describe "Bio::Ucsc::Hg19::Reference" do
   describe ".find_by_interval_raw" do
     context "given range chr1:1,000,000-1,000,030" do
       it 'returens "TGGGCACAGCCTCACCCAGGAAAGCAGCTGG"' do
-        Bio::Ucsc::Hg19::Reference.load("samples/hg19.2bit")
+        Bio::Ucsc::Hg19::ReferenceSequence.load("samples/hg19.2bit")
         itv = Bio::GenomicInterval.parse("chr1:1,000,000-1,000,030")
-        r = Bio::Ucsc::Hg19::Reference.find_by_interval_raw(itv)
+        r = Bio::Ucsc::Hg19::ReferenceSequence.find_by_interval_raw(itv)
         r.should == "TGGGCACAGCCTCACCCAGGAAAGCAGCTGG"
       end
     end
 
     context "given range chr2:1,123,456-1,123,499" do
       it 'returens "GTACTTAGAACACTATTGATTTCTGTACGTTGATTTTGTATTCT"' do
-        Bio::Ucsc::Hg19::Reference.load("samples/hg19.2bit")
+        Bio::Ucsc::Hg19::ReferenceSequence.load("samples/hg19.2bit")
         itv = Bio::GenomicInterval.parse("chr2:1,123,456-1,123,499")
-        r = Bio::Ucsc::Hg19::Reference.find_by_interval_raw(itv)
+        r = Bio::Ucsc::Hg19::ReferenceSequence.find_by_interval_raw(itv)
         r.should == "GTACTTAGAACACTATTGATTTCTGTACGTTGATTTTGTATTCT"
       end
     end
 
     context "given range chr2:1,123,456-1,123,456" do
       it 'returens "G"' do
-        Bio::Ucsc::Hg19::Reference.load("samples/hg19.2bit")
+        Bio::Ucsc::Hg19::ReferenceSequence.load("samples/hg19.2bit")
         itv = Bio::GenomicInterval.parse("chr2:1,123,456-1,123,456")
-        r = Bio::Ucsc::Hg19::Reference.find_by_interval_raw(itv)
+        r = Bio::Ucsc::Hg19::ReferenceSequence.find_by_interval_raw(itv)
         r.should == "G"
       end
     end
@@ -115,9 +115,9 @@ describe "Bio::Ucsc::Hg19::Reference" do
  describe ".find_by_interval" do
     context "given range chr1:9,980-10,020" do
       it 'returns "NNNNNNNNNNNNNNNNNNNNNTAACCCTAACCCTAACCCTA"' do
-        Bio::Ucsc::Hg19::Reference.load("samples/hg19.2bit")
+        Bio::Ucsc::Hg19::ReferenceSequence.load("samples/hg19.2bit")
         itv = Bio::GenomicInterval.parse("chr1:9,980-10,020")
-        r = Bio::Ucsc::Hg19::Reference.find_by_interval(itv)
+        r = Bio::Ucsc::Hg19::ReferenceSequence.find_by_interval(itv)
         r.should == "NNNNNNNNNNNNNNNNNNNNNTAACCCTAACCCTAACCCTA"
       end
     end
@@ -125,9 +125,9 @@ describe "Bio::Ucsc::Hg19::Reference" do
     # N-block => chr1:267,720-317,719
     context "given range chr1:267,690-267,735" do
       it 'returns "GGGACTACAGGCGCCCGCATCCAGCTGGATNNNNNNNNNNNNNNNN' do
-        Bio::Ucsc::Hg19::Reference.load("samples/hg19.2bit")
+        Bio::Ucsc::Hg19::ReferenceSequence.load("samples/hg19.2bit")
         itv = Bio::GenomicInterval.parse("chr1:267,690-267,735")
-        r = Bio::Ucsc::Hg19::Reference.find_by_interval(itv)
+        r = Bio::Ucsc::Hg19::ReferenceSequence.find_by_interval(itv)
         r.should == "GGGACTACAGGCGCCCGCATCCAGCTGGATNNNNNNNNNNNNNNNN"
       end
     end

metadata

@@ -2,17 +2,16 @@
 name: bio-ucsc-api
 version: !ruby/object:Gem::Version 
   prerelease: 
-  version: 0.0.5
+  version: 0.1.0
 platform: ruby
 authors: 
 - Hiroyuki Mishima
-- Francesco Strozzi
 - Jan Aerts
 autorequire: 
 bindir: bin
 cert_chain: []
 
-date: 2011-06-19 00:00:00 Z
+date: 2011-07-07 00:00:00 Z
 dependencies: 
 - !ruby/object:Gem::Dependency 
   name: activerecord
@@ -113,7 +112,7 @@ dependencies:
   type: :development
   prerelease: false
   version_requirements: *id009
-description: "A Bioruby plugin: an API for UCSC Genome Browser database (experimental)"
+description: "Ruby UCSC API: accessing the UCSC Genome Database using Ruby"
 email: missy@be.to
 executables: []
 
@@ -1115,6 +1114,7 @@ files:
 - lib/bio-ucsc/hg18/rdmrraw.rb
 - lib/bio-ucsc/hg18/recombrate.rb
 - lib/bio-ucsc/hg18/reference.rb
+- lib/bio-ucsc/hg18/reference_sequence.rb
 - lib/bio-ucsc/hg18/refflat.rb
 - lib/bio-ucsc/hg18/refgene.rb
 - lib/bio-ucsc/hg18/reflink.rb
@@ -3757,6 +3757,7 @@ files:
 - lib/bio-ucsc/hg19/polyapredict.rb
 - lib/bio-ucsc/hg19/recombrate.rb
 - lib/bio-ucsc/hg19/reference.rb
+- lib/bio-ucsc/hg19/reference_sequence.rb
 - lib/bio-ucsc/hg19/refflat.rb
 - lib/bio-ucsc/hg19/refgene.rb
 - lib/bio-ucsc/hg19/reflink.rb
@@ -6020,7 +6021,7 @@ files:
 - spec/hg18/rdmr_spec.rb
 - spec/hg18/rdmrraw_spec.rb
 - spec/hg18/recombrate_spec.rb
-- spec/hg18/reference_spec.rb
+- spec/hg18/reference_sequence_spec.rb
 - spec/hg18/refflat_spec.rb
 - spec/hg18/refgene_spec.rb
 - spec/hg18/reflink_spec.rb
@@ -8659,7 +8660,7 @@ files:
 - spec/hg19/polyadb_spec.rb
 - spec/hg19/polyapredict_spec.rb
 - spec/hg19/recombrate_spec.rb
-- spec/hg19/reference_spec.rb
+- spec/hg19/reference_sequence_spec.rb
 - spec/hg19/refflat_spec.rb
 - spec/hg19/refgene_spec.rb
 - spec/hg19/reflink_spec.rb
@@ -9954,7 +9955,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
   requirements: 
   - - ">="
     - !ruby/object:Gem::Version 
-      hash: -3461379058262703329
+      hash: -4523550702802348992
       segments: 
       - 0
       version: "0"
@@ -9970,7 +9971,7 @@ rubyforge_project:
 rubygems_version: 1.7.2
 signing_key: 
 specification_version: 3
-summary: "A Bioruby plugin: an API for UCSC Genome Browser (experimental)"
+summary: "The Ruby UCSC API: accessing the UCSC Genome Database using Ruby"
 test_files: 
 - spec/hg18/acembly_spec.rb
 - spec/hg18/acemblyclass_spec.rb
@@ -10952,7 +10953,7 @@ test_files:
 - spec/hg18/rdmr_spec.rb
 - spec/hg18/rdmrraw_spec.rb
 - spec/hg18/recombrate_spec.rb
-- spec/hg18/reference_spec.rb
+- spec/hg18/reference_sequence_spec.rb
 - spec/hg18/refflat_spec.rb
 - spec/hg18/refgene_spec.rb
 - spec/hg18/reflink_spec.rb
@@ -13591,7 +13592,7 @@ test_files:
 - spec/hg19/polyadb_spec.rb
 - spec/hg19/polyapredict_spec.rb
 - spec/hg19/recombrate_spec.rb
-- spec/hg19/reference_spec.rb
+- spec/hg19/reference_sequence_spec.rb
 - spec/hg19/refflat_spec.rb
 - spec/hg19/refgene_spec.rb
 - spec/hg19/reflink_spec.rb