bio-ucsc-api 0.0.1 → 0.0.3

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

@@ -0,0 +1,23 @@
+#
+# = hg19/descriptioin.rb
+# Copyright::
+#  Copyright (C) 2011 MISHIMA, Hiroyuki <missy at be.to / hmishima at nagasaki-u.ac.jp> 
+# License::     The Ruby licence (Ryby's / GPLv2 dual)
+#
+# = Table description in UCSC Table Browser This track shows multiple
+# Description of a genbank sequence
+
+module Bio
+  module Ucsc
+    module Hg19
+      class Description < DBConnection
+        set_table_name 'description'
+        set_primary_key :id
+        Bio::Ucsc::Hg19::GbCdnaInfo
+        belongs_to(:gbCdnaInfo,
+                   :class_name => "Bio::Ucsc::Hg19::GbCdnaInfo",
+                   :foreign_key => :id)
+       end
+    end
+  end
+end

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

@@ -0,0 +1,24 @@
+#
+# = hg19/gbcdnainfo.rb
+# Copyright::
+#  Copyright (C) 2011 MISHIMA, Hiroyuki <missy at be.to / hmishima at nagasaki-u.ac.jp> 
+# License::     The Ruby licence (Ryby's / GPLv2 dual)
+#
+# = Table description in UCSC Table Browser This track shows multiple
+# Links together various info associated with a GenBank mRNA or EST
+
+module Bio
+  module Ucsc
+    module Hg19
+      class GbCdnaInfo < DBConnection
+        set_table_name 'gbCdnaInfo'
+        set_primary_key :id
+        Bio::Ucsc::Hg19::Description
+        has_one(:description,
+                :class_name => "Bio::Ucsc::Hg19::Description",
+                :foreign_key => :id)
+        columns_hash.delete("type")
+       end
+    end
+  end
+end

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

@@ -0,0 +1,19 @@
+#
+# = hg19/kgxref.rb
+# Copyright::
+#  Copyright (C) 2011 MISHIMA, Hiroyuki <missy at be.to / hmishima at nagasaki-u.ac.jp> 
+# License::     The Ruby licence (Ryby's / GPLv2 dual)
+#
+# = Table description in UCSC Table Browser This track shows multiple
+# Link together a Known Gene ID and a gene alias
+
+module Bio
+  module Ucsc
+    module Hg19
+      class KgXref < DBConnection
+        set_table_name 'kgXref'
+        set_primary_key nil
+      end
+    end
+  end
+end

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

@@ -0,0 +1,171 @@
+#
+# = reference.rb
+# handle UCSC's 2bit file (locally stored) to retrieve the reference sequence
+#
+# Copyright::   Cioyrught (C) 2011
+#               MISHIMA, Hiroyuki <missy at be.to / hmishima at nagasaki-u.ac.jp> 
+# License::     Ruby license (Ryby's / GPLv2 dual)
+
+# require 'bio'
+
+module Bio
+  module Ucsc
+    module Hg19
+      TwoBitHeader = 
+        Struct.new(:signature, :version, :sequence_count, :reserved)
+      TwoBitRecord =
+        Struct.new(:dna_size,
+                   :n_block_intervals, :mask_block_intervals,
+                   :reserved, :packed_dna_offset)
+
+      class ByteQueue
+        def initialize(str)
+          @str = str
+          @index = 0
+        end
+
+        attr_accessor :index
+
+        def next(n)
+          result = @str[@index, n]
+          @index += n
+          result
+        end
+      end # class ByteQueue
+
+      class Reference
+        BINCODE = {0b00 => "T", 0b01 => "C", 0b10 => "A", 0b11 => "G"}
+
+        cattr_reader :filename, :header, :offsets
+
+        def self.load(filename)
+          two_bit = nil
+          open(filename, 'rb') {|f| two_bit = f.read}
+          @@tbq = ByteQueue.new(two_bit)
+          @@filename = filename
+
+          twobit_header = TwoBitHeader.new
+          twobit_header.signature      = @@tbq.next(4).unpack('L').first
+          twobit_header.version        = @@tbq.next(4).unpack('L').first
+          twobit_header.sequence_count = @@tbq.next(4).unpack('L').first
+          twobit_header.reserved       = @@tbq.next(4).unpack('L').first
+          @@header = twobit_header
+
+          @@offsets = Hash.new
+          @@header.sequence_count.times do
+            name_length = @@tbq.next(1).unpack('C').first
+            @@offsets[@@tbq.next(name_length).unpack('a*').first] =
+              @@tbq.next(4).unpack('L').first
+          end
+          @@records = Hash.new
+        end
+
+        def self.records(chrom)
+          return @@records[chrom] if @@records[chrom]
+          
+          @@tbq.index = @@offsets[chrom]
+          @@records[chrom] = TwoBitRecord.new
+          @@records[chrom].dna_size = @@tbq.next(4).unpack('L').first
+ 
+          n_block_count = @@tbq.next(4).unpack('L').first
+          n_block_starts = Array.new
+          n_block_count.times do
+            n_block_starts << @@tbq.next(4).unpack('L').first
+          end
+          n_block_sizes = Array.new
+          n_block_count.times do
+            n_block_sizes << @@tbq.next(4).unpack('L').first
+          end
+          @@records[chrom].n_block_intervals = Array.new
+          n_block_count.times do |idx|
+            @@records[chrom].n_block_intervals << 
+              Bio::GenomicInterval.zero_based(chrom,
+                                             n_block_starts[idx],
+                                             n_block_starts[idx]+n_block_sizes[idx])
+          end
+          
+          mask_block_count = @@tbq.next(4).unpack('L').first
+          mask_block_starts = Array.new
+          mask_block_count.times do
+            mask_block_starts << @@tbq.next(4).unpack('L').first
+          end
+          mask_block_sizes = Array.new
+          mask_block_count.times do
+            mask_block_sizes << @@tbq.next(4).unpack('L').first
+          end
+          @@records[chrom].mask_block_intervals = Array.new
+          mask_block_count.times do |idx|
+            @@records[chrom].mask_block_intervals << 
+              Bio::GenomicInterval.zero_based(chrom,
+                                             mask_block_starts[idx],
+                                             mask_block_starts[idx]+mask_block_sizes[idx])
+          end
+  
+          @@records[chrom].reserved = @@tbq.next(4).unpack('L').first
+          @@records[chrom].packed_dna_offset = @@tbq.index
+
+          @@records[chrom]
+        end
+
+        def self.find_by_interval(interval)
+          seq = self.find_by_interval_raw(interval)
+          @@records[interval.chrom].n_block_intervals.map do |nb|
+            if interval.overlapped?(nb)
+              case interval.compare(nb)
+              when :equal,:contained_by
+                seq = 'N' * interval.overlap(nb)
+              when :contains
+                left_len  = nb.chr_start - interval.chr_start + 1
+                right_len = interval.chr_end - nb.chr_end + 1
+                seq[0, left_len] = 'N' * left_len
+                seq[-right_len, right_len] = 'N' * right_len
+              when :left_overlapped
+                left_len = nb.chr_end - interval.chr_start + 1
+                seq[0, left_len] = 'N' * left_len
+              when :right_overlapped
+                right_len = interval.chr_end - nb.chr_start + 1
+                seq[-right_len, right_len] = 'N' * right_len
+              when :right_adjacent, :right_off
+                # expecting that N-blocks are sorted
+                # return Bio::Sequence::NA.new(seq) 
+                seq
+              end
+            end
+          end
+          #Bio::Sequence::NA.new(seq)
+          seq
+        end
+
+        def self.find_by_interval_raw(interval)
+          byte_count, byte_mod = interval.zero_start.divmod 4
+          chrom_top = self.records(interval.chrom).packed_dna_offset
+          div_start, mod_start = interval.zero_start.divmod 4
+          div_end, mod_end     = interval.zero_end.divmod 4
+          div_len, mod_len     = interval.length.divmod 4
+
+          byte_length = div_end - div_start + 1
+          @@tbq.index = chrom_top + div_start
+          bytes = @@tbq.next(byte_length).unpack('C*')
+          seq = Bio::Ucsc::Hg19::Reference.bytes_to_nucleotides(bytes)
+          seq[mod_start..(-1-(4-mod_end))]
+        end
+
+        def self.bytes_to_nucleotides(bytes) 
+          results = ""
+          bytes.each do |byte|
+            results << Bio::Ucsc::Hg19::Reference.byte_to_nucleotides(byte)
+          end
+          results
+        end
+
+        def self.byte_to_nucleotides(byte)
+          BINCODE[byte >> 6] +
+            BINCODE[(byte >> 4) & 0b11] +
+            BINCODE[(byte >> 2) & 0b11] +
+            BINCODE[byte & 0b11]
+        end
+      end # class Reference
+
+    end # module Hg19
+  end # module Ucsc
+end # module Bio

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

@@ -0,0 +1,23 @@
+#
+# = hg19/refseqsummary.rb
+# Copyright::
+#  Copyright (C) 2011 MISHIMA, Hiroyuki <missy at be.to / hmishima at nagasaki-u.ac.jp> 
+# License::     The Ruby licence (Ryby's / GPLv2 dual)
+#
+# = Table description in UCSC Table Browser This track shows multiple
+# Summary or completeness info for RefSeqs (when given in comments)
+#
+# mrnaAcc column: see http://www.ncbi.nlm.nih.gov/RefSeq/key.html#accessions 
+# exsamples - NM_000546 (mRNA), NR_029476 (small RNA, unaligned)
+#
+
+module Bio
+  module Ucsc
+    module Hg19
+      class RefSeqSummary < DBConnection
+        set_table_name 'refSeqSummary'
+        set_primary_key nil
+      end
+    end
+  end
+end

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

@@ -0,0 +1,20 @@
+#
+# = hg19/trnas.rb
+# Copyright::
+#  Copyright (C) 2011 MISHIMA, Hiroyuki <missy at be.to / hmishima at nagasaki-u.ac.jp> 
+# License::     The Ruby licence (Ryby's / GPLv2 dual)
+#
+# = Table description in UCSC Table Browser
+# This track displays tRNA genes predicted by using tRNAscan-SE v.1.23.
+
+module Bio
+  module Ucsc
+    module Hg19
+      class TRNAs < DBConnection
+        extend Bio::Ucsc::Hg19::QueryUsingChromBin
+        set_table_name 'tRNAs'
+        set_primary_key nil
+      end
+    end
+  end
+end

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

@@ -0,0 +1,39 @@
+#!/usr/local/bin/ruby-1.9
+#
+# Usage:: hg19-2bit-retrieve.rb <genomic interval>
+#         (default is "chr1:9,500-10,499")
+#
+# Copyright::
+#   Copyright (C) 2011 MISHIMA, Hiroyuki
+#                      <missy at be.to / hmishima at ngit agasaki-u.ac.jp>
+# License::     The Ruby licence (Ryby's / GPLv2 dual)
+#
+
+require 'nkf'
+
+HG19_2BIT_FILE = "hg19.2bit"
+
+require File.dirname(__FILE__) + '/../lib/bio-ucsc'
+
+class Hg19Ref
+  include Bio::Ucsc::Hg19
+
+  def run(interval)
+    DBConnection.connect
+    Reference.load(HG19_2BIT_FILE)
+    itv = Bio::GenomicInterval.parse(interval)
+
+    puts itv.to_s
+    puts NKF.nkf("-wf50-0", Reference.find_by_interval(itv))
+  end
+end
+
+if $0 == __FILE__
+  interval = ARGV[0]
+  interval ||= "chr1:9,500-10,999"
+  Hg19Ref.new.run(interval)
+end
+
+
+
+

data/samples/hg19-sample.rb

@@ -1,5 +1,7 @@
 #!/usr/local/bin/ruby-1.9
 #
+# hg19-sample.rb: chunks of codes handling hg19 tables
+#
 # Copyright::
 #   Copyright (C) 2011 MISHIMA, Hiroyuki
 #                      <missy at be.to / hmishima at nagasaki-u.ac.jp>
@@ -7,10 +9,10 @@
 #
 
 require File.dirname(__FILE__) + '/../lib/bio-ucsc'
+require 'nkf'
 
 include Bio::Ucsc
 
-Hg19::DBConnection.default
 Hg19::DBConnection.connect
 
 itvs_a =
@@ -64,3 +66,22 @@ names.each do |n|
   i = Bio::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/symbol2summary.rb

@@ -0,0 +1,47 @@
+#!/usr/local/bin/ruby-1.9
+#
+# Usage:: symbol2summary.rb <Gene_Symbol> (default is "TP53")
+#
+# Copyright::
+#   Copyright (C) 2011 MISHIMA, Hiroyuki
+#                      <missy at be.to / hmishima at ngit agasaki-u.ac.jp>
+# License::     The Ruby licence (Ryby's / GPLv2 dual)
+#
+
+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
+
+    puts "---"
+    puts "Gene symbol: #{genesym}" if known_gene
+    puts "Description: #{known_gene.description}" if known_gene
+    if summary
+      puts "Summary:"
+      puts NKF.nkf("-wF72", summary)
+    end
+  end
+end
+
+if $0 == __FILE__
+  genesym = ARGV[0]
+  genesym ||= "TP53"
+  Sym2Sum.new.run(genesym)
+end
+
+
+   
+
+
+
+
+
+
+

data/spec/hg18/reference_spec.rb

@@ -0,0 +1,144 @@
+require 'bio-ucsc'
+
+describe "Bio::Ucsc::Hg18::Reference" do 
+  
+  describe ".load" do
+    context 'given "../samples/hg18.2bit"' do
+      it "returns true" do
+        Bio::Ucsc::Hg18::Reference.load("samples/hg18.2bit")
+      end
+    end
+  end
+
+  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
+      end
+    end
+  end
+
+  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
+      end
+    end
+  end
+
+  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
+      end
+    end
+  end
+
+  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
+      end
+    end
+  end
+
+  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
+      end
+    end
+  end
+
+  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
+      end
+    end
+  end
+
+  describe ".byte_to_nucleotides" do
+    context 'given 0b00011011' do
+      it 'returns "TCAG"' do
+        r = Bio::Ucsc::Hg18::Reference.byte_to_nucleotides(0b00011011)
+        r.should == "TCAG"
+      end
+    end
+  end
+
+  describe ".bytes_to_nucleotides" do
+    context 'given [0b00011011, 0b11100100]' do
+      it 'returns "TCAGGACT"' do
+        ary = [0b00011011, 0b11100100]
+        r = Bio::Ucsc::Hg18::Reference.bytes_to_nucleotides(ary)
+        r.should == "TCAGGACT"
+      end
+    end
+  end
+
+  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")
+        itv = Bio::GenomicInterval.parse("chr1:1,000,000-1,000,030")
+        r = Bio::Ucsc::Hg18::Reference.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")
+        itv = Bio::GenomicInterval.parse("chr2:1,123,456-1,123,499")
+        r = Bio::Ucsc::Hg18::Reference.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")
+        itv = Bio::GenomicInterval.parse("chr2:1,123,456-1,123,456")
+        r = Bio::Ucsc::Hg18::Reference.find_by_interval_raw(itv)
+        r.should == "T"
+      end
+    end
+  end
+
+ describe ".find_by_interval" do
+    context "given range chr1:217,260-217,299" do
+      it 'returns "NNNNNNNNNNNNNNNNNNNNNGATTCATGGCTGAAATCGT"' do
+
+        Bio::Ucsc::Hg18::Reference.load("samples/hg18.2bit")
+        itv = Bio::GenomicInterval.parse("chr1:217,260-217,299")
+        r = Bio::Ucsc::Hg18::Reference.find_by_interval(itv)
+        r.should == "NNNNNNNNNNNNNNNNNNNNNGATTCATGGCTGAAATCGT"
+      end
+    end
+    
+    # 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")
+        itv = Bio::GenomicInterval.parse("chr1:257,560-257,600")
+        r = Bio::Ucsc::Hg18::Reference.find_by_interval(itv)
+        r.should == "CAGGCGCCCGCATCCAGCTGGATNNNNNNNNNNNNNNNNNN"
+      end
+    end
+  end
+
+end
+
+# N-Blocks
+#  chr1:167281-217280,
+#  chr1:257583-307582,
+#  chr1:461232-511231,
+#  chr1:2624081-2674080,
+