bio-ucsc-api 0.0.5 → 0.1.0

data/lib/bio-ucsc/hg18/reference_sequence.rb

@@ -0,0 +1,171 @@
+#
+# = reference_sequence.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 Hg18
+      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 ReferenceSequence
+        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::Hg18::ReferenceSequence.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::Hg18::ReferenceSequence.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 ReferenceSequence
+
+    end # module Hg18
+  end # module Ucsc
+end # module Bio

data/lib/bio-ucsc/hg18/refgene.rb

@@ -2,7 +2,6 @@
 # = hg18/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/hg18/snp130.rb

@@ -2,7 +2,6 @@
 # = hg18/snp130.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.rb

@@ -16,7 +16,8 @@ module Bio
 
       # Reference sequence retrieval via the 2bit fil
       #
-      autoload :Reference,            "#{base}/reference"
+      autoload :Reference, "#{base}/reference" # OBSOLETE
+      autoload :ReferenceSequence, "#{base}/reference_sequence"
 
       # group: Mapping and Sequencing Tracks ----------
       #

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

@@ -3,7 +3,7 @@
 # 
 # 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>
+#   Copyright (C) 2010 Jan Aerts <jan.aerts@gmail.com>
 # License::     The Ruby licence (Ryby's / GPLv2 dual)
 #
 # = DESCRIPTION

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

@@ -2,7 +2,6 @@
 # = hg19/cytoband.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/cytobandideo.rb

@@ -2,7 +2,6 @@
 # = hg19/cytobandideo.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/db_connection.rb

@@ -3,7 +3,7 @@
 #
 # Copyright::   Cioyrught (C) 2011
 #               MISHIMA, Hiroyuki <missy at be.to / hmishima at nagasaki-u.ac.jp> 
-# Copyright::   Copyright (C) 2008
+# Copyright::   Copyright (C) 2010
 #               Jan Aerts <jan.aerts@gmail.com>
 # License::     Ruby licence (Ryby's / GPLv2 dual)
 

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

@@ -2,7 +2,6 @@
 # = hg19/dgv.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/ensgene.rb

@@ -2,7 +2,6 @@
 # = hg19/ensgene.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/reference.rb

@@ -2,170 +2,11 @@
 # = reference.rb
 # handle UCSC's 2bit file (locally stored) to retrieve the reference sequence
 #
+# In version 0.1.0, this file is OBSOLETE.
+# Use Ucsc::Hg18::ReferenceSequence instead.
+#
 # 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
+raise "Bio::Ucsc::Hg19::Reference is OBSOLETE. Use Bio::Ucsc::Hg19::ReferenceSequence instead."

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

@@ -0,0 +1,171 @@
+#
+# = reference_sequence.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 ReferenceSequence
+        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::ReferenceSequence.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::ReferenceSequence.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 ReferenceSequence
+
+    end # module Hg19
+  end # module Ucsc
+end # module Bio