bio 1.4.1 → 1.4.2
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- data/ChangeLog +954 -0
- data/KNOWN_ISSUES.rdoc +40 -5
- data/README.rdoc +36 -35
- data/RELEASE_NOTES.rdoc +87 -59
- data/bioruby.gemspec +24 -2
- data/doc/RELEASE_NOTES-1.4.1.rdoc +104 -0
- data/doc/Tutorial.rd +162 -200
- data/doc/Tutorial.rd.html +149 -146
- data/lib/bio.rb +1 -0
- data/lib/bio/appl/blast.rb +1 -1
- data/lib/bio/appl/blast/ddbj.rb +26 -34
- data/lib/bio/appl/blast/genomenet.rb +21 -11
- data/lib/bio/db/embl/sptr.rb +193 -21
- data/lib/bio/db/fasta.rb +1 -1
- data/lib/bio/db/fastq.rb +14 -0
- data/lib/bio/db/fastq/format_fastq.rb +2 -2
- data/lib/bio/db/genbank/ddbj.rb +1 -2
- data/lib/bio/db/genbank/format_genbank.rb +1 -1
- data/lib/bio/db/medline.rb +1 -0
- data/lib/bio/db/newick.rb +3 -1
- data/lib/bio/db/pdb/pdb.rb +9 -9
- data/lib/bio/db/pdb/residue.rb +2 -2
- data/lib/bio/io/ddbjrest.rb +344 -0
- data/lib/bio/io/ncbirest.rb +121 -1
- data/lib/bio/location.rb +2 -2
- data/lib/bio/reference.rb +3 -4
- data/lib/bio/shell/plugin/entry.rb +7 -3
- data/lib/bio/shell/plugin/ncbirest.rb +5 -1
- data/lib/bio/util/restriction_enzyme.rb +3 -0
- data/lib/bio/util/restriction_enzyme/dense_int_array.rb +195 -0
- data/lib/bio/util/restriction_enzyme/range/sequence_range.rb +7 -7
- data/lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb +57 -18
- data/lib/bio/util/restriction_enzyme/range/sequence_range/fragment.rb +2 -2
- data/lib/bio/util/restriction_enzyme/sorted_num_array.rb +219 -0
- data/lib/bio/version.rb +1 -1
- data/sample/test_restriction_enzyme_long.rb +4403 -0
- data/test/data/fasta/EFTU_BACSU.fasta +8 -0
- data/test/data/genbank/CAA35997.gp +48 -0
- data/test/data/genbank/SCU49845.gb +167 -0
- data/test/data/litdb/1717226.litdb +13 -0
- data/test/data/pir/CRAB_ANAPL.pir +6 -0
- data/test/functional/bio/appl/blast/test_remote.rb +93 -0
- data/test/functional/bio/appl/test_blast.rb +61 -0
- data/test/functional/bio/io/test_ddbjrest.rb +47 -0
- data/test/functional/bio/test_command.rb +3 -3
- data/test/unit/bio/db/embl/test_sptr.rb +6 -6
- data/test/unit/bio/db/embl/test_uniprot_new_part.rb +208 -0
- data/test/unit/bio/db/genbank/test_common.rb +274 -0
- data/test/unit/bio/db/genbank/test_genbank.rb +401 -0
- data/test/unit/bio/db/genbank/test_genpept.rb +81 -0
- data/test/unit/bio/db/pdb/test_pdb.rb +3287 -11
- data/test/unit/bio/db/test_fasta.rb +34 -12
- data/test/unit/bio/db/test_fastq.rb +26 -0
- data/test/unit/bio/db/test_litdb.rb +95 -0
- data/test/unit/bio/db/test_medline.rb +1 -0
- data/test/unit/bio/db/test_nbrf.rb +82 -0
- data/test/unit/bio/db/test_newick.rb +22 -4
- data/test/unit/bio/test_reference.rb +35 -0
- data/test/unit/bio/util/restriction_enzyme/test_dense_int_array.rb +201 -0
- data/test/unit/bio/util/restriction_enzyme/test_sorted_num_array.rb +281 -0
- metadata +44 -38
@@ -34,13 +34,40 @@ class CalculatedCuts
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include StringFormatting
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# +Array+ of vertical cuts on the primary strand in 0-based index notation
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-
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def vc_primary
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#$stderr.puts caller[0].inspect ###DEBUG
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@vc_primary.to_a
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end
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+
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# Returns the same contents as vc_primary, but returns original data
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# structure used in the class.
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def vc_primary_as_original_class
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@vc_primary
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end
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# +Array+ of vertical cuts on the complementary strand in 0-based index notation
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-
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def vc_complement
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#$stderr.puts caller[0].inspect ###DEBUG
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@vc_complement.to_a
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end
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+
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# Returns the same contents as vc_complement, but returns original data
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# structure used in the class.
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def vc_complement_as_original_class
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@vc_complement
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end
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# +Array+ of horizontal cuts between strands in 0-based index notation
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-
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def hc_between_strands
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#$stderr.puts caller[0].inspect ###DEBUG
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@hc_between_strands.to_a
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end
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+
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# Returns the same contents as hc_between_strands, but returns original data
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# structure used in the class.
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def hc_between_strands_as_original_class
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@hc_between_strands
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end
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# Set to +true+ if the fragment CalculatedCuts is working on is circular
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attr_accessor :circular
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def initialize(size=nil, circular=false)
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@size = size
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@circular = circular
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-
@vc_primary = []
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@vc_complement = []
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@hc_between_strands = []
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@vc_primary = SortedNumArray[]
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@vc_complement = SortedNumArray[]
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@hc_between_strands = SortedNumArray[]
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end
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# Accepts an +Array+ of CutRange type objects and applies them to
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def add_cuts_from_cut_ranges(cut_ranges)
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@strands_for_display_current = false
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@vc_primary = @vc_primary.dup
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@vc_complement = @vc_complement.dup
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+
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cut_ranges.each do |cut_range|
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-
@vc_primary
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-
@vc_complement
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@vc_primary.concat [cut_range.p_cut_left, cut_range.p_cut_right]
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@vc_complement.concat [cut_range.c_cut_left, cut_range.c_cut_right]
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# Add horizontal cut ranges. This may happen from cuts made inbetween a
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# VerticalCutRange or may be specifically defined by a HorizontalCutRange.
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@@ -124,10 +154,10 @@ class CalculatedCuts
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@size = size if size
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raise IndexError, "Size of the strand must be provided here or during initalization." if !@size.kind_of?(Fixnum) and not @circular
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-
vcuts =
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vcuts = @vc_primary + @vc_complement
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hcuts = @hc_between_strands
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last_index = @size - 1
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-
good_hcuts = []
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good_hcuts = SortedNumArray[]
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potential_hcuts = []
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if @circular
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@@ -146,13 +176,14 @@ class CalculatedCuts
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if potential_hcuts.empty?
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if vcuts.include?( hcut ) and vcuts.include?( hcut - 1 )
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-
good_hcuts
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good_hcuts << hcut
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elsif vcuts.include?( hcut - 1 )
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potential_hcuts << hcut
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end
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else
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if vcuts.include?( hcut )
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-
good_hcuts
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good_hcuts.concat(potential_hcuts)
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good_hcuts << hcut
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potential_hcuts.clear
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else
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potential_hcuts << hcut
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@@ -163,7 +194,7 @@ class CalculatedCuts
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check_vc = lambda do |vertical_cuts, opposing_vcuts|
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# opposing_vcuts is here only to check for blunt cuts, so there shouldn't
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# be any out-of-order problems with this
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-
good_vc = []
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+
good_vc = SortedNumArray[]
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vertical_cuts.each { |vc| good_vc << vc if good_hcuts.include?( vc ) or good_hcuts.include?( vc + 1 ) or opposing_vcuts.include?( vc ) }
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good_vc
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end
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@@ -192,18 +223,26 @@ class CalculatedCuts
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hcs = '-' # Horizontal cut symbol
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vhcs = '+' # Intersection of vertical and horizontal cut symbol
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-
num_txt_repeat = lambda { num_txt = '0123456789'; (num_txt * (
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num_txt_repeat = lambda { num_txt = '0123456789'; (num_txt * (@size.div(num_txt.size) + 1))[0..@size-1] }
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(str1 == nil) ? a = num_txt_repeat.call : a = str1.dup
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(str2 == nil) ? b = num_txt_repeat.call : b = str2.dup
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if vcp and !vcp.is_a?(SortedNumArray) then
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vcp = SortedNumArray.new.concat(vcp)
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end
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if vcc and !vcc.is_a?(SortedNumArray) then
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vcc = SortedNumArray.new.concat(vcc)
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end
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if hc and !hc.is_a?(SortedNumArray) then
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hc = SortedNumArray.new.concat(hc)
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end
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+
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vcp = @vc_primary if vcp==nil
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vcc = @vc_complement if vcc==nil
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hc = @hc_between_strands if hc==nil
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-
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-
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vcp.reverse.each { |c| a.insert(c+1, vcs) }
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vcc.reverse.each { |c| b.insert(c+1, vcs) }
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vcp.reverse_each { |c| a.insert(c+1, vcs) }
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vcc.reverse_each { |c| b.insert(c+1, vcs) }
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between = ' ' * @size
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hc.each {|hcut| between[hcut,1] = hcs }
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@@ -5,7 +5,7 @@
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# Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
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# License:: The Ruby License
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#
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# $Id
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# $Id:$
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#
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require 'bio/util/restriction_enzyme'
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@@ -31,7 +31,7 @@ class Fragment
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df.primary = ''
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df.complement = ''
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both_bins =
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both_bins = @primary_bin + @complement_bin
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both_bins.each do |item|
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@primary_bin.include?(item) ? df.primary << p_str[item] : df.primary << ' '
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@complement_bin.include?(item) ? df.complement << c_str[item] : df.complement << ' '
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#
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# bio/util/restriction_enzyme/sorted_num_array.rb - Internal data storage for Bio::RestrictionEnzyme::Range::SequenceRange
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#
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# Copyright:: Copyright (C) 2011
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# Naohisa Goto <ng@bioruby.org>
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# License:: The Ruby License
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#
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module Bio
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class RestrictionEnzyme
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# a class to store sorted numerics.
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#
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# Bio::RestrictionEnzyme internal use only.
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# Please do not create the instance outside Bio::RestrictionEnzyme.
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class SortedNumArray
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# Same usage as Array.[]
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def self.[](*args)
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a = self.new
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args.each do |elem|
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a.push elem
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end
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a
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end
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# Creates a new object
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def initialize
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@hash = {}
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#clear_cache
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end
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# initialize copy
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def initialize_copy(other)
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super(other)
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@hash = @hash.dup
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end
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# sets internal hash object
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def internal_data_hash=(h)
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#clear_cache
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@hash = h
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self
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end
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protected :internal_data_hash=
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# gets internal hash object
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def internal_data_hash
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@hash
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end
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protected :internal_data_hash
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#---
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## clear the internal cache
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#def clear_cache
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# @sorted_keys = nil
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#end
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#protected :clear_cache
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#+++
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+
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# sorted keys
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def sorted_keys
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#@sorted_keys ||= @hash.keys.sort
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#@sorted_keys
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@hash.keys.sort
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end
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private :sorted_keys
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+
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# adds a new element
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def push_element(n)
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#return if @hash.has_key?(n) #already existed; do nothing
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@hash.store(n, true)
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#if @sorted_keys then
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# if thelast = @sorted_keys[-1] and n > thelast then
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# @sorted_keys.push n
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# else
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# clear_cache
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# end
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#end
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nil
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end
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private :push_element
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+
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# adds a new element in the beginning of the array
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def unshift_element(n)
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#return if @hash.has_key?(n) #already existed; do nothing
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@hash.store(n, true)
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#if @sorted_keys then
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# if thefirst = @sorted_keys[0] and n < thefirst then
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# @sorted_keys.unshift n
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# else
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# clear_cache
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# end
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#end
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nil
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end
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private :unshift_element
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+
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# Same usage as Array#[]
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def [](*arg)
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#$stderr.puts "SortedNumArray#[]"
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sorted_keys[*arg]
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end
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# Not implemented
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def []=(*arg)
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raise NotImplementedError, 'SortedNumArray#[]= is not implemented.'
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end
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+
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# Same usage as Array#each
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def each(&block)
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sorted_keys.each(&block)
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end
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+
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# Same usage as Array#reverse_each
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def reverse_each(&block)
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sorted_keys.reverse_each(&block)
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+
end
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+
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# Same usage as Array#+, but accepts only the same classes instance.
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def +(other)
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unless other.is_a?(self.class) then
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raise TypeError, 'unsupported data type'
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end
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new_hash = @hash.merge(other.internal_data_hash)
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result = self.class.new
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result.internal_data_hash = new_hash
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result
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end
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+
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# Same usage as Array#==
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def ==(other)
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if r = super(other) then
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r
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elsif other.is_a?(self.class) then
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other.internal_data_hash == @hash
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else
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false
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end
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end
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+
|
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+
# Same usage as Array#concat
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def concat(ary)
|
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+
ary.each { |elem| push_element(elem) }
|
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self
|
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+
end
|
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+
|
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+
# Same usage as Array#push
|
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+
def push(*args)
|
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+
args.each do |elem|
|
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+
push_element(elem)
|
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+
end
|
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self
|
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+
end
|
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+
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+
# Same usage as Array#unshift
|
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+
def unshift(*arg)
|
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+
arg.reverse_each do |elem|
|
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+
unshift_element(elem)
|
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+
end
|
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+
self
|
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+
end
|
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+
|
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+
# Same usage as Array#<<
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165
|
+
def <<(elem)
|
166
|
+
push_element(elem)
|
167
|
+
self
|
168
|
+
end
|
169
|
+
|
170
|
+
# Same usage as Array#include?
|
171
|
+
def include?(elem)
|
172
|
+
@hash.has_key?(elem)
|
173
|
+
end
|
174
|
+
|
175
|
+
# Same usage as Array#first
|
176
|
+
def first
|
177
|
+
sorted_keys.first
|
178
|
+
end
|
179
|
+
|
180
|
+
# Same usage as Array#last
|
181
|
+
def last
|
182
|
+
sorted_keys.last
|
183
|
+
end
|
184
|
+
|
185
|
+
# Same usage as Array#size
|
186
|
+
def size
|
187
|
+
@hash.size
|
188
|
+
end
|
189
|
+
alias length size
|
190
|
+
|
191
|
+
# Same usage as Array#delete
|
192
|
+
def delete(elem)
|
193
|
+
#clear_cache
|
194
|
+
@hash.delete(elem) ? elem : nil
|
195
|
+
end
|
196
|
+
|
197
|
+
# Does nothing
|
198
|
+
def sort!(&block)
|
199
|
+
# does nothing
|
200
|
+
self
|
201
|
+
end
|
202
|
+
|
203
|
+
# Does nothing
|
204
|
+
def uniq!
|
205
|
+
# does nothing
|
206
|
+
self
|
207
|
+
end
|
208
|
+
|
209
|
+
# Converts to an array
|
210
|
+
def to_a
|
211
|
+
#sorted_keys.dup
|
212
|
+
sorted_keys
|
213
|
+
end
|
214
|
+
end #class SortedNumArray
|
215
|
+
|
216
|
+
end #class RestrictionEnzyme
|
217
|
+
end #module Bio
|
218
|
+
|
219
|
+
|
data/lib/bio/version.rb
CHANGED
@@ -10,7 +10,7 @@
|
|
10
10
|
module Bio
|
11
11
|
|
12
12
|
# BioRuby version (Array containing Integer)
|
13
|
-
BIORUBY_VERSION = [1, 4,
|
13
|
+
BIORUBY_VERSION = [1, 4, 2].extend(Comparable).freeze
|
14
14
|
|
15
15
|
# Extra version specifier (String or nil).
|
16
16
|
# Existance of the value indicates pre-release version or modified version.
|
@@ -0,0 +1,4403 @@
|
|
1
|
+
#
|
2
|
+
# = sample/test_restriction_enzyme_long.rb - Benchmark tests for Bio::RestrictionEnzyme::Analysis.cut for long sequences
|
3
|
+
#
|
4
|
+
# Copyright:: Copyright (C) 2011
|
5
|
+
# Naohisa Goto <ng@bioruby.org>
|
6
|
+
# License:: The Ruby License
|
7
|
+
#
|
8
|
+
# Acknowledgements: The idea of the test is based on the issue report
|
9
|
+
# https://github.com/bioruby/bioruby/issues/10
|
10
|
+
# posted by ray1729 (https://github.com/ray1729).
|
11
|
+
#
|
12
|
+
|
13
|
+
require 'test/unit'
|
14
|
+
require 'benchmark'
|
15
|
+
require 'bio'
|
16
|
+
|
17
|
+
entry = Bio::TogoWS::REST.entry('genbank', 'BA000007.2')
|
18
|
+
EcoliO157H7Seq = Bio::GenBank.new(entry).naseq.freeze
|
19
|
+
|
20
|
+
module TestRestrictionEnzymeAnalysisCutLong
|
21
|
+
|
22
|
+
# dummy benchmarch class
|
23
|
+
class DummyBench
|
24
|
+
def report(str); yield; end
|
25
|
+
end
|
26
|
+
|
27
|
+
module HelperMethods
|
28
|
+
def _truncate_cut_ranges(cut_ranges, len)
|
29
|
+
limit = len - 1
|
30
|
+
ret = cut_ranges.collect do |a|
|
31
|
+
if a[0] > limit || a[2] > limit then
|
32
|
+
nil
|
33
|
+
else
|
34
|
+
a.collect { |pos| pos > limit ? limit : pos }
|
35
|
+
end
|
36
|
+
end
|
37
|
+
ret.compact!
|
38
|
+
if last_a = ret[-1] then
|
39
|
+
last_a[1] = limit
|
40
|
+
last_a[3] = limit
|
41
|
+
end
|
42
|
+
ret
|
43
|
+
end
|
44
|
+
|
45
|
+
def _collect_cut_ranges(cuts)
|
46
|
+
cuts.collect do |f|
|
47
|
+
[ f.p_left, f.p_right, f.c_left, f.c_right ]
|
48
|
+
end
|
49
|
+
end
|
50
|
+
|
51
|
+
def _test_by_size(len, bench = DummyBench.new)
|
52
|
+
cuts = nil
|
53
|
+
bench.report("#{self.class::TestLabel} #{len}") {
|
54
|
+
cuts = _cut(self.class::SampleSequence[0, len])
|
55
|
+
}
|
56
|
+
cut_ranges = _collect_cut_ranges(cuts)
|
57
|
+
expected = _truncate_cut_ranges(self.class::SampleCutRanges, len)
|
58
|
+
assert_equal(expected, cut_ranges)
|
59
|
+
end
|
60
|
+
|
61
|
+
def test_10k_to_100k
|
62
|
+
$stderr.print "\n"
|
63
|
+
Benchmark.bm(26) do |bench|
|
64
|
+
10_000.step(100_000, 10_000) do |len|
|
65
|
+
_test_by_size(len, bench)
|
66
|
+
end
|
67
|
+
end
|
68
|
+
end
|
69
|
+
|
70
|
+
def test_100k_to_1M
|
71
|
+
$stderr.print "\n"
|
72
|
+
Benchmark.bm(26) do |bench|
|
73
|
+
100_000.step(1_000_000, 100_000) do |len|
|
74
|
+
_test_by_size(len, bench)
|
75
|
+
end
|
76
|
+
end
|
77
|
+
end
|
78
|
+
|
79
|
+
def test_1M_to_5M_and_whole
|
80
|
+
$stderr.print "\n"
|
81
|
+
Benchmark.bm(26) do |bench|
|
82
|
+
1_000_000.step(5_000_000, 1_000_000) do |len|
|
83
|
+
_test_by_size(len, bench)
|
84
|
+
end
|
85
|
+
_test_by_size(self.class::SampleSequence.length, bench)
|
86
|
+
end
|
87
|
+
end if defined? Bio::RestrictionEnzyme::SortedNumArray
|
88
|
+
|
89
|
+
def disabled_test_whole
|
90
|
+
cuts = _cut(self.class::SampleSequence)
|
91
|
+
cut_ranges = _collect_cut_ranges(cuts)
|
92
|
+
cut_ranges.each do |a|
|
93
|
+
$stderr.print " [ ", a.join(", "), " ], \n"
|
94
|
+
end
|
95
|
+
assert_equal(self.class::SampleCutRanges, cut_ranges)
|
96
|
+
end
|
97
|
+
end #module HelperMethods
|
98
|
+
|
99
|
+
|
100
|
+
class TestEcoliO157H7_BstEII < Test::Unit::TestCase
|
101
|
+
|
102
|
+
include HelperMethods
|
103
|
+
|
104
|
+
TestLabel = 'BstEII'
|
105
|
+
|
106
|
+
SampleSequence = EcoliO157H7Seq
|
107
|
+
|
108
|
+
SampleCutRanges = BstEII_WHOLE =
|
109
|
+
[ [ 0, 79, 0, 84 ],
|
110
|
+
[ 80, 4612, 85, 4617 ],
|
111
|
+
[ 4613, 13483, 4618, 13488 ],
|
112
|
+
[ 13484, 15984, 13489, 15989 ],
|
113
|
+
[ 15985, 21462, 15990, 21467 ],
|
114
|
+
[ 21463, 27326, 21468, 27331 ],
|
115
|
+
[ 27327, 30943, 27332, 30948 ],
|
116
|
+
[ 30944, 34888, 30949, 34893 ],
|
117
|
+
[ 34889, 35077, 34894, 35082 ],
|
118
|
+
[ 35078, 35310, 35083, 35315 ],
|
119
|
+
[ 35311, 36254, 35316, 36259 ],
|
120
|
+
[ 36255, 41885, 36260, 41890 ],
|
121
|
+
[ 41886, 43070, 41891, 43075 ],
|
122
|
+
[ 43071, 45689, 43076, 45694 ],
|
123
|
+
[ 45690, 52325, 45695, 52330 ],
|
124
|
+
[ 52326, 55703, 52331, 55708 ],
|
125
|
+
[ 55704, 58828, 55709, 58833 ],
|
126
|
+
[ 58829, 59178, 58834, 59183 ],
|
127
|
+
[ 59179, 72610, 59184, 72615 ],
|
128
|
+
[ 72611, 72739, 72616, 72744 ],
|
129
|
+
[ 72740, 73099, 72745, 73104 ],
|
130
|
+
[ 73100, 75123, 73105, 75128 ],
|
131
|
+
[ 75124, 77366, 75129, 77371 ],
|
132
|
+
[ 77367, 77810, 77372, 77815 ],
|
133
|
+
[ 77811, 78740, 77816, 78745 ],
|
134
|
+
[ 78741, 79717, 78746, 79722 ],
|
135
|
+
[ 79718, 82250, 79723, 82255 ],
|
136
|
+
[ 82251, 84604, 82256, 84609 ],
|
137
|
+
[ 84605, 95491, 84610, 95496 ],
|
138
|
+
[ 95492, 95785, 95497, 95790 ],
|
139
|
+
[ 95786, 95794, 95791, 95799 ],
|
140
|
+
[ 95795, 96335, 95800, 96340 ],
|
141
|
+
[ 96336, 102044, 96341, 102049 ],
|
142
|
+
[ 102045, 102541, 102050, 102546 ],
|
143
|
+
[ 102542, 103192, 102547, 103197 ],
|
144
|
+
[ 103193, 104722, 103198, 104727 ],
|
145
|
+
[ 104723, 110883, 104728, 110888 ],
|
146
|
+
[ 110884, 120090, 110889, 120095 ],
|
147
|
+
[ 120091, 120657, 120096, 120662 ],
|
148
|
+
[ 120658, 128308, 120663, 128313 ],
|
149
|
+
[ 128309, 138305, 128314, 138310 ],
|
150
|
+
[ 138306, 141147, 138311, 141152 ],
|
151
|
+
[ 141148, 143724, 141153, 143729 ],
|
152
|
+
[ 143725, 143838, 143730, 143843 ],
|
153
|
+
[ 143839, 144303, 143844, 144308 ],
|
154
|
+
[ 144304, 148199, 144309, 148204 ],
|
155
|
+
[ 148200, 149577, 148205, 149582 ],
|
156
|
+
[ 149578, 149731, 149583, 149736 ],
|
157
|
+
[ 149732, 156115, 149737, 156120 ],
|
158
|
+
[ 156116, 161126, 156121, 161131 ],
|
159
|
+
[ 161127, 162856, 161132, 162861 ],
|
160
|
+
[ 162857, 170693, 162862, 170698 ],
|
161
|
+
[ 170694, 170944, 170699, 170949 ],
|
162
|
+
[ 170945, 171201, 170950, 171206 ],
|
163
|
+
[ 171202, 173241, 171207, 173246 ],
|
164
|
+
[ 173242, 177283, 173247, 177288 ],
|
165
|
+
[ 177284, 178177, 177289, 178182 ],
|
166
|
+
[ 178178, 178781, 178183, 178786 ],
|
167
|
+
[ 178782, 181610, 178787, 181615 ],
|
168
|
+
[ 181611, 181706, 181616, 181711 ],
|
169
|
+
[ 181707, 185661, 181712, 185666 ],
|
170
|
+
[ 185662, 193407, 185667, 193412 ],
|
171
|
+
[ 193408, 195511, 193413, 195516 ],
|
172
|
+
[ 195512, 195754, 195517, 195759 ],
|
173
|
+
[ 195755, 197247, 195760, 197252 ],
|
174
|
+
[ 197248, 200659, 197253, 200664 ],
|
175
|
+
[ 200660, 201820, 200665, 201825 ],
|
176
|
+
[ 201821, 202300, 201826, 202305 ],
|
177
|
+
[ 202301, 202686, 202306, 202691 ],
|
178
|
+
[ 202687, 206289, 202692, 206294 ],
|
179
|
+
[ 206290, 206466, 206295, 206471 ],
|
180
|
+
[ 206467, 207011, 206472, 207016 ],
|
181
|
+
[ 207012, 208159, 207017, 208164 ],
|
182
|
+
[ 208160, 209976, 208165, 209981 ],
|
183
|
+
[ 209977, 210078, 209982, 210083 ],
|
184
|
+
[ 210079, 211485, 210084, 211490 ],
|
185
|
+
[ 211486, 212377, 211491, 212382 ],
|
186
|
+
[ 212378, 213569, 212383, 213574 ],
|
187
|
+
[ 213570, 216005, 213575, 216010 ],
|
188
|
+
[ 216006, 220098, 216011, 220103 ],
|
189
|
+
[ 220099, 224063, 220104, 224068 ],
|
190
|
+
[ 224064, 228604, 224069, 228609 ],
|
191
|
+
[ 228605, 239993, 228610, 239998 ],
|
192
|
+
[ 239994, 247914, 239999, 247919 ],
|
193
|
+
[ 247915, 251579, 247920, 251584 ],
|
194
|
+
[ 251580, 257092, 251585, 257097 ],
|
195
|
+
[ 257093, 261621, 257098, 261626 ],
|
196
|
+
[ 261622, 263030, 261627, 263035 ],
|
197
|
+
[ 263031, 265084, 263036, 265089 ],
|
198
|
+
[ 265085, 265243, 265090, 265248 ],
|
199
|
+
[ 265244, 265534, 265249, 265539 ],
|
200
|
+
[ 265535, 266117, 265540, 266122 ],
|
201
|
+
[ 266118, 274428, 266123, 274433 ],
|
202
|
+
[ 274429, 282285, 274434, 282290 ],
|
203
|
+
[ 282286, 286948, 282291, 286953 ],
|
204
|
+
[ 286949, 292547, 286954, 292552 ],
|
205
|
+
[ 292548, 297678, 292553, 297683 ],
|
206
|
+
[ 297679, 308161, 297684, 308166 ],
|
207
|
+
[ 308162, 308706, 308167, 308711 ],
|
208
|
+
[ 308707, 313482, 308712, 313487 ],
|
209
|
+
[ 313483, 337118, 313488, 337123 ],
|
210
|
+
[ 337119, 337935, 337124, 337940 ],
|
211
|
+
[ 337936, 338781, 337941, 338786 ],
|
212
|
+
[ 338782, 339493, 338787, 339498 ],
|
213
|
+
[ 339494, 341025, 339499, 341030 ],
|
214
|
+
[ 341026, 344424, 341031, 344429 ],
|
215
|
+
[ 344425, 348384, 344430, 348389 ],
|
216
|
+
[ 348385, 354781, 348390, 354786 ],
|
217
|
+
[ 354782, 356692, 354787, 356697 ],
|
218
|
+
[ 356693, 357008, 356698, 357013 ],
|
219
|
+
[ 357009, 357305, 357014, 357310 ],
|
220
|
+
[ 357306, 357328, 357311, 357333 ],
|
221
|
+
[ 357329, 358126, 357334, 358131 ],
|
222
|
+
[ 358127, 359472, 358132, 359477 ],
|
223
|
+
[ 359473, 362160, 359478, 362165 ],
|
224
|
+
[ 362161, 365395, 362166, 365400 ],
|
225
|
+
[ 365396, 365704, 365401, 365709 ],
|
226
|
+
[ 365705, 381746, 365710, 381751 ],
|
227
|
+
[ 381747, 381994, 381752, 381999 ],
|
228
|
+
[ 381995, 383335, 382000, 383340 ],
|
229
|
+
[ 383336, 385141, 383341, 385146 ],
|
230
|
+
[ 385142, 390171, 385147, 390176 ],
|
231
|
+
[ 390172, 392764, 390177, 392769 ],
|
232
|
+
[ 392765, 394338, 392770, 394343 ],
|
233
|
+
[ 394339, 394686, 394344, 394691 ],
|
234
|
+
[ 394687, 398703, 394692, 398708 ],
|
235
|
+
[ 398704, 404095, 398709, 404100 ],
|
236
|
+
[ 404096, 408361, 404101, 408366 ],
|
237
|
+
[ 408362, 413032, 408367, 413037 ],
|
238
|
+
[ 413033, 414563, 413038, 414568 ],
|
239
|
+
[ 414564, 416901, 414569, 416906 ],
|
240
|
+
[ 416902, 417419, 416907, 417424 ],
|
241
|
+
[ 417420, 421777, 417425, 421782 ],
|
242
|
+
[ 421778, 423748, 421783, 423753 ],
|
243
|
+
[ 423749, 431903, 423754, 431908 ],
|
244
|
+
[ 431904, 440000, 431909, 440005 ],
|
245
|
+
[ 440001, 448040, 440006, 448045 ],
|
246
|
+
[ 448041, 452994, 448046, 452999 ],
|
247
|
+
[ 452995, 453075, 453000, 453080 ],
|
248
|
+
[ 453076, 454950, 453081, 454955 ],
|
249
|
+
[ 454951, 455888, 454956, 455893 ],
|
250
|
+
[ 455889, 460160, 455894, 460165 ],
|
251
|
+
[ 460161, 463076, 460166, 463081 ],
|
252
|
+
[ 463077, 465003, 463082, 465008 ],
|
253
|
+
[ 465004, 466828, 465009, 466833 ],
|
254
|
+
[ 466829, 467686, 466834, 467691 ],
|
255
|
+
[ 467687, 468596, 467692, 468601 ],
|
256
|
+
[ 468597, 479953, 468602, 479958 ],
|
257
|
+
[ 479954, 480538, 479959, 480543 ],
|
258
|
+
[ 480539, 482869, 480544, 482874 ],
|
259
|
+
[ 482870, 489378, 482875, 489383 ],
|
260
|
+
[ 489379, 492241, 489384, 492246 ],
|
261
|
+
[ 492242, 495406, 492247, 495411 ],
|
262
|
+
[ 495407, 495712, 495412, 495717 ],
|
263
|
+
[ 495713, 497829, 495718, 497834 ],
|
264
|
+
[ 497830, 501698, 497835, 501703 ],
|
265
|
+
[ 501699, 504565, 501704, 504570 ],
|
266
|
+
[ 504566, 505105, 504571, 505110 ],
|
267
|
+
[ 505106, 508452, 505111, 508457 ],
|
268
|
+
[ 508453, 515947, 508458, 515952 ],
|
269
|
+
[ 515948, 519141, 515953, 519146 ],
|
270
|
+
[ 519142, 519398, 519147, 519403 ],
|
271
|
+
[ 519399, 521386, 519404, 521391 ],
|
272
|
+
[ 521387, 526115, 521392, 526120 ],
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[ 4904985, 4914224, 4904990, 4914229 ],
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1579
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[ 4914225, 4916537, 4914230, 4916542 ],
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1580
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[ 4916538, 4919908, 4916543, 4919913 ],
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1581
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[ 4919909, 4926663, 4919914, 4926668 ],
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1582
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[ 4926664, 4929329, 4926669, 4929334 ],
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1583
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[ 4929330, 4930673, 4929335, 4930678 ],
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1584
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[ 4930674, 4930954, 4930679, 4930959 ],
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1585
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[ 4930955, 4931594, 4930960, 4931599 ],
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1586
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[ 4931595, 4937282, 4931600, 4937287 ],
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1587
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[ 4937283, 4939667, 4937288, 4939672 ],
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1588
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[ 4939668, 4941837, 4939673, 4941842 ],
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1589
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[ 4941838, 4947030, 4941843, 4947035 ],
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1590
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[ 4947031, 4951071, 4947036, 4951076 ],
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1591
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[ 4951072, 4953999, 4951077, 4954004 ],
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1592
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[ 4954000, 4955481, 4954005, 4955486 ],
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1593
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[ 4955482, 4959224, 4955487, 4959229 ],
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1594
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[ 4959225, 4974624, 4959230, 4974629 ],
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1595
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[ 4974625, 4977429, 4974630, 4977434 ],
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1596
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[ 4977430, 4984448, 4977435, 4984453 ],
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1597
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[ 4984449, 4986670, 4984454, 4986675 ],
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1598
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[ 4986671, 4992038, 4986676, 4992043 ],
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1599
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[ 4992039, 4993811, 4992044, 4993816 ],
|
1600
|
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[ 4993812, 4995631, 4993817, 4995636 ],
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1601
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[ 4995632, 4996624, 4995637, 4996629 ],
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1602
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[ 4996625, 4996668, 4996630, 4996673 ],
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1603
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[ 4996669, 4998818, 4996674, 4998823 ],
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1604
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[ 4998819, 5004186, 4998824, 5004191 ],
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1605
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[ 5004187, 5013598, 5004192, 5013603 ],
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1606
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[ 5013599, 5016180, 5013604, 5016185 ],
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1607
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[ 5016181, 5018455, 5016186, 5018460 ],
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1608
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[ 5018456, 5026770, 5018461, 5026775 ],
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1609
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[ 5026771, 5028841, 5026776, 5028846 ],
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1610
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[ 5028842, 5031862, 5028847, 5031867 ],
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1611
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[ 5031863, 5036331, 5031868, 5036336 ],
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1612
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[ 5036332, 5037861, 5036337, 5037866 ],
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1613
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[ 5037862, 5038887, 5037867, 5038892 ],
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1614
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[ 5038888, 5040440, 5038893, 5040445 ],
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1615
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[ 5040441, 5042902, 5040446, 5042907 ],
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1616
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[ 5042903, 5044827, 5042908, 5044832 ],
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1617
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[ 5044828, 5050524, 5044833, 5050529 ],
|
1618
|
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[ 5050525, 5053866, 5050530, 5053871 ],
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1619
|
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[ 5053867, 5054707, 5053872, 5054712 ],
|
1620
|
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[ 5054708, 5055021, 5054713, 5055026 ],
|
1621
|
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[ 5055022, 5057873, 5055027, 5057878 ],
|
1622
|
+
[ 5057874, 5059734, 5057879, 5059739 ],
|
1623
|
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[ 5059735, 5061548, 5059740, 5061553 ],
|
1624
|
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[ 5061549, 5063342, 5061554, 5063347 ],
|
1625
|
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[ 5063343, 5064119, 5063348, 5064124 ],
|
1626
|
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[ 5064120, 5064638, 5064125, 5064643 ],
|
1627
|
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[ 5064639, 5068774, 5064644, 5068779 ],
|
1628
|
+
[ 5068775, 5069157, 5068780, 5069162 ],
|
1629
|
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[ 5069158, 5069375, 5069163, 5069380 ],
|
1630
|
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[ 5069376, 5071533, 5069381, 5071538 ],
|
1631
|
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[ 5071534, 5072259, 5071539, 5072264 ],
|
1632
|
+
[ 5072260, 5072332, 5072265, 5072337 ],
|
1633
|
+
[ 5072333, 5074288, 5072338, 5074293 ],
|
1634
|
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[ 5074289, 5087508, 5074294, 5087513 ],
|
1635
|
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[ 5087509, 5088409, 5087514, 5088414 ],
|
1636
|
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[ 5088410, 5093963, 5088415, 5093968 ],
|
1637
|
+
[ 5093964, 5098261, 5093969, 5098266 ],
|
1638
|
+
[ 5098262, 5116037, 5098267, 5116042 ],
|
1639
|
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[ 5116038, 5116647, 5116043, 5116652 ],
|
1640
|
+
[ 5116648, 5119282, 5116653, 5119287 ],
|
1641
|
+
[ 5119283, 5132940, 5119288, 5132945 ],
|
1642
|
+
[ 5132941, 5133405, 5132946, 5133410 ],
|
1643
|
+
[ 5133406, 5134558, 5133411, 5134563 ],
|
1644
|
+
[ 5134559, 5138432, 5134564, 5138437 ],
|
1645
|
+
[ 5138433, 5138944, 5138438, 5138949 ],
|
1646
|
+
[ 5138945, 5139157, 5138950, 5139162 ],
|
1647
|
+
[ 5139158, 5139587, 5139163, 5139592 ],
|
1648
|
+
[ 5139588, 5142617, 5139593, 5142622 ],
|
1649
|
+
[ 5142618, 5148183, 5142623, 5148188 ],
|
1650
|
+
[ 5148184, 5148672, 5148189, 5148677 ],
|
1651
|
+
[ 5148673, 5150053, 5148678, 5150058 ],
|
1652
|
+
[ 5150054, 5151087, 5150059, 5151092 ],
|
1653
|
+
[ 5151088, 5153217, 5151093, 5153222 ],
|
1654
|
+
[ 5153218, 5154383, 5153223, 5154388 ],
|
1655
|
+
[ 5154384, 5155016, 5154389, 5155021 ],
|
1656
|
+
[ 5155017, 5156599, 5155022, 5156604 ],
|
1657
|
+
[ 5156600, 5157802, 5156605, 5157807 ],
|
1658
|
+
[ 5157803, 5157970, 5157808, 5157975 ],
|
1659
|
+
[ 5157971, 5160625, 5157976, 5160630 ],
|
1660
|
+
[ 5160626, 5162852, 5160631, 5162857 ],
|
1661
|
+
[ 5162853, 5164824, 5162858, 5164829 ],
|
1662
|
+
[ 5164825, 5171077, 5164830, 5171082 ],
|
1663
|
+
[ 5171078, 5180591, 5171083, 5180596 ],
|
1664
|
+
[ 5180592, 5188235, 5180597, 5188240 ],
|
1665
|
+
[ 5188236, 5194013, 5188241, 5194018 ],
|
1666
|
+
[ 5194014, 5200363, 5194019, 5200368 ],
|
1667
|
+
[ 5200364, 5200380, 5200369, 5200385 ],
|
1668
|
+
[ 5200381, 5212416, 5200386, 5212421 ],
|
1669
|
+
[ 5212417, 5214189, 5212422, 5214194 ],
|
1670
|
+
[ 5214190, 5218448, 5214195, 5218453 ],
|
1671
|
+
[ 5218449, 5221514, 5218454, 5221519 ],
|
1672
|
+
[ 5221515, 5222405, 5221520, 5222410 ],
|
1673
|
+
[ 5222406, 5223121, 5222411, 5223126 ],
|
1674
|
+
[ 5223122, 5225062, 5223127, 5225067 ],
|
1675
|
+
[ 5225063, 5227034, 5225068, 5227039 ],
|
1676
|
+
[ 5227035, 5237062, 5227040, 5237067 ],
|
1677
|
+
[ 5237063, 5238549, 5237068, 5238554 ],
|
1678
|
+
[ 5238550, 5239941, 5238555, 5239946 ],
|
1679
|
+
[ 5239942, 5241160, 5239947, 5241165 ],
|
1680
|
+
[ 5241161, 5245009, 5241166, 5245014 ],
|
1681
|
+
[ 5245010, 5245420, 5245015, 5245425 ],
|
1682
|
+
[ 5245421, 5246665, 5245426, 5246670 ],
|
1683
|
+
[ 5246666, 5246882, 5246671, 5246887 ],
|
1684
|
+
[ 5246883, 5252321, 5246888, 5252326 ],
|
1685
|
+
[ 5252322, 5261182, 5252327, 5261187 ],
|
1686
|
+
[ 5261183, 5273111, 5261188, 5273116 ],
|
1687
|
+
[ 5273112, 5273132, 5273117, 5273137 ],
|
1688
|
+
[ 5273133, 5273680, 5273138, 5273685 ],
|
1689
|
+
[ 5273681, 5274282, 5273686, 5274287 ],
|
1690
|
+
[ 5274283, 5277485, 5274288, 5277490 ],
|
1691
|
+
[ 5277486, 5278602, 5277491, 5278607 ],
|
1692
|
+
[ 5278603, 5286668, 5278608, 5286673 ],
|
1693
|
+
[ 5286669, 5288844, 5286674, 5288849 ],
|
1694
|
+
[ 5288845, 5295426, 5288850, 5295431 ],
|
1695
|
+
[ 5295427, 5299331, 5295432, 5299336 ],
|
1696
|
+
[ 5299332, 5299740, 5299337, 5299745 ],
|
1697
|
+
[ 5299741, 5302074, 5299746, 5302079 ],
|
1698
|
+
[ 5302075, 5304927, 5302080, 5304932 ],
|
1699
|
+
[ 5304928, 5316196, 5304933, 5316201 ],
|
1700
|
+
[ 5316197, 5321884, 5316202, 5321889 ],
|
1701
|
+
[ 5321885, 5327443, 5321890, 5327448 ],
|
1702
|
+
[ 5327444, 5333009, 5327449, 5333014 ],
|
1703
|
+
[ 5333010, 5335558, 5333015, 5335563 ],
|
1704
|
+
[ 5335559, 5337934, 5335564, 5337939 ],
|
1705
|
+
[ 5337935, 5340296, 5337940, 5340301 ],
|
1706
|
+
[ 5340297, 5342510, 5340302, 5342515 ],
|
1707
|
+
[ 5342511, 5343834, 5342516, 5343839 ],
|
1708
|
+
[ 5343835, 5359283, 5343840, 5359288 ],
|
1709
|
+
[ 5359284, 5362544, 5359289, 5362549 ],
|
1710
|
+
[ 5362545, 5375729, 5362550, 5375734 ],
|
1711
|
+
[ 5375730, 5375790, 5375735, 5375795 ],
|
1712
|
+
[ 5375791, 5377253, 5375796, 5377258 ],
|
1713
|
+
[ 5377254, 5378696, 5377259, 5378701 ],
|
1714
|
+
[ 5378697, 5382060, 5378702, 5382065 ],
|
1715
|
+
[ 5382061, 5388224, 5382066, 5388229 ],
|
1716
|
+
[ 5388225, 5391633, 5388230, 5391638 ],
|
1717
|
+
[ 5391634, 5401417, 5391639, 5401422 ],
|
1718
|
+
[ 5401418, 5406537, 5401423, 5406542 ],
|
1719
|
+
[ 5406538, 5408637, 5406543, 5408642 ],
|
1720
|
+
[ 5408638, 5417270, 5408643, 5417275 ],
|
1721
|
+
[ 5417271, 5419353, 5417276, 5419358 ],
|
1722
|
+
[ 5419354, 5420144, 5419359, 5420149 ],
|
1723
|
+
[ 5420145, 5420216, 5420150, 5420221 ],
|
1724
|
+
[ 5420217, 5420740, 5420222, 5420745 ],
|
1725
|
+
[ 5420741, 5427477, 5420746, 5427482 ],
|
1726
|
+
[ 5427478, 5429323, 5427483, 5429328 ],
|
1727
|
+
[ 5429324, 5441634, 5429329, 5441639 ],
|
1728
|
+
[ 5441635, 5448663, 5441640, 5448668 ],
|
1729
|
+
[ 5448664, 5452231, 5448669, 5452236 ],
|
1730
|
+
[ 5452232, 5458274, 5452237, 5458279 ],
|
1731
|
+
[ 5458275, 5459524, 5458280, 5459529 ],
|
1732
|
+
[ 5459525, 5468509, 5459530, 5468514 ],
|
1733
|
+
[ 5468510, 5469773, 5468515, 5469778 ],
|
1734
|
+
[ 5469774, 5475379, 5469779, 5475384 ],
|
1735
|
+
[ 5475380, 5476063, 5475385, 5476068 ],
|
1736
|
+
[ 5476064, 5477860, 5476069, 5477865 ],
|
1737
|
+
[ 5477861, 5478124, 5477866, 5478129 ],
|
1738
|
+
[ 5478125, 5478577, 5478130, 5478582 ],
|
1739
|
+
[ 5478578, 5479176, 5478583, 5479181 ],
|
1740
|
+
[ 5479177, 5483012, 5479182, 5483017 ],
|
1741
|
+
[ 5483013, 5483809, 5483018, 5483814 ],
|
1742
|
+
[ 5483810, 5495234, 5483815, 5495239 ],
|
1743
|
+
[ 5495235, 5498449, 5495240, 5498449 ]
|
1744
|
+
]
|
1745
|
+
|
1746
|
+
def _cut(seq)
|
1747
|
+
cuts = Bio::RestrictionEnzyme::Analysis.cut(seq, "BstEII",
|
1748
|
+
{:view_ranges => true})
|
1749
|
+
end
|
1750
|
+
|
1751
|
+
def test_BstEII_edge_cases
|
1752
|
+
(13481..13492).each do |len|
|
1753
|
+
_test_by_size(len)
|
1754
|
+
end
|
1755
|
+
end
|
1756
|
+
|
1757
|
+
end # class TestEcoliO157H7_BstEII
|
1758
|
+
|
1759
|
+
class TestEcoliO157H7_3enzymes < Test::Unit::TestCase
|
1760
|
+
include HelperMethods
|
1761
|
+
|
1762
|
+
TestLabel = 'SacI+EcoRI+BstEII'
|
1763
|
+
|
1764
|
+
SampleSequence = EcoliO157H7Seq
|
1765
|
+
|
1766
|
+
|
1767
|
+
SampleCutRanges = The3Enzymes_WHOLE =
|
1768
|
+
[ [ 0, 79, 0, 84 ],
|
1769
|
+
[ 80, 3858, 85, 3862 ],
|
1770
|
+
[ 3859, 4612, 3863, 4617 ],
|
1771
|
+
[ 4613, 5619, 4618, 5623 ],
|
1772
|
+
[ 5620, 7472, 5624, 7468 ],
|
1773
|
+
[ 7473, 12905, 7469, 12909 ],
|
1774
|
+
[ 12906, 13483, 12910, 13488 ],
|
1775
|
+
[ 13484, 14551, 13489, 14547 ],
|
1776
|
+
[ 14552, 15984, 14548, 15989 ],
|
1777
|
+
[ 15985, 20045, 15990, 20049 ],
|
1778
|
+
[ 20046, 21462, 20050, 21467 ],
|
1779
|
+
[ 21463, 27326, 21468, 27331 ],
|
1780
|
+
[ 27327, 30943, 27332, 30948 ],
|
1781
|
+
[ 30944, 34888, 30949, 34893 ],
|
1782
|
+
[ 34889, 35077, 34894, 35082 ],
|
1783
|
+
[ 35078, 35310, 35083, 35315 ],
|
1784
|
+
[ 35311, 36254, 35316, 36259 ],
|
1785
|
+
[ 36255, 36648, 36260, 36652 ],
|
1786
|
+
[ 36649, 36918, 36653, 36922 ],
|
1787
|
+
[ 36919, 41885, 36923, 41890 ],
|
1788
|
+
[ 41886, 43070, 41891, 43075 ],
|
1789
|
+
[ 43071, 45689, 43076, 45694 ],
|
1790
|
+
[ 45690, 48588, 45695, 48584 ],
|
1791
|
+
[ 48589, 52325, 48585, 52330 ],
|
1792
|
+
[ 52326, 54650, 52331, 54654 ],
|
1793
|
+
[ 54651, 54728, 54655, 54732 ],
|
1794
|
+
[ 54729, 55703, 54733, 55708 ],
|
1795
|
+
[ 55704, 58828, 55709, 58833 ],
|
1796
|
+
[ 58829, 59178, 58834, 59183 ],
|
1797
|
+
[ 59179, 59800, 59184, 59796 ],
|
1798
|
+
[ 59801, 61256, 59797, 61260 ],
|
1799
|
+
[ 61257, 72610, 61261, 72615 ],
|
1800
|
+
[ 72611, 72739, 72616, 72744 ],
|
1801
|
+
[ 72740, 73099, 72745, 73104 ],
|
1802
|
+
[ 73100, 75123, 73105, 75128 ],
|
1803
|
+
[ 75124, 77366, 75129, 77371 ],
|
1804
|
+
[ 77367, 77810, 77372, 77815 ],
|
1805
|
+
[ 77811, 78740, 77816, 78745 ],
|
1806
|
+
[ 78741, 79717, 78746, 79722 ],
|
1807
|
+
[ 79718, 82250, 79723, 82255 ],
|
1808
|
+
[ 82251, 84604, 82256, 84609 ],
|
1809
|
+
[ 84605, 95491, 84610, 95496 ],
|
1810
|
+
[ 95492, 95785, 95497, 95790 ],
|
1811
|
+
[ 95786, 95794, 95791, 95799 ],
|
1812
|
+
[ 95795, 96335, 95800, 96340 ],
|
1813
|
+
[ 96336, 96489, 96341, 96493 ],
|
1814
|
+
[ 96490, 101464, 96494, 101468 ],
|
1815
|
+
[ 101465, 102044, 101469, 102049 ],
|
1816
|
+
[ 102045, 102541, 102050, 102546 ],
|
1817
|
+
[ 102542, 103192, 102547, 103197 ],
|
1818
|
+
[ 103193, 103397, 103198, 103393 ],
|
1819
|
+
[ 103398, 104722, 103394, 104727 ],
|
1820
|
+
[ 104723, 106365, 104728, 106369 ],
|
1821
|
+
[ 106366, 106896, 106370, 106900 ],
|
1822
|
+
[ 106897, 107735, 106901, 107739 ],
|
1823
|
+
[ 107736, 110020, 107740, 110024 ],
|
1824
|
+
[ 110021, 110883, 110025, 110888 ],
|
1825
|
+
[ 110884, 112524, 110889, 112528 ],
|
1826
|
+
[ 112525, 113324, 112529, 113328 ],
|
1827
|
+
[ 113325, 115867, 113329, 115871 ],
|
1828
|
+
[ 115868, 117723, 115872, 117727 ],
|
1829
|
+
[ 117724, 118742, 117728, 118738 ],
|
1830
|
+
[ 118743, 120090, 118739, 120095 ],
|
1831
|
+
[ 120091, 120657, 120096, 120662 ],
|
1832
|
+
[ 120658, 128060, 120663, 128064 ],
|
1833
|
+
[ 128061, 128308, 128065, 128313 ],
|
1834
|
+
[ 128309, 136112, 128314, 136116 ],
|
1835
|
+
[ 136113, 138305, 136117, 138310 ],
|
1836
|
+
[ 138306, 138996, 138311, 139000 ],
|
1837
|
+
[ 138997, 139146, 139001, 139142 ],
|
1838
|
+
[ 139147, 141147, 139143, 141152 ],
|
1839
|
+
[ 141148, 143724, 141153, 143729 ],
|
1840
|
+
[ 143725, 143838, 143730, 143843 ],
|
1841
|
+
[ 143839, 144303, 143844, 144308 ],
|
1842
|
+
[ 144304, 148199, 144309, 148204 ],
|
1843
|
+
[ 148200, 149577, 148205, 149582 ],
|
1844
|
+
[ 149578, 149731, 149583, 149736 ],
|
1845
|
+
[ 149732, 152137, 149737, 152141 ],
|
1846
|
+
[ 152138, 156115, 152142, 156120 ],
|
1847
|
+
[ 156116, 161126, 156121, 161131 ],
|
1848
|
+
[ 161127, 162856, 161132, 162861 ],
|
1849
|
+
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4251
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[ 5171078, 5176566, 5171083, 5176570 ],
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4254
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4255
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[ 5180105, 5180591, 5180109, 5180596 ],
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4256
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[ 5184143, 5188235, 5184139, 5188240 ],
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4258
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[ 5188236, 5190430, 5188241, 5190434 ],
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4259
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[ 5190431, 5194013, 5190435, 5194018 ],
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4260
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[ 5194014, 5194634, 5194019, 5194638 ],
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4261
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[ 5194635, 5199338, 5194639, 5199342 ],
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4262
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[ 5199339, 5200363, 5199343, 5200368 ],
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4263
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[ 5200364, 5200380, 5200369, 5200385 ],
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4264
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[ 5200381, 5207919, 5200386, 5207923 ],
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4265
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[ 5207920, 5210484, 5207924, 5210480 ],
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4266
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[ 5210485, 5211327, 5210481, 5211331 ],
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4267
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[ 5211328, 5212227, 5211332, 5212231 ],
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4268
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[ 5212228, 5212416, 5212232, 5212421 ],
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4269
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[ 5212417, 5214189, 5212422, 5214194 ],
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4270
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[ 5214190, 5218448, 5214195, 5218453 ],
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4271
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[ 5218449, 5221514, 5218454, 5221519 ],
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4272
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[ 5221515, 5222166, 5221520, 5222170 ],
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4273
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[ 5222167, 5222235, 5222171, 5222239 ],
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4274
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[ 5222236, 5222405, 5222240, 5222410 ],
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4275
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[ 5222406, 5223121, 5222411, 5223126 ],
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4276
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[ 5223122, 5225062, 5223127, 5225067 ],
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4277
|
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[ 5225063, 5227034, 5225068, 5227039 ],
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4278
|
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[ 5227035, 5230060, 5227040, 5230064 ],
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4279
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[ 5230061, 5235911, 5230065, 5235915 ],
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4280
|
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[ 5235912, 5237062, 5235916, 5237067 ],
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4281
|
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[ 5237063, 5238549, 5237068, 5238554 ],
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4282
|
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[ 5238550, 5239941, 5238555, 5239946 ],
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4283
|
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[ 5239942, 5241160, 5239947, 5241165 ],
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4284
|
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[ 5241161, 5243887, 5241166, 5243891 ],
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4285
|
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[ 5243888, 5244364, 5243892, 5244368 ],
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4286
|
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[ 5244365, 5245009, 5244369, 5245014 ],
|
4287
|
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[ 5245010, 5245420, 5245015, 5245425 ],
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4288
|
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[ 5245421, 5246665, 5245426, 5246670 ],
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4289
|
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[ 5246666, 5246882, 5246671, 5246887 ],
|
4290
|
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[ 5246883, 5252321, 5246888, 5252326 ],
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4291
|
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[ 5252322, 5258113, 5252327, 5258117 ],
|
4292
|
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[ 5258114, 5259300, 5258118, 5259304 ],
|
4293
|
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[ 5259301, 5261182, 5259305, 5261187 ],
|
4294
|
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[ 5261183, 5261507, 5261188, 5261503 ],
|
4295
|
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[ 5261508, 5268860, 5261504, 5268864 ],
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4296
|
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[ 5268861, 5269941, 5268865, 5269945 ],
|
4297
|
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[ 5269942, 5270945, 5269946, 5270949 ],
|
4298
|
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[ 5270946, 5271167, 5270950, 5271171 ],
|
4299
|
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[ 5271168, 5273111, 5271172, 5273116 ],
|
4300
|
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[ 5273112, 5273132, 5273117, 5273137 ],
|
4301
|
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[ 5273133, 5273680, 5273138, 5273685 ],
|
4302
|
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[ 5273681, 5274282, 5273686, 5274287 ],
|
4303
|
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[ 5274283, 5277485, 5274288, 5277490 ],
|
4304
|
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[ 5277486, 5278602, 5277491, 5278607 ],
|
4305
|
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[ 5278603, 5279312, 5278608, 5279316 ],
|
4306
|
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[ 5279313, 5279965, 5279317, 5279969 ],
|
4307
|
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[ 5279966, 5286668, 5279970, 5286673 ],
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4308
|
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[ 5286669, 5288844, 5286674, 5288849 ],
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4309
|
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[ 5288845, 5292505, 5288850, 5292509 ],
|
4310
|
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[ 5292506, 5295145, 5292510, 5295149 ],
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4311
|
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[ 5295146, 5295426, 5295150, 5295431 ],
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4312
|
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[ 5295427, 5296411, 5295432, 5296407 ],
|
4313
|
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[ 5296412, 5299331, 5296408, 5299336 ],
|
4314
|
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[ 5299332, 5299740, 5299337, 5299745 ],
|
4315
|
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[ 5299741, 5302074, 5299746, 5302079 ],
|
4316
|
+
[ 5302075, 5304927, 5302080, 5304932 ],
|
4317
|
+
[ 5304928, 5309929, 5304933, 5309925 ],
|
4318
|
+
[ 5309930, 5311027, 5309926, 5311023 ],
|
4319
|
+
[ 5311028, 5313142, 5311024, 5313138 ],
|
4320
|
+
[ 5313143, 5313612, 5313139, 5313616 ],
|
4321
|
+
[ 5313613, 5316196, 5313617, 5316201 ],
|
4322
|
+
[ 5316197, 5320424, 5316202, 5320428 ],
|
4323
|
+
[ 5320425, 5321884, 5320429, 5321889 ],
|
4324
|
+
[ 5321885, 5327443, 5321890, 5327448 ],
|
4325
|
+
[ 5327444, 5333009, 5327449, 5333014 ],
|
4326
|
+
[ 5333010, 5335558, 5333015, 5335563 ],
|
4327
|
+
[ 5335559, 5337934, 5335564, 5337939 ],
|
4328
|
+
[ 5337935, 5340296, 5337940, 5340301 ],
|
4329
|
+
[ 5340297, 5341322, 5340302, 5341326 ],
|
4330
|
+
[ 5341323, 5342510, 5341327, 5342515 ],
|
4331
|
+
[ 5342511, 5343834, 5342516, 5343839 ],
|
4332
|
+
[ 5343835, 5351733, 5343840, 5351737 ],
|
4333
|
+
[ 5351734, 5355838, 5351738, 5355842 ],
|
4334
|
+
[ 5355839, 5359283, 5355843, 5359288 ],
|
4335
|
+
[ 5359284, 5362430, 5359289, 5362434 ],
|
4336
|
+
[ 5362431, 5362544, 5362435, 5362549 ],
|
4337
|
+
[ 5362545, 5364468, 5362550, 5364472 ],
|
4338
|
+
[ 5364469, 5369245, 5364473, 5369241 ],
|
4339
|
+
[ 5369246, 5375729, 5369242, 5375734 ],
|
4340
|
+
[ 5375730, 5375790, 5375735, 5375795 ],
|
4341
|
+
[ 5375791, 5377253, 5375796, 5377258 ],
|
4342
|
+
[ 5377254, 5378696, 5377259, 5378701 ],
|
4343
|
+
[ 5378697, 5382060, 5378702, 5382065 ],
|
4344
|
+
[ 5382061, 5388003, 5382066, 5388007 ],
|
4345
|
+
[ 5388004, 5388224, 5388008, 5388229 ],
|
4346
|
+
[ 5388225, 5389155, 5388230, 5389159 ],
|
4347
|
+
[ 5389156, 5391633, 5389160, 5391638 ],
|
4348
|
+
[ 5391634, 5399712, 5391639, 5399716 ],
|
4349
|
+
[ 5399713, 5401417, 5399717, 5401422 ],
|
4350
|
+
[ 5401418, 5406297, 5401423, 5406301 ],
|
4351
|
+
[ 5406298, 5406537, 5406302, 5406542 ],
|
4352
|
+
[ 5406538, 5406850, 5406543, 5406854 ],
|
4353
|
+
[ 5406851, 5408637, 5406855, 5408642 ],
|
4354
|
+
[ 5408638, 5410093, 5408643, 5410097 ],
|
4355
|
+
[ 5410094, 5417270, 5410098, 5417275 ],
|
4356
|
+
[ 5417271, 5419353, 5417276, 5419358 ],
|
4357
|
+
[ 5419354, 5420144, 5419359, 5420149 ],
|
4358
|
+
[ 5420145, 5420216, 5420150, 5420221 ],
|
4359
|
+
[ 5420217, 5420740, 5420222, 5420745 ],
|
4360
|
+
[ 5420741, 5423081, 5420746, 5423085 ],
|
4361
|
+
[ 5423082, 5424075, 5423086, 5424079 ],
|
4362
|
+
[ 5424076, 5425137, 5424080, 5425141 ],
|
4363
|
+
[ 5425138, 5427477, 5425142, 5427482 ],
|
4364
|
+
[ 5427478, 5429323, 5427483, 5429328 ],
|
4365
|
+
[ 5429324, 5429631, 5429329, 5429635 ],
|
4366
|
+
[ 5429632, 5432849, 5429636, 5432853 ],
|
4367
|
+
[ 5432850, 5432874, 5432854, 5432878 ],
|
4368
|
+
[ 5432875, 5440584, 5432879, 5440588 ],
|
4369
|
+
[ 5440585, 5440833, 5440589, 5440837 ],
|
4370
|
+
[ 5440834, 5441634, 5440838, 5441639 ],
|
4371
|
+
[ 5441635, 5446602, 5441640, 5446606 ],
|
4372
|
+
[ 5446603, 5448663, 5446607, 5448668 ],
|
4373
|
+
[ 5448664, 5452231, 5448669, 5452236 ],
|
4374
|
+
[ 5452232, 5453350, 5452237, 5453354 ],
|
4375
|
+
[ 5453351, 5455164, 5453355, 5455168 ],
|
4376
|
+
[ 5455165, 5458274, 5455169, 5458279 ],
|
4377
|
+
[ 5458275, 5459524, 5458280, 5459529 ],
|
4378
|
+
[ 5459525, 5468509, 5459530, 5468514 ],
|
4379
|
+
[ 5468510, 5469773, 5468515, 5469778 ],
|
4380
|
+
[ 5469774, 5474040, 5469779, 5474044 ],
|
4381
|
+
[ 5474041, 5475379, 5474045, 5475384 ],
|
4382
|
+
[ 5475380, 5476063, 5475385, 5476068 ],
|
4383
|
+
[ 5476064, 5477860, 5476069, 5477865 ],
|
4384
|
+
[ 5477861, 5478124, 5477866, 5478129 ],
|
4385
|
+
[ 5478125, 5478577, 5478130, 5478582 ],
|
4386
|
+
[ 5478578, 5479176, 5478583, 5479181 ],
|
4387
|
+
[ 5479177, 5483012, 5479182, 5483017 ],
|
4388
|
+
[ 5483013, 5483809, 5483018, 5483814 ],
|
4389
|
+
[ 5483810, 5490967, 5483815, 5490963 ],
|
4390
|
+
[ 5490968, 5491739, 5490964, 5491743 ],
|
4391
|
+
[ 5491740, 5495234, 5491744, 5495239 ],
|
4392
|
+
[ 5495235, 5498449, 5495240, 5498449 ]
|
4393
|
+
]
|
4394
|
+
|
4395
|
+
def _cut(seq)
|
4396
|
+
cuts = Bio::RestrictionEnzyme::Analysis.cut(seq,
|
4397
|
+
"SacI", "EcoRI", "BstEII",
|
4398
|
+
{:view_ranges => true})
|
4399
|
+
end
|
4400
|
+
end #TestEcoliO157H7_3enzymes
|
4401
|
+
|
4402
|
+
|
4403
|
+
end #module TestRestrictionEnzymeAnalysisCutLong
|