wwood-bioruby 1.2.11

data/lib/bio/util/restriction_enzyme/single_strand_complement.rb

@@ -0,0 +1,23 @@
+#
+# bio/util/restriction_enzyme/single_strand_complement.rb - Single strand restriction enzyme sequence in complement orientation
+#
+# Author::    Trevor Wennblom  <mailto:trevor@corevx.com>
+# Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
+# License::   The Ruby License
+#
+#  $Id: single_strand_complement.rb,v 1.5 2007/07/16 19:28:48 k Exp $
+#
+
+require 'bio/util/restriction_enzyme'
+
+module Bio
+class RestrictionEnzyme
+
+# A single strand of restriction enzyme sequence pattern with a 3' to 5' orientation.
+#
+class SingleStrandComplement < SingleStrand
+  # Orientation of the strand, 3' to 5'
+  def orientation; [3, 5]; end
+end # SingleStrandComplement
+end # RestrictionEnzyme
+end # Bio

data/lib/bio/util/restriction_enzyme/string_formatting.rb

@@ -0,0 +1,111 @@
+#
+# bio/util/restriction_enzyme/string_formatting.rb - Useful functions for string manipulation
+#
+# Author::    Trevor Wennblom  <mailto:trevor@corevx.com>
+# Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
+# License::   The Ruby License
+#
+#  $Id: string_formatting.rb,v 1.6 2007/07/16 19:28:48 k Exp $
+#
+
+require 'bio/util/restriction_enzyme'
+
+module Bio
+class RestrictionEnzyme
+
+module StringFormatting
+  include CutSymbol
+  extend CutSymbol
+
+  # Return the sequence with spacing for alignment.  Does not add whitespace
+  # around cut symbols.
+  #
+  # Example:
+  #   pattern = 'n^ng^arraxt^n'
+  #   add_spacing( pattern )      # => "n^n g^a r r a x t^n"
+  #
+  # ---
+  # *Arguments*
+  # * +seq+: sequence with cut symbols
+  # * +cs+: (_optional_) Cut symbol along the string.  The reason this is
+  #   definable outside of CutSymbol is that this is a utility function used
+  #   to form vertical and horizontal cuts such as:
+  #
+  #     a|t g c
+  #      +---+
+  #     t a c|g
+  # *Returns*:: +String+ sequence with single character distance between bases
+  def add_spacing( seq, cs = cut_symbol )
+    str = ''
+    flag = false
+    seq.each_byte do |c|
+      c = c.chr
+      if c == cs
+        str += c
+        flag = false
+      elsif flag
+        str += ' ' + c
+      else
+        str += c
+        flag = true
+      end
+    end
+    str
+  end
+
+  # Remove extraneous nucleic acid wildcards ('n' padding) from the
+  # left and right sides
+  #
+  # ---
+  # *Arguments*
+  # * +s+: sequence with extraneous 'n' padding
+  # *Returns*:: +String+ sequence without 'n' padding on the sides
+  def strip_padding( s )
+    if s[0].chr == 'n'
+      s =~ %r{(n+)(.+)}
+      s = $2
+    end
+    if s[-1].chr == 'n'
+      s =~ %r{(.+?)(n+)$}
+      s = $1
+    end
+    s
+  end
+
+  # Remove extraneous nucleic acid wildcards ('n' padding) from the
+  # left and right sides and remove cut symbols
+  #
+  # ---
+  # *Arguments*
+  # * +s+: sequence with extraneous 'n' padding and cut symbols
+  # *Returns*:: +String+ sequence without 'n' padding on the sides or cut symbols
+  def strip_cuts_and_padding( s )
+    strip_padding( s.tr(cut_symbol, '') )
+  end
+
+  # Return the 'n' padding on the left side of the strand
+  #
+  # ---
+  # *Arguments*
+  # * +s+: sequence with extraneous 'n' padding on the left side of the strand
+  # *Returns*:: +String+ the 'n' padding from the left side
+  def left_padding( s )
+    s =~ %r{^n+}
+    ret = $&
+    ret ? ret : ''  # Don't pass nil values
+  end
+
+  # Return the 'n' padding on the right side of the strand
+  #
+  # ---
+  # *Arguments*
+  # * +s+: sequence with extraneous 'n' padding on the right side of the strand
+  # *Returns*:: +String+ the 'n' padding from the right side
+  def right_padding( s )
+    s =~ %r{n+$}
+    ret = $&
+    ret ? ret : ''  # Don't pass nil values
+  end
+end # StringFormatting
+end # RestrictionEnzyme
+end # Bio

data/lib/bio/util/sirna.rb

@@ -0,0 +1,288 @@
+#
+# = bio/util/sirna.rb - Class for designing small inhibitory RNAs
+#
+# Copyright::   Copyright (C) 2004, 2005
+#               Itoshi NIKAIDO <dritoshi@gmail.com>
+# License::     The Ruby License
+#
+# $Id: sirna.rb,v 1.11 2007/04/05 23:35:41 trevor Exp $
+#
+# == Bio::SiRNA - Designing siRNA.
+#
+# This class implements the selection rules described by Kumiko Ui-Tei
+# et al. (2004) and Reynolds et al. (2004).
+#
+# == Example
+#
+#  seq = Bio::Sequence::NA.new(ARGF.read)
+#  
+#  sirna = Bio::SiRNA.new(seq)
+#  pairs = sirna.design
+#  
+#  pairs.each do |pair|
+#    puts pair.report
+#    shrna = Bio::SiRNA::ShRNA.new(pair)
+#    shrna.design
+#    puts shrna.report
+#    
+#    puts shrna.top_strand.dna
+#    puts shrna.bottom_strand.dna
+#  end
+#
+# == References
+# 
+# * Kumiko Ui-Tei et al.  Guidelines for the selection of highly effective
+#   siRNA sequences for mammalian and chick RNA interference.
+#   Nucl. Acids. Res. 2004 32: 936-948.
+#    
+# * Angela Reynolds et al.  Rational siRNA design for RNA interference.
+#   Nature Biotech. 2004 22: 326-330.
+#
+
+require 'bio/sequence'
+
+module Bio
+
+  # = Bio::SiRNA
+  # Designing siRNA.
+  #
+  # This class implements the selection rules described by Kumiko Ui-Tei
+  # et al. (2004) and Reynolds et al. (2004).
+  class SiRNA
+
+    # A parameter of size of antisense.
+    attr_accessor :antisense_size
+
+    # A parameter of maximal %GC.
+    attr_accessor :max_gc_percent
+
+    # A parameter of minimum %GC.
+    attr_accessor :min_gc_percent
+
+    # Input is a Bio::Sequence::NA object (the target sequence).
+    # Output is a list of Bio::SiRNA::Pair object.
+    def initialize(seq, antisense_size = 21, max_gc_percent = 60.0, min_gc_percent = 40.0)
+      @seq = seq.rna!
+      @pairs = Array.new
+      @antisense_size = antisense_size
+      @max_gc_percent = max_gc_percent
+      @min_gc_percent = min_gc_percent
+    end
+
+    # Ui-Tei's rule.
+    def uitei?(target)
+      return false unless /^.{2}[GC]/i =~ target
+      return false unless /[AU].{2}$/i =~ target
+      return false if     /[GC]{9}/i   =~ target
+
+      one_third  = target.size * 1 / 3
+      start_pos  = @target_size - one_third - 1
+      remain_seq = target.subseq(start_pos, @target_size - 2)
+      au_number  = remain_seq.scan(/[AU]/i).size
+      return false if au_number < 5
+  
+      return true
+    end
+
+    # Reynolds' rule.
+    def reynolds?(target)
+      return false if /[GC]{9}/i =~ target
+      return false unless /^.{4}A.{6}U.{2}[AUC].{5}[AU].{2}$/i =~ target
+      return true
+    end
+
+    # same as design('uitei').
+    def uitei
+      design('uitei')
+    end
+
+    # same as design('reynolds').
+    def reynolds
+      design('reynolds')
+    end
+
+    #  rule can be one of 'uitei' (default) and 'reynolds'.
+    def design(rule = 'uitei')
+      @target_size = @antisense_size + 2
+
+      target_start = 0
+      @seq.window_search(@target_size) do |target|
+        antisense = target.subseq(1, @target_size - 2).complement.rna
+        sense     = target.subseq(3, @target_size)
+
+        target_start += 1
+        target_stop  = target_start + @target_size
+
+        antisense_gc_percent = antisense.gc_percent
+        next if antisense_gc_percent > @max_gc_percent
+        next if antisense_gc_percent < @min_gc_percent
+        
+        case rule
+        when 'uitei'
+          next unless uitei?(target)
+        when 'reynolds'
+          next unless reynolds?(target)
+        else
+          raise NotImplementedError
+        end
+
+        pair = Bio::SiRNA::Pair.new(target, sense, antisense, target_start, target_stop, rule, antisense_gc_percent)
+        @pairs.push(pair)
+      end
+      return @pairs
+    end
+
+    # = Bio::SiRNA::Pair
+    class Pair
+
+      attr_accessor :target
+
+      attr_accessor :sense
+
+      attr_accessor :antisense
+
+      attr_accessor :start
+
+      attr_accessor :stop
+
+      attr_accessor :rule
+
+      attr_accessor :gc_percent
+
+      def initialize(target, sense, antisense, start, stop, rule, gc_percent)
+        @target     = target
+        @sense      = sense
+        @antisense  = antisense
+        @start      = start
+        @stop       = stop
+        @rule       = rule
+        @gc_percent = gc_percent
+      end
+
+      # human readable report
+      def report
+        report =  "### siRNA\n"
+        report << 'Start: ' + @start.to_s + "\n"
+        report << 'Stop:  ' + @stop.to_s  + "\n"
+        report << 'Rule:  ' + @rule.to_s  + "\n"
+        report << 'GC %:  ' + @gc_percent.to_s  + "\n"
+        report << 'Target:    '        + @target.upcase + "\n"
+        report << 'Sense:     ' + '  ' + @sense.upcase  + "\n"
+        report << 'Antisense: '        + @antisense.reverse.upcase + "\n"
+      end
+
+      # computer parsable report
+      #def to_s
+      #  [ @antisense, @start, @stop ].join("\t")
+      #end
+
+    end # class Pair
+
+
+    # = Bio::SiRNA::ShRNA
+    # Designing shRNA.
+    class ShRNA
+
+      # Bio::Sequence::NA
+      attr_accessor :top_strand
+
+      # Bio::Sequence::NA
+      attr_accessor :bottom_strand
+
+      # Input is a Bio::SiRNA::Pair object (the target sequence).    
+      def initialize(pair)
+        @pair = pair
+      end
+
+      # only the 'BLOCK-iT' rule is implemented for now.
+      def design(method = 'BLOCK-iT')
+        case method
+        when 'BLOCK-iT'
+          block_it
+        else
+          raise NotImplementedError
+        end
+      end
+
+
+      # same as design('BLOCK-iT').
+      # method can be one of 'piGENE' (default) and 'BLOCK-iT'.
+      def block_it(method = 'piGENE')
+        top = Bio::Sequence::NA.new('CACC') # top_strand_shrna_overhang
+        bot = Bio::Sequence::NA.new('AAAA') # bottom_strand_shrna_overhang
+        fwd = @pair.sense
+        rev = @pair.sense.complement
+
+        case method
+        when 'BLOCK-iT'
+          # From BLOCK-iT's manual
+          loop_fwd = Bio::Sequence::NA.new('CGAA')
+          loop_rev = loop_fwd.complement
+        when 'piGENE'
+          # From piGENE document
+          loop_fwd = Bio::Sequence::NA.new('GTGTGCTGTCC')
+          loop_rev = loop_fwd.complement
+        else
+          raise NotImplementedError
+        end
+
+        if /^G/i =~ fwd
+          @top_strand    = top + fwd + loop_fwd + rev
+          @bottom_strand = bot + fwd + loop_rev + rev
+        else
+          @top_strand    = top + 'G' + fwd + loop_fwd + rev
+          @bottom_strand = bot + fwd + loop_rev + rev + 'C'
+        end
+      end
+      
+      # human readable report
+      def report
+        report = "### shRNA\n"
+        report << "Top strand shRNA (#{@top_strand.length} nt):\n"
+        report << "  5'-#{@top_strand.upcase}-3'\n"
+        report << "Bottom strand shRNA (#{@bottom_strand.length} nt):\n"
+        report << "      3'-#{@bottom_strand.reverse.upcase}-5'\n"
+      end
+
+    end # class ShRNA
+
+  end # class SiRNA
+
+end # module Bio
+
+
+if __FILE__ == $0
+  
+  seq = Bio::Sequence::NA.new(ARGF.read)
+
+  sirna = Bio::SiRNA.new(seq)
+  pairs = sirna.design # or .design('uitei') or .uitei or .reynolds
+
+  pairs.each do |pair|
+    puts pair.report
+
+    shrna = Bio::SiRNA::ShRNA.new(pair)
+    shrna.design # or .design('BLOCK-iT') or .block_it
+    puts shrna.report
+
+    puts "# as DNA"
+    puts shrna.top_strand.dna
+    puts shrna.bottom_strand.dna
+  end
+
+end  
+
+=begin
+
+= ChangeLog
+
+  2005/03/21 Itoshi NIKAIDO <itoshi.nikaido@nifty.com>
+  Bio::SiRNA#ShRNA_designer method was changed design method.
+
+  2004/06/25
+  Bio::ShRNA class was added.
+
+  2004/06/17 Itoshi NIKAIDO <itoshi.nikaido@nifty.com>
+  We can use shRNA loop sequence from piGene document.
+
+=end

data/test/data/HMMER/hmmpfam.out

@@ -0,0 +1,64 @@
+hmmpfam - search one or more sequences against HMM database
+HMMER 2.3.2 (Oct 2003)
+Copyright (C) 1992-2003 HHMI/Washington University School of Medicine
+Freely distributed under the GNU General Public License (GPL)
+- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+HMM file:                 /Users/nakao/Sites/iprscan/data/Pfam
+Sequence file:            /Users/nakao/Sites/iprscan/tmp/20050517/iprscan-20050517-16244071/chunk_1/iprscan-20050517-16244071.nocrc
+- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+
+Query sequence: 104K_THEPA
+Accession:      [none]
+Description:    [none]
+
+Scores for sequence family classification (score includes all domains):
+Model    Description                                    Score    E-value  N 
+-------- -----------                                    -----    ------- ---
+PF04385.4 Domain of unknown function, DUF529             259.3    6.6e-75   4
+
+Parsed for domains:
+Model    Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
+-------- ------- ----- -----    ----- -----      -----  -------
+PF04385.4   1/4      36   111 ..     1    80 []    65.0    2e-16
+PF04385.4   2/4     149   224 ..     1    80 []    64.7  2.5e-16
+PF04385.4   3/4     265   343 ..     1    80 []    64.6  2.7e-16
+PF04385.4   4/4     379   456 ..     1    80 []    65.0    2e-16
+
+Alignments of top-scoring domains:
+PF04385.4: domain 1 of 4, from 36 to 111: score 65.0, E = 2e-16
+                   *->tLDlndtgstlkqfdykvalngdivvtytpkpGvkftkitdGnevvW
+                      t+D+n++++    f  +v+++g+++ + ++ ++v+++++++Gn+v+W
+  104K_THEPA    36    TFDINSNQTG-PAFLTAVEMAGVKYLQVQHGSNVNIHRLVEGNVVIW 81   
+
+                   eseddpefglivtlsfyldsnkfLvlllintak<-*
+                   e++   + +l++ ++++++++++++++++ +++   
+  104K_THEPA    82 ENA---STPLYTGAIVTNNDGPYMAYVEVLGDP    111  
+
+PF04385.4: domain 2 of 4, from 149 to 224: score 64.7, E = 2.5e-16
+                   *->tLDlndtgstlkqfdykvalngdivvtytpkpGvkftkitdGnevvW
+                      +L++ ++ +++k+ + ++a+ng ++vt++p++G+ +++++++n++++
+  104K_THEPA   149    SLNMAFQLENNKYEVETHAKNGANMVTFIPRNGHICKMVYHKNVRIY 195  
+
+                   eseddpefglivtlsfyldsnkfLvlllintak<-*
+                   ++     ++++vt++++++ +++L+l+++ +     
+  104K_THEPA   196 KA----TGNDTVTSVVGFFRGLRLLLINVFSID    224  
+
+PF04385.4: domain 3 of 4, from 265 to 343: score 64.6, E = 2.7e-16
+                   *->tLDlndtgstlkqfdykvalngdivvtytpkpGvkftkitdGnevvW
+                       +Dl+ +++ +++f+ + a+++ ++++++p++G+++tk++dG++v++
+  104K_THEPA   265    PVDLDIKDIDYTMFHLADATYHEPCFKIIPNTGFCITKLFDGDQVLY 311  
+
+                   eseddpefglivtlsfyldsnkfLvlllintak<-*
+                   es+ + + ++i  +++y+++n ++++l++n+++   
+  104K_THEPA   312 ESFNP-LIHCINEVHIYDRNNGSIICLHLNYSP    343  
+
+PF04385.4: domain 4 of 4, from 379 to 456: score 65.0, E = 2e-16
+                   *->tLDlndtgstlkqfdykvalngdivvty.tpkpGvkftkitdGnevv
+                      +LD+n  ++++k+ +++  +n d  +t+ tp+p+  + +++dG+ev+
+  104K_THEPA   379    ELDVN--FISDKDLYVAALTNADLNYTMvTPRPHRDVIRVSDGSEVL 423  
+
+                   WeseddpefglivtlsfyldsnkfLvlllintak<-*
+                   W++e+  ++ l++++++++d++ +Lv+l+i++     
+  104K_THEPA   424 WYYEGL-DNFLVCAWIYVSDGVASLVHLRIKDRI    456  
+
+//