sequence_logo 1.0.3 → 1.0.4

data/lib/sequence_logo/ytilib/addon.rb

@@ -1,247 +1,247 @@
-#!/usr/bin/ruby
-
-def File.ext_wo_name(what)
-  return what if what.rindex(".") == nil
-  what = File.basename(what)
-  "#{what}"[what.rindex(".")+1..-1]
-end
-
-def File.name_wo_ext(what)
-  return what if what.rindex(".") == nil
-  what = File.basename(what)
-  "#{what}"[0...what.rindex(".")]
-end
-
-class Float
-  def round_to(x)
-    (self * 10**x).round.to_f / 10**x
-  end
-  
-  def cut_to(x)
-    (self.abs * 10**x).floor.to_f * (self == 0.0 ? 0 : self/self.abs).round / 10**x
-  end
-end
-
-class Array
-  def shuffle
-    arr = self.dup
-    arr.size.downto 2 do |j|
-      r = rand j
-      arr[j-1], arr[r] = arr[r], arr[j-1]
-    end
-    arr
-  end
-  
-  def shuffle!
-    (size - 1).downto 1 do |i|
-      j = rand(i + 1)
-      self[i], self[j] = self[j], self[i]
-    end
-    self
-  end
-  
-  def average
-    self.empty? ? nil : self.inject(0) { |sum,s| sum += s } / self.size
-  end
-  alias mean average
-  
-  def variance
-    return self.collect { |s| s*s }.average - average**2
-  end
-  
-  def sum
-    self.inject(self[0]) { |sum,s| sum += s} - self[0]
-  end
-
-end
-
-class String
-  
-  def compl!
-    self.tr!("acgtACGT", "tgcaTGCA")
-    return self
-  end
-  
-  def compl
-    return self.tr("acgtACGT", "tgcaTGCA")
-  end
-  
-  alias comp! compl!
-  alias complement! compl!
-  alias comp compl
-  alias complement compl
-  
-  def revcomp
-    return comp.reverse
-  end
-  
-  def revcomp!
-    return comp!.reverse!
-  end
-  
-  def to_id
-    return self.gsub(/[^.\w]/, '_').upcase
-  end
-  
-end
-
-# Also this can be done is a more sophisticated way
-=begin
-String.class_eval do    
-  def to_id
-    return self.gsub(/[^.\w]/, '_') 
-  end   
-end
-=end
-
-class String
-  # The opposite of String::next / String::succ. It is impossible to be a
-  # *complete* opposite because both "9".next = "10" and "09".next = "10";
-  # if going backwards from "10" there's no way to know whether the result
-  # should be "09" or "9". Where the first ranged character is about to
-  # underflow and the next character is within the same range the result
-  # is shrunk down - that is, "10" goes to "9", "aa" goes to "z"; any non-
-  # range prefix or suffix is OK, e.g. "+!$%10-=+" goes to "+!$%9-=+".
-  # Items in the middle of a string don't do this - e.g. "12.10" goes to
-  # "12.09", to match how "next" would work as best as possible.
-  #
-  # The standard "next" function works on strings that contain *no*
-  # alphanumeric characters, using character codes. This implementation
-  # of "prev" does *not* work on such strings - while strings may contain
-  # any characters you like, only the alphanumeric components are operated
-  # upon.
-  #
-  # Should total underflow result, "nil" will be returned - e.g. "00".prev
-  # returns 'nil', as does "a".prev. This is done even if there are other
-  # characters in the string that were not touched - e.g. "+0.0".prev
-  # also returns "nil". Broadly speaking, a "nil" return value is used for
-  # any attempt to find the previous value of a string that could not have
-  # been generated using "next" in the first place.
-  #
-  # As with "next" sometimes the result of "prev" can be a little obscure
-  # so it is often best to try out things using "irb" if unsure. Note in
-  # particular that software revision numbers do not necessarily behave
-  # predictably, because they don't with "next"! E.g. "12.4.9" might go to
-  # "12.4.10" for a revision number, but "12.4.9".next = "12.5.0". Thus
-  # "12.5.0".prev = "12.4.9" and "12.4.10".prev = "12.4.09" (because the
-  # only way to make "12.4.10" using "next" is to start at "12.4.09").
-  #
-  # Since 'succ' (successor) is an alias for 'next', so 'pred'
-  # (predecessor) is an alias for 'prev'.
-  #
-  def prev(collapse = false)
-    str        = self.dup
-    early_exit = false
-    any_done   = false
-    ranges     = [
-                   ('0'[0]..'9'[0]),
-                   ('a'[0]..'z'[0]),
-                   ('A'[0]..'Z'[0]),
-                   nil
-                 ]
-
-    # Search forward for the first in-range character. If found check
-    # to see if that character is "1", "a" or "A". If it is, record
-    # its index (from 0 to string length - 1). We'll need this if
-    # underflows wrap as far as the found byte because in that case
-    # this first found byte should be deleted ("aa..." -> "z...",
-    # "10..." -> "9...").
-
-    first_ranged = nil
-
-    for index in (1..str.length)
-      byte = str[index - 1]
-
-      # Determine whether or not the current byte is a number, lower case
-      # or upper case letter. We expect 'select' to only find one matching
-      # array entry in 'ranges', thus we dereference index 0 after the
-      # 'end' to put a matching range from within 'ranges' into 'within',
-      # or 'nil' for any unmatched byte.
-
-      within = ranges.select do |range|
-        range.nil? or range.include?(byte)
-      end [0]
-
-      unless within.nil?
-        case within.first
-          when '0'[0]
-            match_byte = '1'[0]
-          else
-            match_byte = within.first
-        end
-
-        first_ranged = index - 1 if (byte == match_byte)
-        first_within = within
-        break
-      end
-    end
-
-    for index in (1..str.length)
-
-      # Process the input string in reverse character order - fetch the
-      # bytes via negative index.
-
-      byte = str[-index]
-
-      within = ranges.select do |range|
-        range.nil? or range.include?(byte)
-      end [0]
-
-      # Skip this letter unless within a known range. Otherwise note that
-      # at least one byte was able to be processed.
-
-      next if within.nil?
-      any_done = true
-
-      # Decrement the current byte. If it is still within its range, set
-      # the byte and bail out - we're finished. Flag the early exit. If
-      # the byte is no longer within range, wrap the character around
-      # and continue the loop to carry the decrement to an earlier byte.
-
-      byte = byte - 1
-
-      if (within.include? byte)
-        str[-index] = byte
-        early_exit  = true
-        break
-      else
-        str[-index] = within.last
-
-        # If we've just wrapped around a character immediately after the
-        # one found right at the start ('0', 'a' or 'A') then this first
-        # ranged character should be deleted (so "10" -> "09"
-
-        if (first_ranged != nil and first_within.include?(byte + 1) and (first_ranged - str.length) == -(index + 1))
-          str.slice!(-(index + 1))
-          early_exit = true
-          break
-        end
-      end
-
-    end # From outer 'for' loop
-
-    # If we did process at least one byte but we did not exit early, then
-    # the loop completed due to carrying a decrement to other bytes. This
-    # means an underflow condition - return 'nil'.
-
-    if (any_done == true and early_exit == false)
-      return nil
-    else
-      return str
-    end
-  end
-
-  # As (extended) String::pred / String::prev, but modifies the string in
-  # place rather than returning a copy. If underflow occurs, the string
-  # will be unchanged. Returns 'self'.
-  #
-  def prev!
-    new_str = prev
-    self.replace(new_str) unless new_str.nil?
-    return self
-  end
-
-  alias pred  prev
-  alias pred! prev!
-
+#!/usr/bin/ruby
+
+def File.ext_wo_name(what)
+  return what if what.rindex(".") == nil
+  what = File.basename(what)
+  "#{what}"[what.rindex(".")+1..-1]
+end
+
+def File.name_wo_ext(what)
+  return what if what.rindex(".") == nil
+  what = File.basename(what)
+  "#{what}"[0...what.rindex(".")]
+end
+
+class Float
+  def round_to(x)
+    (self * 10**x).round.to_f / 10**x
+  end
+  
+  def cut_to(x)
+    (self.abs * 10**x).floor.to_f * (self == 0.0 ? 0 : self/self.abs).round / 10**x
+  end
+end
+
+class Array
+  def shuffle
+    arr = self.dup
+    arr.size.downto 2 do |j|
+      r = rand j
+      arr[j-1], arr[r] = arr[r], arr[j-1]
+    end
+    arr
+  end
+  
+  def shuffle!
+    (size - 1).downto 1 do |i|
+      j = rand(i + 1)
+      self[i], self[j] = self[j], self[i]
+    end
+    self
+  end
+  
+  def average
+    self.empty? ? nil : self.inject(0) { |sum,s| sum += s } / self.size
+  end
+  alias mean average
+  
+  def variance
+    return self.collect { |s| s*s }.average - average**2
+  end
+  
+  def sum
+    self.inject(self[0]) { |sum,s| sum += s} - self[0]
+  end
+
+end
+
+class String
+  
+  def compl!
+    self.tr!("acgtACGT", "tgcaTGCA")
+    return self
+  end
+  
+  def compl
+    return self.tr("acgtACGT", "tgcaTGCA")
+  end
+  
+  alias comp! compl!
+  alias complement! compl!
+  alias comp compl
+  alias complement compl
+  
+  def revcomp
+    return comp.reverse
+  end
+  
+  def revcomp!
+    return comp!.reverse!
+  end
+  
+  def to_id
+    return self.gsub(/[^.\w]/, '_').upcase
+  end
+  
+end
+
+# Also this can be done is a more sophisticated way
+=begin
+String.class_eval do    
+  def to_id
+    return self.gsub(/[^.\w]/, '_') 
+  end   
+end
+=end
+
+class String
+  # The opposite of String::next / String::succ. It is impossible to be a
+  # *complete* opposite because both "9".next = "10" and "09".next = "10";
+  # if going backwards from "10" there's no way to know whether the result
+  # should be "09" or "9". Where the first ranged character is about to
+  # underflow and the next character is within the same range the result
+  # is shrunk down - that is, "10" goes to "9", "aa" goes to "z"; any non-
+  # range prefix or suffix is OK, e.g. "+!$%10-=+" goes to "+!$%9-=+".
+  # Items in the middle of a string don't do this - e.g. "12.10" goes to
+  # "12.09", to match how "next" would work as best as possible.
+  #
+  # The standard "next" function works on strings that contain *no*
+  # alphanumeric characters, using character codes. This implementation
+  # of "prev" does *not* work on such strings - while strings may contain
+  # any characters you like, only the alphanumeric components are operated
+  # upon.
+  #
+  # Should total underflow result, "nil" will be returned - e.g. "00".prev
+  # returns 'nil', as does "a".prev. This is done even if there are other
+  # characters in the string that were not touched - e.g. "+0.0".prev
+  # also returns "nil". Broadly speaking, a "nil" return value is used for
+  # any attempt to find the previous value of a string that could not have
+  # been generated using "next" in the first place.
+  #
+  # As with "next" sometimes the result of "prev" can be a little obscure
+  # so it is often best to try out things using "irb" if unsure. Note in
+  # particular that software revision numbers do not necessarily behave
+  # predictably, because they don't with "next"! E.g. "12.4.9" might go to
+  # "12.4.10" for a revision number, but "12.4.9".next = "12.5.0". Thus
+  # "12.5.0".prev = "12.4.9" and "12.4.10".prev = "12.4.09" (because the
+  # only way to make "12.4.10" using "next" is to start at "12.4.09").
+  #
+  # Since 'succ' (successor) is an alias for 'next', so 'pred'
+  # (predecessor) is an alias for 'prev'.
+  #
+  def prev(collapse = false)
+    str        = self.dup
+    early_exit = false
+    any_done   = false
+    ranges     = [
+                   ('0'[0]..'9'[0]),
+                   ('a'[0]..'z'[0]),
+                   ('A'[0]..'Z'[0]),
+                   nil
+                 ]
+
+    # Search forward for the first in-range character. If found check
+    # to see if that character is "1", "a" or "A". If it is, record
+    # its index (from 0 to string length - 1). We'll need this if
+    # underflows wrap as far as the found byte because in that case
+    # this first found byte should be deleted ("aa..." -> "z...",
+    # "10..." -> "9...").
+
+    first_ranged = nil
+
+    for index in (1..str.length)
+      byte = str[index - 1]
+
+      # Determine whether or not the current byte is a number, lower case
+      # or upper case letter. We expect 'select' to only find one matching
+      # array entry in 'ranges', thus we dereference index 0 after the
+      # 'end' to put a matching range from within 'ranges' into 'within',
+      # or 'nil' for any unmatched byte.
+
+      within = ranges.select do |range|
+        range.nil? or range.include?(byte)
+      end [0]
+
+      unless within.nil?
+        case within.first
+          when '0'[0]
+            match_byte = '1'[0]
+          else
+            match_byte = within.first
+        end
+
+        first_ranged = index - 1 if (byte == match_byte)
+        first_within = within
+        break
+      end
+    end
+
+    for index in (1..str.length)
+
+      # Process the input string in reverse character order - fetch the
+      # bytes via negative index.
+
+      byte = str[-index]
+
+      within = ranges.select do |range|
+        range.nil? or range.include?(byte)
+      end [0]
+
+      # Skip this letter unless within a known range. Otherwise note that
+      # at least one byte was able to be processed.
+
+      next if within.nil?
+      any_done = true
+
+      # Decrement the current byte. If it is still within its range, set
+      # the byte and bail out - we're finished. Flag the early exit. If
+      # the byte is no longer within range, wrap the character around
+      # and continue the loop to carry the decrement to an earlier byte.
+
+      byte = byte - 1
+
+      if (within.include? byte)
+        str[-index] = byte
+        early_exit  = true
+        break
+      else
+        str[-index] = within.last
+
+        # If we've just wrapped around a character immediately after the
+        # one found right at the start ('0', 'a' or 'A') then this first
+        # ranged character should be deleted (so "10" -> "09"
+
+        if (first_ranged != nil and first_within.include?(byte + 1) and (first_ranged - str.length) == -(index + 1))
+          str.slice!(-(index + 1))
+          early_exit = true
+          break
+        end
+      end
+
+    end # From outer 'for' loop
+
+    # If we did process at least one byte but we did not exit early, then
+    # the loop completed due to carrying a decrement to other bytes. This
+    # means an underflow condition - return 'nil'.
+
+    if (any_done == true and early_exit == false)
+      return nil
+    else
+      return str
+    end
+  end
+
+  # As (extended) String::pred / String::prev, but modifies the string in
+  # place rather than returning a copy. If underflow occurs, the string
+  # will be unchanged. Returns 'self'.
+  #
+  def prev!
+    new_str = prev
+    self.replace(new_str) unless new_str.nil?
+    return self
+  end
+
+  alias pred  prev
+  alias pred! prev!
+
 end

data/lib/sequence_logo/ytilib/bismark.rb

@@ -1,71 +1,71 @@
-#!/usr/bin/ruby
-
-module Ytilib
-require "rexml/document"
-include REXML
-
-class Bismark < Document
-  
-  def initialize(source = nil, add_dtd = false)
-    dtd = add_dtd ? "<!DOCTYPE smallbismark SYSTEM 'smallbismark.dtd'>#{$/}" : ""
-    source == nil ? super("<?xml version='1.0' encoding='UTF-8'?>#{$/}#{dtd}") : super(source)
-    super(IO.read(source)) if source != nil && root == nil
-    if source == nil
-      self.add_element("smallbismark")
-      # xmlns breaks XPath for a REXML library under Linux, strange, indeed
-      # self.add_element("smallbismark", {"xmlns" => "http://bioinform.imb.ac.ru/smallBiSMark/smallbismark.dtd"})
-      self.root.add_element("comment", {"name" => "WARNING"}).add_text("This is a draft version of small-BiSMark. Specification is the subject to change!")
-    end
-  end
-  
-  def getXML
-    beautify
-    s = ""; write(s, 1, true)
-    s.rstrip!
-    return s
-  end
-  alias get_xml getXML
-  
-  def get_pm(xpath)
-    pwmnode = self.elements[xpath]
-    pm = PM.new_pm(pwmnode.attribute("length").value.to_i)
-    toi = pwmnode.name == "PCM"
-    pwmnode.elements.each("pm-column") { |c|
-      position = c.attribute("position").value.to_i - 1
-      weights = [c.elements["a"].get_text.value.strip.to_f, 
-                c.elements["c"].get_text.value.strip.to_f, 
-                c.elements["g"].get_text.value.strip.to_f, 
-                c.elements["t"].get_text.value.strip.to_f]
-      weights.collect { |w| w.to_i } if toi
-      pm['A'][position], pm['C'][position], pm['G'][position], pm['T'][position] = weights[0], weights[1], weights[2], weights[3]
-    }
-    return pm
-  end
-  
-private
-  CONTAIN_NO_TEXT = { 
-                      "segment" => :vasya_shmyak,
-                      "group" => :vasya_shmyak,
-                      "smallbismark" => :vasya_shmyak,
-                      "motif" => :vasya_shmyak,
-                      "PWM" => :vasya_shmyak,
-                      "PCM" => :vasya_shmyak,
-                      "PPM" => :vasya_shmyak,
-                      "source" => :vasya_shmyak,
-                      "factor"  => :vasya_shmyak,
-                      "pm-column" => :vasya_shmyak,
-                      "word-list" => :vasya_shmyak}
-  
-  def beautify(node = self)
-    if node == self 
-      self.delete_if { |e| e.is_a?(Text) }
-      self.each { |e| beautify(e) }
-    else
-      node.delete_if { |e| e.is_a?(Text) } if node.respond_to?(:delete_if) && Bismark::CONTAIN_NO_TEXT.has_key?(node.name)
-      node.each { |e| beautify(e) } if node.respond_to?(:each)
-    end 
-  end
-
-end
-
+#!/usr/bin/ruby
+
+module Ytilib
+require "rexml/document"
+include REXML
+
+class Bismark < Document
+  
+  def initialize(source = nil, add_dtd = false)
+    dtd = add_dtd ? "<!DOCTYPE smallbismark SYSTEM 'smallbismark.dtd'>#{$/}" : ""
+    source == nil ? super("<?xml version='1.0' encoding='UTF-8'?>#{$/}#{dtd}") : super(source)
+    super(IO.read(source)) if source != nil && root == nil
+    if source == nil
+      self.add_element("smallbismark")
+      # xmlns breaks XPath for a REXML library under Linux, strange, indeed
+      # self.add_element("smallbismark", {"xmlns" => "http://bioinform.imb.ac.ru/smallBiSMark/smallbismark.dtd"})
+      self.root.add_element("comment", {"name" => "WARNING"}).add_text("This is a draft version of small-BiSMark. Specification is the subject to change!")
+    end
+  end
+  
+  def getXML
+    beautify
+    s = ""; write(s, 1, true)
+    s.rstrip!
+    return s
+  end
+  alias get_xml getXML
+  
+  def get_pm(xpath)
+    pwmnode = self.elements[xpath]
+    pm = PM.new_pm(pwmnode.attribute("length").value.to_i)
+    toi = pwmnode.name == "PCM"
+    pwmnode.elements.each("pm-column") { |c|
+      position = c.attribute("position").value.to_i - 1
+      weights = [c.elements["a"].get_text.value.strip.to_f, 
+                c.elements["c"].get_text.value.strip.to_f, 
+                c.elements["g"].get_text.value.strip.to_f, 
+                c.elements["t"].get_text.value.strip.to_f]
+      weights.collect { |w| w.to_i } if toi
+      pm['A'][position], pm['C'][position], pm['G'][position], pm['T'][position] = weights[0], weights[1], weights[2], weights[3]
+    }
+    return pm
+  end
+  
+private
+  CONTAIN_NO_TEXT = { 
+                      "segment" => :vasya_shmyak,
+                      "group" => :vasya_shmyak,
+                      "smallbismark" => :vasya_shmyak,
+                      "motif" => :vasya_shmyak,
+                      "PWM" => :vasya_shmyak,
+                      "PCM" => :vasya_shmyak,
+                      "PPM" => :vasya_shmyak,
+                      "source" => :vasya_shmyak,
+                      "factor"  => :vasya_shmyak,
+                      "pm-column" => :vasya_shmyak,
+                      "word-list" => :vasya_shmyak}
+  
+  def beautify(node = self)
+    if node == self 
+      self.delete_if { |e| e.is_a?(Text) }
+      self.each { |e| beautify(e) }
+    else
+      node.delete_if { |e| e.is_a?(Text) } if node.respond_to?(:delete_if) && Bismark::CONTAIN_NO_TEXT.has_key?(node.name)
+      node.each { |e| beautify(e) } if node.respond_to?(:each)
+    end 
+  end
+
+end
+
 end