bioroebe 0.10.80 → 0.12.12

data/lib/bioroebe/siRNA/siRNA.rb

@@ -16,6 +16,16 @@
 #       of the antisense strand
 #   (4) the absence of any GC stretch of more than 9 nt in length
 #
+# Reference: Kumiko Ui-Tei et al. "Guidelines for the selection of highly
+# effective siRNA sequences for mammalian and chick RNA interference."
+#
+#   Nucleic Acids Res. 2004 32: 936-948.
+#
+# The other paper is from:
+#
+# Angela Reynolds et al.  Rational siRNA design for RNA interference.
+# Nat. Biotechnol. 2004 22: 326-330.
+#
 # =========================================================================== #
 # require 'bioroebe/siRNA/siRNA.rb'
 # =========================================================================== #
@@ -40,7 +50,8 @@ class SiRNA # === Bioroebe::SiRNA
   # === uitei?
   # ========================================================================= #
   def uitei?(
-      i = @sequence, be_verbose = true
+      i          = @sequence,
+      be_verbose = true
     )
     unless i.size == 23 # 21 nt target + 2 nt overhang
       if be_verbose
@@ -84,10 +95,79 @@ class SiRNA # === Bioroebe::SiRNA
     return true # This is then the new default return value here.
   end; alias uitei_rule? uitei? # === uitei_rule?
 
+  # ========================================================================= #
+  # === reynolds?
+  #
+  # This method implements the reynolds' rule.
+  #
+  # The Reynolds' rule does not require to fulfill all the
+  # criteria simultaneously.
+  #
+  # See: https://www.nature.com/articles/nbt936
+  # ========================================================================= #
+  def reynolds?(
+      i          = @sequence,
+      be_verbose = true
+    )
+    unless i.size == 23 # 21 nt target + 2 nt overhang
+      if be_verbose
+        puts 'The size should be 23; it is '+i.to_s.size.to_s+'.'
+      end
+      return false
+    end
+    score = 0
+    seq19 = i[2 .. 20] # 19 nt double-stranded region of siRNA
+    complement_to_seq19 = ::Bioroebe.reverse_complement(seq19) # This is actually the reverse complement.
+    # ======================================================================= #
+    # === criterium 1
+    # ======================================================================= #
+    gc_number = seq19.scan(/[GC]/i).size
+    if (7 <= gc_number and gc_number <= 10)
+      score += 1
+    end
+    # ======================================================================= #
+    # === criterium 2
+    # ======================================================================= #
+    au_number = seq19[14..18].scan(/[AU]/i).size
+    score += au_number
+    # ======================================================================= #
+    # === criterium 3
+    #
+    # This is not yet implemented: Tm
+    # ======================================================================= #
+    # ======================================================================= #
+    # === criterium 4
+    # ======================================================================= #
+    score += 1 if seq19[18..18].match(/A/i)
+    # ======================================================================= #
+    # === criterium 5
+    # ======================================================================= #
+    score += 1 if seq19[2..2].match(/A/i)
+    # ======================================================================= #
+    # === criterium 6
+    # ======================================================================= #
+    score += 1 if seq19[9..9].match(/[U]/i)
+    # ======================================================================= #
+    # === criterium 7
+    # ======================================================================= #
+    score -= 1 if seq19[18..18].match(/[GC]/i)
+    # ======================================================================= #
+    # === criterium V8
+    # ======================================================================= #
+    score -= 1 if seq19[12..12].match(/G/i)
+    if score >= 6
+      return score
+    else
+      return false
+    end
+  end; alias reynolds_rule? reynolds? # === reynolds_rule?
+
 end; end
 
 if __FILE__ == $PROGRAM_NAME
   alias e puts
   e Bioroebe::SiRNA.new('GAGAAAATCATGCATGCATTTAT').uitei_rule?
   e Bioroebe::SiRNA.new('GAAAAAAAAATGCATGCAAAAAA').uitei_rule?
+  e Bioroebe::SiRNA.new('GAGAAAATCATGCATGCATTTAT').reynolds_rule?
+  e Bioroebe::SiRNA.new('GAAAAAAAAATGCATGCAAAAAA').reynolds_rule?
 end # siRNA.rb

data/lib/bioroebe/string_matching/find_longest_substring.rb

@@ -109,7 +109,8 @@ class FindLongestSubstring < ::Bioroebe::CommandlineApplication # === Bioroebe::
   # === record
   # ========================================================================= #
   def record(
-      i = @_, start_position = nil
+      i              = @_,
+      start_position = nil
     )
     if i.size > @longest_substring.size
       @longest_substring = i
@@ -148,7 +149,7 @@ class FindLongestSubstring < ::Bioroebe::CommandlineApplication # === Bioroebe::
         @_ << entry
         record(@_, index)
       else
-        @_ = ''
+        @_ = ''.dup
       end
     }
     report_longest_substring

data/lib/bioroebe/string_matching/hamming_distance.rb

@@ -20,11 +20,6 @@ module Bioroebe
 
 class HammingDistance < ::Bioroebe::CommandlineApplication
 
-  # ========================================================================= #
-  # === NAMESPACE
-  # ========================================================================= #
-  NAMESPACE = inspect
-
   # ========================================================================= #
   # === SHOW_SPACER
   # ========================================================================= #
@@ -57,10 +52,7 @@ class HammingDistance < ::Bioroebe::CommandlineApplication
   # ========================================================================= #
   def reset
     super()
-    # ======================================================================= #
-    # === @namespace
-    # ======================================================================= #
-    @namespace = NAMESPACE
+    infer_the_namespace
     # ======================================================================= #
     # === @input
     # ======================================================================= #

data/lib/bioroebe/taxonomy/class_methods.rb

@@ -10,6 +10,7 @@ module Taxonomy # === Bioroebe::Taxonomy
 
   require 'bioroebe/taxonomy/shared.rb'
   require 'bioroebe/colours/rev.rb'
+  require 'bioroebe/taxonomy/constants.rb'
 
   require 'bioroebe/toplevel_methods/extract.rb'
   require 'bioroebe/toplevel_methods/time_and_date.rb'
@@ -17,10 +18,11 @@ module Taxonomy # === Bioroebe::Taxonomy
   require 'bioroebe/toplevel_methods/file_and_directory_related_actions.rb'
 
   extend Colours::E
+  extend Colours
   extend Taxonomy::Shared
 
   # ========================================================================= #
-  # === status
+  # === Bioroebe::Taxonomy.status
   #
   # Invoke this method like that:
   #
@@ -128,13 +130,6 @@ module Taxonomy # === Bioroebe::Taxonomy
     Taxonomy.base_dir?
   end; alias base_dir? project_base_dir? # === base_dir?
 
-  # ========================================================================= #
-  # === Taxonomy.base_dir?
-  # ========================================================================= #
-  def self.base_dir?
-    PROJECT_BASE_DIR2
-  end
-
   # ========================================================================= #
   # === Taxonomy.be_verbose?
   # ========================================================================= #

data/lib/bioroebe/taxonomy/constants.rb

@@ -2,6 +2,8 @@
 # Encoding: UTF-8
 # frozen_string_literal: true
 # =========================================================================== #
+# include Bioroebe::Taxonomy::Constants
+# =========================================================================== #
 module Bioroebe
 
 module Taxonomy
@@ -133,8 +135,6 @@ module Constants # === Bioroebe::Taxonomy::Constants
   # === LAST_INTERACTIVE_COMMAND
   #
   # The following line must come after Shared was included.
-  #
-  # In order for this to work, PROJECT_BASE_DIR2 must exist.
   # ========================================================================= #
   LAST_INTERACTIVE_COMMAND = TEMP_DIR+'LAST_INTERACTIVE_COMMAND.md'
 
@@ -165,7 +165,8 @@ module Constants # === Bioroebe::Taxonomy::Constants
   # ========================================================================= #
   # === URL1
   # ========================================================================= #
-  URL1 = NCBI_CGI_SCRIPT+'mode=Undef&name=Arabidopsis+thaliana&lvl=0&srchmode=1&keep=1&unlock'
+  URL1 = NCBI_CGI_SCRIPT+
+         'mode=Undef&name=Arabidopsis+thaliana&lvl=0&srchmode=1&keep=1&unlock'
 
   # ========================================================================= #
   # == Taxonomy entries

data/lib/bioroebe/taxonomy/edit.rb

@@ -54,7 +54,8 @@ module Taxonomy # === Bioroebe::Taxonomy
     # ======================================================================= #
     # === login
     # ======================================================================= #
-    when 'login','main'
+    when 'login',
+         'main'
       edit_login_file
     # ======================================================================= #
     # === instructions

data/lib/bioroebe/taxonomy/help/help.rb

@@ -36,19 +36,19 @@ module Taxonomy
         Helpline[:nocolours,'# Use this to disable the '+
           'colours. (Use "yescolours" to enable them again)']
       end
-      Helpline[:taxid,'# Find out the name of the organism through the '+
-        'input ID from the NCBI dataset. For example: "taxid 33"']
-      Helpline[:table_names?,'# Use this to show the SQL command '+
+      Helpline[:taxid,'# Find out the name of the organism through '\
+        'the input ID from the NCBI dataset. For example: "taxid 33"']
+      Helpline[:table_names?,'# Use this to show the SQL command '\
         'that was used to generate the SQL Tables.']
-      Helpline[:verify,'# Use this to verify that the '+
+      Helpline[:verify,'# Use this to verify that the '\
         '.sql files (nodes and names) are valid.']
-      Helpline[:verbose,'# be verbose, in other words provide '+
+      Helpline[:verbose,'# be verbose, in other words provide '\
         'extra information to us whenever feasible']
-      Helpline[:ll, '# Show the content of the current working '+
+      Helpline[:ll, '# Show the content of the current working '\
         'directory.']
-      Helpline[:id,'# Query the postgre database to get the ID of '+
+      Helpline[:id,'# Query the postgre database to get the ID of '\
         'a given species.']
-      Helpline[:download,'# Download the remote NCBI database '+
+      Helpline[:download,'# Download the remote NCBI database '\
         '(at '+simp(URL_TO_TAXONOMY_ARCHIVE)+')']
       if SHALL_WE_LOG_LAST_UPDATE
         Helpline[:last_update?,'# When did we last update the database']
@@ -56,8 +56,8 @@ module Taxonomy
       Helpline[:update_database, '# download the remote NCBI database, '+
         'extract it, generate nodes.sql and names.sql,']
       _ = ' ' * Helpline::LJUST
-      e _+Helpline::PADDING+' # and then populate the postgresql-database '+
-        'with this information'
+      e _+Helpline::PADDING+' # and then populate the '\
+        'postgresql-database with this information'
       e # This here to keep a trailing newline.
     }
   end

data/lib/bioroebe/taxonomy/help/helpline.rb

@@ -14,8 +14,8 @@ class Helpline # === Bioroebe::Taxonomy::Helpline
 
   begin
     require 'colours'
-    include Colours
-    extend  Colours::E
+    include ::Colours
+    extend  ::Colours::E
   rescue LoadError; end
 
   # ========================================================================= #

data/lib/bioroebe/taxonomy/info/check_available.rb

@@ -10,7 +10,7 @@ module Bioroebe
 
 module Taxonomy
 
-class CheckAvailable # Taxonomy::CheckAvailable
+class CheckAvailable # === Bioroebe::Taxonomy::CheckAvailable
 
   require 'bioroebe/taxonomy/shared.rb'
  
@@ -49,11 +49,17 @@ class CheckAvailable # Taxonomy::CheckAvailable
   # === reset
   # ========================================================================= #
   def reset
+    # ======================================================================= #
     # === @shall_we_copy
+    # ======================================================================= #
     @shall_we_copy    = SHALL_WE_COPY
+    # ======================================================================= #
     # === @array_duplicates
+    # ======================================================================= #
     @array_duplicates = []
+    # ======================================================================= #
     # === @array_no_match
+    # ======================================================================= #
     @array_no_match   = []
   end
 
@@ -63,9 +69,9 @@ class CheckAvailable # Taxonomy::CheckAvailable
   def show_important_directories
     e 'We will now run through some important local directories.'
     e
-    e '  '+sfancy(INFO_DIR)
-    e '  '+sfancy(AA_DIR)
-    e '  '+sfancy(LOCALOME_DIR)
+    e "  #{sfancy(INFO_DIR)}"
+    e "  #{sfancy(AA_DIR)}"
+    e "  #{sfancy(LOCALOME_DIR)}"
     e
   end
 
@@ -73,8 +79,8 @@ class CheckAvailable # Taxonomy::CheckAvailable
   # === scan_info_directory
   # ========================================================================= #
   def scan_info_directory
-    Dir[INFO_DIR+'*.INFO'].each {|entry|
-      e '  → '+sfile(entry)+' ('+sfancy(File.basename(entry))+')'
+    Dir["#{INFO_DIR}*.INFO"].each {|entry|
+      e "  → #{sfile(entry)} (#{sfancy(File.basename(entry))})"
       show_similar_entries_in_aa_dir(entry)
     }
   end
@@ -89,7 +95,7 @@ class CheckAvailable # Taxonomy::CheckAvailable
     query_string = AA_DIR+_+'*'
     result = Dir[query_string]
     unless result.empty?
-      e 'The corresponding match should be '+sfile(result.first.to_s)
+      e "The corresponding match should be #{sfile(result.first.to_s)}"
       if result.size > 1
         e red('!!!')+' At least one more entry was '+
           'found though, at '+sfile(result[1])
@@ -98,7 +104,7 @@ class CheckAvailable # Taxonomy::CheckAvailable
         if @shall_we_copy
           e 'We will now copy these two entries.'
           copy(original_input, TEST_DIR)
-          copy(result.first, TEST_DIR)
+          copy(result.first,   TEST_DIR)
         end
       end
     else
@@ -140,4 +146,4 @@ end; end; end
  
 if __FILE__ == $PROGRAM_NAME
   Bioroebe::Taxonomy::CheckAvailable.new(ARGV)
-end # taxonomy_check_available
+end # taxonomycheckavailable

data/lib/bioroebe/taxonomy/info/info.rb

@@ -14,7 +14,7 @@
 # If however had an .INFO file is found in localomes, we will instead
 # assume that a fasta file will also be nearby.
 # =========================================================================== #
-# require 'taxonomy/info.rb'
+# require 'bioroebe/taxonomy/info.rb'
 # =========================================================================== #
 require 'bioroebe/base/commandline_application/commandline_application.rb'
 
@@ -27,10 +27,7 @@ class Info < ::Bioroebe::CommandlineApplication
   require 'bioroebe/taxonomy/constants.rb'
   require 'bioroebe/taxonomy/shared.rb'
 
-  # ========================================================================= #
-  # === NAMESPACE
-  # ========================================================================= #
-  NAMESPACE = inspect
+  include Bioroebe::Taxonomy::Constants
 
   # ========================================================================= #
   # === DEFAULT_TARGET
@@ -40,7 +37,6 @@ class Info < ::Bioroebe::CommandlineApplication
 
   attr_accessor :location
     alias location? location
-  attr_accessor :taxonomy_id
 
   # ========================================================================= #
   # === initialize
@@ -87,14 +83,11 @@ class Info < ::Bioroebe::CommandlineApplication
   # ========================================================================= #
   def reset
     super()
-    # ======================================================================= #
-    # === @namespace
-    # ======================================================================= #
-    @namespace = NAMESPACE
+    infer_the_namespace
     # ======================================================================= #
     # === @be_verbose
     # ======================================================================= #
-    @be_verbose = true
+    set_be_verbose
     # ======================================================================= #
     # === @location
     # ======================================================================= #
@@ -320,6 +313,20 @@ class Info < ::Bioroebe::CommandlineApplication
     @data
   end
 
+  # ========================================================================= #
+  # === set_taxonomy_id
+  # ========================================================================= #
+  def set_taxonomy_id(i)
+    @taxonomy_id = i
+  end; alias taxonomy_id= set_taxonomy_id # === taxonomy_id=
+
+  # ========================================================================= #
+  # === taxonomy_id?
+  # ========================================================================= #
+  def taxonomy_id?
+    @taxonomy_id
+  end; alias taxonomy_id taxonomy_id? # === taxonomy
+
   # ========================================================================= #
   # === run
   #

data/lib/bioroebe/taxonomy/info/is_dna.rb

@@ -28,7 +28,6 @@ class IsDNA # === Bioroebe::Taxonomy::IsDNA['ATTAAA']
   #   - min-Zeichen
 
   attr_reader :n_entries # How many characters we will process in total.
-  attr_reader :total_characters
 
   # ========================================================================= #
   # === initialize
@@ -50,6 +49,9 @@ class IsDNA # === Bioroebe::Taxonomy::IsDNA['ATTAAA']
     # === @be_verbose
     # ======================================================================= #
     @be_verbose = false
+    # ======================================================================= #
+    # === @n_entries
+    # ======================================================================= #
     @n_entries = 0
   end
 
@@ -75,38 +77,11 @@ class IsDNA # === Bioroebe::Taxonomy::IsDNA['ATTAAA']
   end
 
   # ========================================================================= #
-  # === IsDNA['ABC']
-  #
-  # Class method for a more convenient output.
+  # === total_characters?
   # ========================================================================= #
-  def self.[](i)
-    return IsDNA.new(i).result
-  end
-
-  # ========================================================================= #
-  # === run
-  # ========================================================================= #
-  def run
-    result = true
-    # @input is an array.
-    @input.each {|entry|
-      splitted = entry.chars
-      splitted.each {|inner_entry|
-        @n_entries += 1
-        if ARRAY_VALID_DNA_SEQUENCES.include? inner_entry
-        else # else it can not be DNA.
-          if @be_verbose
-            e 'Nope, '+sfancy(inner_entry)+' is not DNA.'
-            pp splitted
-          end
-          result = false
-          break
-        end
-      }
-    }
-    @result = result
-    return result
-  end
+  def total_characters?
+    @total_characters
+  end; alias total_characters total_characters? # === total_characters
 
   # ========================================================================= #
   # === is_dna?
@@ -139,12 +114,47 @@ class IsDNA # === Bioroebe::Taxonomy::IsDNA['ATTAAA']
     @result
   end; alias result result? # === result
 
+  # ========================================================================= #
+  # === run
+  # ========================================================================= #
+  def run
+    result = true
+    # @input is an array.
+    @input.each {|entry|
+      splitted = entry.chars
+      splitted.each {|inner_entry|
+        @n_entries += 1
+        if ARRAY_VALID_DNA_SEQUENCES.include? inner_entry
+        else # else it can not be DNA.
+          if @be_verbose
+            e "Nope, #{sfancy(inner_entry)} is not DNA."
+            pp splitted
+          end
+          result = false
+          break
+        end
+      }
+    }
+    @result = result
+    return result
+  end
+
+  # ========================================================================= #
+  # === IsDNA['ABC']
+  #
+  # Class method for a more convenient output.
+  # ========================================================================= #
+  def self.[](i = ARGV)
+    return new(i).result
+  end
+
 end; end; end
 
 if __FILE__ == $PROGRAM_NAME
+  alias e puts
   include Bioroebe::Taxonomy
-  puts IsDNA.new('ATTTAAA').result
-  puts IsDNA.new().result
-  puts IsDNA.new('TGGGGTACTACTTTGATGAGTACTGTCAGGTGAACGCCACGACACGAAGCATTTCTTCTGTTGCATCCTTCATTGACTTTGATGTATTTGGCTTTGTCAATGAGATTTGCAGTGACTCATTTGAGACATACGAAGCAGTATACAACGCTTCTTACAGTTGCACCACTAACGGCGGTGCTTATCTTGAATCGGATGATAGTGGGTACGATAATTCTGGAGACCAAGGCAAAGATGGAAACAACGAAGAAAGGCACGAGCGCGAAGATAACAGAGAAGAGGAAGATAGGAACTCAAGAGACAGCCAGGAGTTTGAGATGTCAGGAGAGGACGTATGTTTTGCAGTTTACACAGCTGAACATTTTCAATCTATAAGAAACAAGGAGATCGCAGTGCACTACCTCAAGACACTGGTGC').result
-  puts IsDNA['ABC']
+  e IsDNA.new('ATTTAAA').result
+  e IsDNA.new.result
+  e IsDNA.new('TGGGGTACTACTTTGATGAGTACTGTCAGGTGAACGCCACGACACGAAGCATTTCTTCTGTTGCATCCTTCATTGACTTTGATGTATTTGGCTTTGTCAATGAGATTTGCAGTGACTCATTTGAGACATACGAAGCAGTATACAACGCTTCTTACAGTTGCACCACTAACGGCGGTGCTTATCTTGAATCGGATGATAGTGGGTACGATAATTCTGGAGACCAAGGCAAAGATGGAAACAACGAAGAAAGGCACGAGCGCGAAGATAACAGAGAAGAGGAAGATAGGAACTCAAGAGACAGCCAGGAGTTTGAGATGTCAGGAGAGGACGTATGTTTTGCAGTTTACACAGCTGAACATTTTCAATCTATAAGAAACAAGGAGATCGCAGTGCACTACCTCAAGACACTGGTGC').result
+  e IsDNA['ABC']
 end # rb is_dna.rb