bioroebe 0.12.24 → 0.13.31

data/lib/bioroebe/images/misc/README.md

@@ -0,0 +1,6 @@
+This directory may contain some small-ish images or icons that
+may be useful - such as for display in a widget, or on a 
+webpage.
+
+They were largely inspired from having a look at different
+books and the illustrations therein.

data/lib/bioroebe/{constants/base_directory.rb → log_directory/log_directory.rb}

@@ -2,66 +2,106 @@
 # Encoding: UTF-8
 # frozen_string_literal: true
 # =========================================================================== #
-# Do note that in the past, this .rb file contained several hardcoded
-# constants. Since as of September 2019 this older approach was deprecated,
-# mostly because hardcoded constants do not allow for as much flexibility
-# as method calls do. Even if a method call is slightly slower, I found
-# that in the long run it greatly makes the resulting code significantly
-# simpler to maintain, rather than having to deal with hardcoded constants
-# that may lead to inflexibility. This happened to me in a restricted
-# university setting, so I don't quite fancy hardcoded constants anymore
-# as much - at the least not for important variables.
-# =========================================================================== #
-# require 'bioroebe/constants/base_directory.rb'
+# require 'bioroebe/log_directory/log_directory.rb'
 # =========================================================================== #
 module Bioroebe
 
-  require 'bioroebe/project/project.rb'
-  require 'bioroebe/toplevel_methods/is_on_roebe.rb'
+  # ========================================================================= #
+  # === Bioroebe.user_home_directory?
+  #
+  # This method will either refer to the home directory of the user at hand,
+  # or, if unavailable, simply refer to '/tmp/' as hardcoded target.
+  #
+  # The main assumption here is that the home directory is writable and
+  # readable for the user, by default.
+  # ========================================================================= #
+  def self.user_home_directory?
+    begin
+      # ===================================================================== #
+      # Expand to find the proper directory.
+      # ===================================================================== #
+      return "#{File.expand_path('~')}/"
+    rescue ArgumentError
+      # ===================================================================== #
+      # Rescued in .cgi environments, where it will default to /tmp/.
+      # ===================================================================== #
+      return '/tmp/'
+    end
+  end
 
   # ========================================================================= #
-  # === Bioroebe.base_directory?
+  # === @log_directory
   #
-  # This method will return the stored value for the @base_directory,
-  # which is typically a String such as "/root/Bioroebe/".
+  # Keep track where to log output into, through this variable.
   # ========================================================================= #
-  def self.base_directory?
-    @base_directory
-  end; self.instance_eval { alias base_dir? base_directory? } # === Bioroebe.base_dir?
+  @log_directory = nil
 
   # ========================================================================= #
-  # === Bioroebe.set_base_directory
+  # === Bioroebe.log_directory?
   #
-  # This method can be used to set the main @base_dir variable
-  # for the Bioroebe-project.
+  # This method will keep track over where we will store output,
+  # related to the Bioroebe project. On my home system this will
+  # default to "/root/Bioroebe" usually.
+  # ========================================================================= #
+  def self.log_directory?
+    @log_directory
+  end; self.instance_eval { alias log_dir                log_directory? } # === Bioroebe.log_dir
+       self.instance_eval { alias store_here?            log_directory? } # === Bioroebe.store_here?
+       self.instance_eval { alias save_dir?              log_directory? } # === Bioroebe.save_dir?
+       self.instance_eval { alias log_dir?               log_directory? } # === Bioroebe.log_dir?
+       self.instance_eval { alias project_log_directory? log_directory? } # === Bioroebe.project_log_directory?
+       self.instance_eval { alias base_directory?        log_directory? } # === Bioroebe.base_directory?
+       self.instance_eval { alias base_dir?              log_directory? } # === Bioroebe.base_dir?
+
+  # ========================================================================= #
+  # === Bioroebe.set_log_dir
   #
-  # By default this method will append the name "Bioroebe/" to the
-  # target directory, if :default is given as argument - which is
-  # also the default argument, hence the name. If you do not want
-  # this behaviour then you have to call Bioroebe.set_base_directory()
-  # by yourself, with the desired base directory to use.
+  # This method will set the log-directory for the Bioroebe project.
+  #
+  # Usually this will be in the user's home directory, and then a
+  # 'Bioroebe/' suffix appended onto it. The default input-value is
+  # the symbol :default.
+  #
+  # The user can set to use another log-directory through this method.
+  #
+  # By default this method will append the name "bioroebe/" to the
+  # target directory, if :default is given as argument to this method -
+  # which is also the default argument, hence the name. If you do not
+  # want this behaviour then you have to call Bioroebe.set_base_directory()
+  # on your own by yourself, with the desired base directory to use.
   # ========================================================================= #
-  def self.set_base_directory(
+  def self.set_log_directory(
       i = :default
     )
     # ======================================================================= #
     # We may need YAML support in this method.
     # ======================================================================= #
     require 'bioroebe/requires/require_yaml.rb'
-    case i
+    require 'bioroebe/project/project.rb'        # ← For Bioroebe.project_yaml_directory?
+    require 'bioroebe/toplevel_methods/roebe.rb' # ← For Bioroebe.is_on_roebe?
+    case i # case tag
     # ======================================================================= #
     # === :default
+    #
+    # This is the default value, aka the primary entry point into this
+    # method.
     # ======================================================================= #
     when :default
       user_home_directory = user_home_directory?
       unless File.directory? user_home_directory
         # =================================================================== #
+        # === Expand the file path
+        #
         # Enter this clause for regular systems that do not have a
         # /Depot/Temp/ directory. Such systems will store output
         # into the home directory of the user.
         # =================================================================== #
         i = "#{File.expand_path('~')}/"
       end
+      # ===================================================================== #
+      # Query the default path to be used, as stored in the configuration
+      # file.
+      # ===================================================================== #
       file_temp_dir = "#{Bioroebe.project_yaml_directory?}configuration/temp_dir.yml"
       if File.exist?(file_temp_dir) and !File.empty?(file_temp_dir)
         i = YAML.load_file(file_temp_dir)
@@ -76,45 +116,25 @@ module Bioroebe
       end
     end
     # ======================================================================= #
-    # Keep a trailing '/' for the variable at all times.
+    # Keep a trailing '/' for this variable, at all times.
     # ======================================================================= #
     unless i.end_with? '/'
       i = i.dup if i.frozen?
       i << '/'
     end
-    @base_directory = i
-  end; self.instance_eval { alias set_base_dir set_base_directory } # === Bioroebe.set_base_dir
+    @log_directory = i
+  end; self.instance_eval { alias set_log_dir        set_log_directory } # === Bioroebe.set_log_dir
+       self.instance_eval { alias set_base_directory set_log_directory } # === Bioroebe.set_base_directory
+       self.instance_eval { alias set_base_dir       set_log_directory } # === Bioroebe.set_base_dir
 
   # ========================================================================= #
-  # === Bioroebe.user_home_directory?
-  #
-  # This method will either refer to the home directory of the user at hand,
-  # or, if unavailable, simply refer to '/tmp/' as hardcoded target.
-  #
-  # The main assumption here is that the home directory is writable and
-  # readable for the user, by default.
+  # === Initialize it at once, with the default value.
   # ========================================================================= #
-  def self.user_home_directory?
-    begin
-      # ===================================================================== #
-      # Expand to find the proper directory.
-      # ===================================================================== #
-      return "#{File.expand_path('~')}/"
-    rescue ArgumentError
-      # ===================================================================== #
-      # Rescued in .cgi environments, where it will default to /tmp/.
-      # ===================================================================== #
-      return '/tmp/'
-    end
+  _ = :default # Uses the default path.
+  if ENV.has_key? 'BIOROEBE_DEFAULT_LOG_DIRECTORY'
+    _ = ENV['BIOROEBE_DEFAULT_LOG_DIRECTORY']
   end
 
-  set_base_directory # Initialize it at once.
-
-end
+  set_log_directory(_)
 
-if __FILE__ == $PROGRAM_NAME
-  alias e puts
-  e 'Base directory for the Bioroebe project: '+
-    Bioroebe.base_directory?
-  e Bioroebe.user_home_directory?
 end

data/lib/bioroebe/matplotlib/matplotlib_generator.rb

@@ -11,7 +11,7 @@
 # =========================================================================== #
 # require 'bioroebe/matplotlib/matplotlib_generator.rb'
 # =========================================================================== #
-require 'bioroebe/base/commandline_application/commandline_application.rb'
+require 'bioroebe/requires/commandline_application.rb'
 
 module Bioroebe
 

data/lib/bioroebe/misc/quiz/three_letter_to_aminoacid.rb

@@ -14,7 +14,7 @@
 # =========================================================================== #
 # require 'bioroebe/misc/quiz/three_letter_to_aminoacid.rb'
 # =========================================================================== #
-require 'bioroebe/base/commandline_application/commandline_application.rb'
+require 'bioroebe/requires/commandline_application.rb'
 
 module Bioroebe
 

data/lib/bioroebe/misc/ruler.rb

@@ -28,7 +28,7 @@
 # Bioroebe.ruler_return_as_string_without_colours 'ATGCTGACAGGGGGGGEEEEEE'
 # Bioroebe::Ruler.new(ARGV)
 # =========================================================================== #
-require 'bioroebe/base/commandline_application/commandline_application.rb'
+require 'bioroebe/requires/commandline_application.rb'
 
 module Bioroebe
 
@@ -76,7 +76,7 @@ class Ruler < ::Bioroebe::CommandlineApplication # === Bioroebe::Ruler
           # ================================================================= #
           when :no_colours,
                :without_colours
-            @highlight_numbers = false
+            @internal_hash[:highlight_numbers] = false
           end
         end
       else
@@ -86,7 +86,7 @@ class Ruler < ::Bioroebe::CommandlineApplication # === Bioroebe::Ruler
         # =================================================================== #
         when :no_colours,
              :without_colours
-          @highlight_numbers = false
+          @internal_hash[:highlight_numbers] = false
         end
       end
     end
@@ -110,7 +110,7 @@ class Ruler < ::Bioroebe::CommandlineApplication # === Bioroebe::Ruler
     # If the next variable is set to true then we will highlight the
     # positions at 1, 5 and 10. This can be toggled to false by the user.
     # ======================================================================= #
-    @highlight_numbers = true
+    @internal_hash[:highlight_numbers] = true
   end
 
   # ========================================================================= #
@@ -177,7 +177,7 @@ class Ruler < ::Bioroebe::CommandlineApplication # === Bioroebe::Ruler
       _ = ''.dup
       sequence.chars.each_with_index {|char, index| index += 1
         result = index % 10
-        if @highlight_numbers
+        if @internal_hash[:highlight_numbers]
           case result
           when 1
             result = crimson(result)+rev

data/lib/bioroebe/misc/useful_formulas.rb

@@ -14,7 +14,7 @@
 # =========================================================================== #
 # require 'bioroebe/misc/useful_formulas.rb'
 # =========================================================================== #
-require 'bioroebe/base/commandline_application/commandline_application.rb'
+require 'bioroebe/requires/commandline_application.rb'
 
 module Bioroebe
 
@@ -112,13 +112,13 @@ class UsefulFormulas < ::Bioroebe::CommandlineApplication # === Bioroebe::Useful
     working_with_rna
     working_with_temperatures_and_pressure
     quantification_of_proteins
-    e # And a happy trailing newline.
+    # e # And a happy trailing newline. No longer needed as of Nov 2023.
   end
 
   # ========================================================================= #
   # === Bioroebe::UsefulFormulas[]
   # ========================================================================= #
-  def self.[](i = '')
+  def self.[](i = ARGV)
     new
   end
 

data/lib/bioroebe/ncbi/efetch.rb

@@ -40,8 +40,7 @@ module Bioroebe # === Bioroebe::Ncbi
 
 class Ncbi < ::Bioroebe::Base
 
-  require 'bioroebe/toplevel_methods/fasta_and_fastq.rb'
-  require 'bioroebe/toplevel_methods/log_directory.rb'
+  require 'bioroebe/toplevel_methods/toplevel_methods.rb'
 
   require 'open-uri'
 

data/lib/bioroebe/ngs/phred_quality_score_table.rb

@@ -26,13 +26,13 @@
 # =========================================================================== #
 # require 'bioroebe/ngs/phred_quality_score_table.rb'
 # =========================================================================== #
-require 'bioroebe/base/commandline_application/commandline_application.rb'
+require 'bioroebe/requires/commandline_application.rb'
 
 module Bioroebe
 
 class PhredQualityScoreTable < ::Bioroebe::CommandlineApplication # === Bioroebe::PhredQualityScoreTable
 
-  require 'bioroebe/toplevel_methods/phred_error_probability.rb'
+  require 'bioroebe/toplevel_methods/toplevel_methods.rb'
 
   # ========================================================================= #
   # === initialize
@@ -112,7 +112,7 @@ class PhredQualityScoreTable < ::Bioroebe::CommandlineApplication # === Bioroebe
   # ========================================================================= #
   # === Bioroebe::PhredQualityScoreTable[]
   # ========================================================================= #
-  def self.[](i = '')
+  def self.[](i = ARGV)
     new(i)
   end
 

data/lib/bioroebe/nucleotides/complementary_dna_strand.rb

@@ -11,15 +11,11 @@
 # require 'bioroebe/nucleotides/complementary_dna_strand.rb'
 # Bioroebe::ComplementaryDnaStrand.new(ARGV)
 # =========================================================================== #
-require 'bioroebe/base/commandline_application/commandline_arguments.rb'
+require 'bioroebe/requires/commandline_application.rb'
 
 module Bioroebe
 
-class ComplementaryDnaStrand # === Bioroebe::ComplementaryDnaStrand
-
-  include Bioroebe::CommandlineArguments
-
-  require 'bioroebe/toplevel_methods/nucleotides.rb'
+class ComplementaryDnaStrand < ::Bioroebe::CommandlineApplication # === Bioroebe::ComplementaryDnaStrand
 
   # ========================================================================= #
   # === initialize
@@ -37,6 +33,7 @@ class ComplementaryDnaStrand # === Bioroebe::ComplementaryDnaStrand
   # === reset                                                     (reset tag)
   # ========================================================================= #
   def reset
+    super()
     # ======================================================================= #
     # === @continue
     # ======================================================================= #

data/lib/bioroebe/nucleotides/molecular_weight_of_nucleotides.rb

@@ -14,8 +14,8 @@ module Bioroebe
 
 module MolecularWeightOfNucleotides # === Bioroebe::MolecularWeightOfNucleotides
 
-  require 'bioroebe/toplevel_methods/e.rb'
-  require 'bioroebe/colours/misc_colours.rb'
+  require 'bioroebe/toplevel_methods/toplevel_methods.rb'
+  require 'bioroebe/colours/colours.rb'
 
   # ========================================================================= #
   # === MolecularWeightOfNucleotides::GUANINE
@@ -110,7 +110,7 @@ module MolecularWeightOfNucleotides # === Bioroebe::MolecularWeightOfNucleotides
   # === MolecularWeightOfNucleotides.report_weight
   # ========================================================================= #
   def self.report_weight
-    e 'The molecular weight of the four main nucleotides are:'; e
+    e ::Colours.rev+'The molecular weight of the four main nucleotides are:'; e
     MolecularWeightOfNucleotides.hash.each_pair {|nucleotide, weight|
       weight = ('%.3f' % weight.to_f).to_s
       e '  '+

data/lib/bioroebe/nucleotides/most_likely_nucleotide_sequence_for_this_aminoacid_sequence.rb

@@ -18,7 +18,7 @@
 # =========================================================================== #
 # require 'bioroebe/nucleotides/most_likely_nucleotide_sequence_for_this_aminoacid_sequence.rb'
 # =========================================================================== #
-require 'bioroebe/base/commandline_application/commandline_application.rb'
+require 'bioroebe/requires/commandline_application.rb'
 
 module Bioroebe
 
@@ -60,10 +60,6 @@ class MostLikelyNucleotideSequenceForThisAminoacidSequence < ::Bioroebe::Command
     super()
     infer_the_namespace
     # ======================================================================= #
-    # === @internal_hash
-    # ======================================================================= #
-    @internal_hash = {}
-    # ======================================================================= #
     # === :codon_percentage
     # ======================================================================= #
     @internal_hash[:codon_percentage] = Bioroebe::CodonPercentage.new
@@ -80,13 +76,13 @@ class MostLikelyNucleotideSequenceForThisAminoacidSequence < ::Bioroebe::Command
   # === name_of_the_codon_table?
   # ========================================================================= #
   def name_of_the_codon_table?
-    @internal_hash[:codon_percentage].name_of_the_codon_table?
+    codon_percentage?.name_of_the_codon_table?
   end
 
   # ========================================================================= #
   # === codon_percentage?
   # ========================================================================= #
-  def codon_percenage?
+  def codon_percentage?
     @internal_hash[:codon_percentage]
   end
 
@@ -97,7 +93,7 @@ class MostLikelyNucleotideSequenceForThisAminoacidSequence < ::Bioroebe::Command
     _ = first?.delete('-').split(//)
     erev 'The aminoacid sequence '+steelblue(_.join)+rev+
          ' is best represented by:' if be_verbose?
-    codon_percentage = codon_percenage?
+    codon_percentage = codon_percentage?
     all_codons = ::Bioroebe.possible_codons_for_these_aminoacids(_)
     final_sequence = ''.dup
     all_codons.each {|array_codons|
@@ -132,7 +128,7 @@ class MostLikelyNucleotideSequenceForThisAminoacidSequence < ::Bioroebe::Command
   # ========================================================================= #
   # === Bioroebe::MostLikelyNucleotideSequenceForThisAminoacidSequence[]
   # ========================================================================= #
-  def self.[](i = '')
+  def self.[](i = ARGV)
     new(i)
   end
 
@@ -187,4 +183,4 @@ if __FILE__ == $PROGRAM_NAME
   Bioroebe::MostLikelyNucleotideSequenceForThisAminoacidSequence.new(ARGV)
 end # mostlikelynucleotides HLI
     # mostlikelynucleotides MTTAGP
-    # mostlikelynucleotides M-T-T-A-G-P
+    # mostlikelynucleotides M-T-T-A-G-P