bioroebe 0.12.24 → 0.13.31

data/lib/bioroebe/toplevel_methods/extract.rb

@@ -1,56 +0,0 @@
-#!/usr/bin/ruby -w
-# Encoding: UTF-8
-# frozen_string_literal: true
-# =========================================================================== #
-# require 'bioroebe/toplevel_methods/extract.rb'
-# =========================================================================== #
-module Bioroebe
-
-  require 'bioroebe/toplevel_methods/file_and_directory_related_actions.rb'
-  require 'bioroebe/toplevel_methods/esystem.rb'
-  require 'bioroebe/toplevel_methods/verbose.rb'
-
-  # ========================================================================= #
-  # === Bioroebe.extract
-  #
-  # This method can be used to quickly extract a local archive.
-  # ========================================================================= #
-  def self.extract(
-      i = ARGV
-    )
-    require 'bioroebe/colours/sfancy.rb'
-    require 'bioroebe/colours/swarn.rb'
-    if i.is_a? Array
-      i = i.join(' ').strip
-    end
-    unless i.include?('/')
-      unless File.exist? i
-        i = return_pwd+
-            File.basename(i)
-      end
-    end
-    if File.exist? i
-      case i
-      when /bz2$/
-        _ = "tar -xfv #{i}"
-      when /xz$/
-        _ = "tar -xvf #{i}"
-      end
-      if be_verbose?
-        e "Now extracting `#{sfancy((i).squeeze('/'))}`."
-        esystem(_)
-        e 'Done extracting!'
-      else
-        system _
-      end
-    else
-      ewarn "Can not extract #{sfile(i)} because it does "\
-            "not appear to exist."
-    end
-  end
-
-end
-
-if __FILE__ == $PROGRAM_NAME
-  Bioroebe.extract(ARGV)
-end # ruby extract.rb /home/x/src/htop/htop-3.0.5.tar.xz

data/lib/bioroebe/toplevel_methods/file_and_directory_related_actions.rb

@@ -1,269 +0,0 @@
-#!/usr/bin/ruby -w
-# Encoding: UTF-8
-# frozen_string_literal: true
-# =========================================================================== #
-# require 'bioroebe/toplevel_methods/file_and_directory_related_actions.rb'
-# =========================================================================== #
-module Bioroebe
-
-  require 'fileutils'
-  require 'bioroebe/toplevel_methods/e.rb'
-  require 'bioroebe/toplevel_methods/log_directory.rb'
-  require 'bioroebe/colours/rev.rb'
-  require 'bioroebe/colours/sfile.rb'
-  require 'bioroebe/colours/sdir.rb'
-
-  # ========================================================================= #
-  # === Bioroebe.move_file
-  # ========================================================================= #
-  def self.move_file(a, b)
-    FileUtils.mv(a, b)
-  end
-
-  # ========================================================================= #
-  # === Bioroebe.pwd                                                (pwd tag)
-  #
-  # Feedback the current working directory (it will be returned, as a
-  # String).
-  # ========================================================================= #
-  def self.pwd
-    "#{Dir.pwd}/".squeeze('/')
-  end; self.instance_eval { alias return_pwd pwd } # === Bioroebe.return_pwd
-
-  # ========================================================================= #
-  # === pwd
-  # ========================================================================= #
-  def pwd
-    ::Bioroebe.pwd
-  end
-
-  # ========================================================================= #
-  # === Bioroebe.no_file_exists_at
-  # ========================================================================= #
-  def self.no_file_exists_at(i)
-    erev "No file exists at `#{sfile(i)}#{rev}`."
-  end
-
-  # ========================================================================= #
-  # === Bioroebe.mv
-  #
-  # This method can be used to rename or move a (local) file.
-  # ========================================================================= #
-  def self.mv(old, new)
-    FileUtils.mv(old, new)
-  end; self.instance_eval { alias rename mv } # === Bioroebe.rename
-
-  # ========================================================================= #
-  # === Bioroebe.create_file
-  #
-  # This method can be used to create a file.
-  # ========================================================================= #
-  def self.create_file(i)
-    FileUtils.touch(i) unless File.file?(i)
-  end
-
-  # ========================================================================= #
-  # === Bioroebe.append_what_into
-  #
-  # This method can be used to append content onto a file.
-  # ========================================================================= #
-  def self.append_what_into(
-      what = 'Hello world!',
-      into = 'test.md'
-    )
-    unless File.exist? into
-      base_dir = File.dirname(into)
-      unless File.directory? base_dir
-        e rev+
-        'No directory exists at '+sdir(base_dir)+
-        rev+'. Thus creating it now.'
-        create_directory(base_dir)
-      end
-      e rev+
-        'No file exists at '+sfile(into)+rev+
-        '. Thus creating it now.'
-      create_file(into)
-    end
-    File.open(into, 'a') { |file|
-      file << what
-    }
-  end
-
-  # ========================================================================= #
-  # === Bioroebe.write_what_into
-  #
-  # This method will simply write the content of the variable `what`
-  # into the file called `into`.
-  # ========================================================================= #
-  def self.write_what_into(
-      what = 'Hello world!',
-      into = 'test.md'
-    )
-    base_directory = File.dirname(into)
-    if File.directory? base_directory
-      File.open(into, 'w') { |file|
-        file << what
-      }
-    else
-      e "No directory exists at #{base_directory}. Thus, "\
-        "no file could be saved."
-    end
-  end; self.instance_eval { alias save_file       write_what_into } # === Bioroebe.save_file
-       self.instance_eval { alias save_what_where write_what_into } # === Bioroebe.save_what_where
-
-  # ========================================================================= #
-  # === Bioroebe.remove_file
-  #
-  # Use this method to remove a file.
-  # ========================================================================= #
-  def self.remove_file(
-      i, be_verbose = false
-    )
-    if File.exist? i
-      File.delete(i)
-      if be_verbose
-        this_file = "#{return_pwd}#{i}"
-        e 'File '+sfile(this_file)+' exists, '\
-          'we will thus remove it now.'
-      end
-    end
-  end; self.instance_eval { alias remove remove_file } # === Bioroebe.remove
-
-  # ========================================================================= #
-  # === Bioroebe.change_directory
-  #
-  # This method allows us to change the directory.
-  #
-  # Bioroebe.cd() is an alias to the method here.
-  # ========================================================================= #
-  def self.change_directory(
-      i          = '$HOME',
-      be_verbose = false
-    )
-    case be_verbose
-    # ======================================================================= #
-    # === :do_report_current_directory
-    # ======================================================================= #
-    when :do_report_current_directory,
-         :be_verbose
-      be_verbose = true
-    end
-    case i # Do some sanitizing here. (case tag)
-    # ======================================================================= #
-    # === :home_directory
-    # ======================================================================= #
-    when :home_directory,
-         :default,
-         nil # ← Nil is also assumed to refer to this :default value.
-      # ===================================================================== #
-      # In this case we will try to cd into the base-directory of the
-      # Bioroebe shell.
-      # ===================================================================== #
-      i = log_dir?
-    # ======================================================================= #
-    # === :download_dir
-    # ======================================================================= #
-    when :download_dir,':download_dir',
-         :download_directory,':download_directory'
-      i = download_dir?
-    # ======================================================================= #
-    # Bioroebe.save_dir? is defined in bioroebe/toplevel_methods/store_here.rb.
-    # ======================================================================= #
-    when 'base',
-         'logdir',
-         :bioroebe_log_directory
-      # ===================================================================== #
-      # Enter the main log dir, unless a file exists with the same name.
-      # ===================================================================== #
-      i = save_dir? unless File.exist?(i.to_s) # .to_s to avoid Symbols here.
-    end
-    i = i.dup if i.is_a?(String) and i.frozen?
-    i << '/' unless i.end_with? '/'
-    if File.directory? i
-      e sdir(i) if be_verbose # Also colourize the directory and output it.
-      Dir.chdir(i)
-    else
-      if be_verbose
-        erev "No directory called `#{sdir(i)}#{rev}` exists,"
-        erev 'thus we can not cd to this target.'
-      end
-    end
-  end; self.instance_eval { alias cd    change_directory } # === Bioroebe.cd
-       self.instance_eval { alias chdir change_directory } # === Bioroebe.chdir
-
-  # ========================================================================= #
-  # === Bioroebe.pdb_directory?
-  #
-  # This refers to the local pdb/ directory.
-  # ========================================================================= #
-  def self.pdb_directory?
-    return "#{log_dir?}pdb/"
-  end
-
-  # ========================================================================= #
-  # === Bioroebe.ensure_that_the_base_directories_exist
-  #
-  # This method will ensure that the base directory for the
-  # Bioroebe project exist.
-  # ========================================================================= #
-  def self.ensure_that_the_base_directories_exist
-    # ======================================================================= #
-    # We also need to create the temp directory, as well as having to
-    # notify the user that this will be done. The taxonomy subdirectory
-    # will also be created.
-    # ======================================================================= #
-    use_this_log_dir = log_dir?
-    unless File.exist? use_this_log_dir
-      erev "The base directory at `#{sdir(use_this_log_dir)}#{rev}` does not exist."
-      erev 'It will thus be created next.'
-      mkdir use_this_log_dir
-    end
-    # ======================================================================= #
-    # === Ensure that the Downloads/ directory exists
-    # ======================================================================= #
-    _ = "#{use_this_log_dir}Downloads/"
-    unless File.exist? _
-      erev "The directory at `#{sdir(_)}#{rev}` does not exist."
-      erev 'It will thus be created next.'
-      mkdir _
-    end
-    # ======================================================================= #
-    # === Ensure that the pdb/ directory exists
-    # ======================================================================= #
-    _ = "#{use_this_log_dir}pdb/"
-    unless File.exist? _
-      erev "The directory at `#{sdir(_)}#{rev}` does not exist."
-      erev 'It will thus be created next.'
-      mkdir _
-    end
-    autogenerated_sql_files_dir =
-      AUTOGENERATED_SQL_FILES_DIR
-    unless Dir.exist? autogenerated_sql_files_dir
-      erev 'The directory at `'+sdir(autogenerated_sql_files_dir)+
-           rev+'` does not exist.'
-      erev 'It will thus be created next.'
-      mkdir(autogenerated_sql_files_dir)
-    end
-  end
-
-  # ========================================================================= #
-  # === Bioroebe.mkdir                                            (mkdir tag)
-  # ========================================================================= #
-  def self.mkdir(i)
-    FileUtils.mkdir_p(i)
-  end; self.instance_eval { alias create_directory mkdir } # === Bioroebe.create_directory
-       self.instance_eval { alias mkdir_p          mkdir } # === Bioroebe.mkdir_p
-
-  # ========================================================================= #
-  # === mkdir
-  # ========================================================================= #
-  def mkdir(i)
-    ::Bioroebe.mkdir(i)
-  end
-
-end
-
-if __FILE__ == $PROGRAM_NAME
-  Bioroebe.ensure_that_the_base_directories_exist
-  Bioroebe.write_what_into(ARGV[0], ARGV[1])
-end

data/lib/bioroebe/toplevel_methods/frequencies.rb

@@ -1,99 +0,0 @@
-#!/usr/bin/ruby -w
-# Encoding: UTF-8
-# frozen_string_literal: true
-# =========================================================================== #
-# require 'bioroebe/frequencies.rb'
-# Bioroebe.aminoacid_frequency
-# =========================================================================== #
-module Bioroebe
-
-  require 'bioroebe/project/project.rb'
-  require 'bioroebe/toplevel_methods/e.rb'
-  require 'bioroebe/colours/colours.rb'
-  require 'bioroebe/codons/convert_this_codon_to_that_aminoacid.rb'
-
-  # ========================================================================= #
-  # === Bioroebe.calculate_the_frequencies_of_this_species
-  # ========================================================================= #
-  def self.calculate_the_frequencies_of_this_species(
-      i = :homo_sapiens
-    )
-    require 'bioroebe/sequence/dna.rb'
-    require 'yaml'
-    if i and i.is_a?(Array) and i.empty?
-      i << :homo_sapiens
-    end
-    hash_aminoacids = {}
-    hash_aminoacids.default = 0
-    if i.is_a? Array
-      i = i.first
-    end
-    case i.to_sym
-    # ======================================================================= #
-    # === :homo_sapiens
-    # ======================================================================= #
-    when :homo_sapiens,
-         :homo,
-         :human
-      i = "#{project_base_directory?}"\
-          "codon_tables/frequencies/9606_Homo_sapiens.yml"
-    end
-    hash = YAML.load_file(i)
-    # "GAC"=>25.1
-    hash.each_pair {|key, value|
-      this_aminoacid = Bioroebe.to_aa(key)
-      hash_aminoacids[this_aminoacid] += value
-    }
-    e
-    # ======================================================================= #
-    # Convert it into percent:
-    # ======================================================================= #
-    hash_aminoacids.each_pair {|key, value_for_percentage|
-      value_for_percentage = ((value_for_percentage * 100.0) / 1000.0).round(3).to_s
-      value_for_percentage = '%.2f' % value_for_percentage
-      e '  '+
-        steelblue(key).to_s+' '+
-        royalblue(
-          value_for_percentage.rjust(6)+'%'
-        )
-    }
-    e
-  end
-
-  # ========================================================================= #
-  # === Bioroebe.aminoacid_frequency
-  #
-  # Usage example:
-  #
-  #   Bioroebe.aminoacid_frequency('MVTDEGAIYFTKDAARNWKAAVEETVSATLNRTVSSGITGASYYTGTFST')
-  #
-  # Would yield the following Hash:
-  #
-  #   {"M"=>1, "V"=>4, "T"=>9, "D"=>2, "E"=>3, "G"=>4, "A"=>7, "I"=>2, "Y"=>3, "F"=>2, "K"=>2, "R"=>2, "N"=>2, "W"=>1, "S"=>5, "L"=>1}
-  #
-  # ========================================================================= #
-  def self.aminoacid_frequency(
-      of_this_sequence = ''
-    )
-    if of_this_sequence.is_a? Array
-      of_this_sequence = of_this_sequence.first 
-    end
-    chars = of_this_sequence.split(//)
-    hash = {}
-    hash.default = 0
-    chars.each {|this_char| hash[this_char] += 1 }
-    return hash
-  end; self.instance_eval { alias aminoacid_frequencies aminoacid_frequency } # === Bioroebe.aminoacid_frequencies
-
-end
-
-if __FILE__ == $PROGRAM_NAME
-  alias e puts
-  e
-  Bioroebe.calculate_the_frequencies_of_this_species(ARGV)
-  e
-  e 'Aminoacid frequency:'
-  e; print '  '
-  pp Bioroebe.aminoacid_frequency('MVTDEGAIYFTKDAARNWKAAVEETVSATLNRTVSSGITGASYYTGTFST')
-  e
-end # calculatethefrequenciesofthisspecies

data/lib/bioroebe/toplevel_methods/hamming_distance.rb

@@ -1,60 +0,0 @@
-#!/usr/bin/ruby -w
-# Encoding: UTF-8
-# frozen_string_literal: true
-# =========================================================================== #
-# require 'bioroebe/toplevel_methods/hamming_distance.rb'
-# Bioroebe.hamming_distance('ATCG','ATCC')
-# puts Bioroebe.hamming_distance(ARGV[0], ARGV[1])
-# =========================================================================== #
-module Bioroebe
-
-  # ========================================================================= #
-  # === Bioroebe.hamming_distance
-  #
-  # This method will return an Integer, aka a number, which represents
-  # the hamming distance between two sequences of equal length. This
-  # will state how many differences exist between two same-sized
-  # sequences (aka sequences that have the same length).
-  #
-  # Do note that a second implementation may exist for the hamming
-  # distance, in the Bioroebe project.
-  #
-  # Usage example:
-  #
-  #   Bioroebe.hamming_distance('ATCG','ATCC') # => 1
-  #
-  # ========================================================================= #
-  def self.hamming_distance(
-      sequence1 = 'ATCG',
-      sequence2 = 'ATCC'
-    )
-    if sequence1.nil?
-      e 'Please provide a sequence (String) as input to this method.'
-      return
-    end
-    if sequence1.is_a? String
-      sequence1 = sequence1.split(//)
-    end
-    if sequence2.is_a? String
-      sequence2 = sequence2.split(//)
-    end
-    array_sequence1 = [sequence1].flatten
-    array_sequence2 = [sequence2].flatten
-    # ======================================================================= #
-    # Zip the two sequences together, then reduce this Array of
-    # zipped values to an integer value, which will be returned.
-    # ======================================================================= #
-    zipped_array = array_sequence1.zip(array_sequence2)
-    hamming_value = 0
-    zipped_array.each { |left, right|
-      hamming_value += 1 unless left == right
-    }
-    return hamming_value
-  end; self.instance_eval { alias hamming hamming_distance } # === Bioroebe.hamming
-
-end
-
-if __FILE__ == $PROGRAM_NAME
-  puts Bioroebe.hamming_distance(ARGV[0], ARGV[1])
-end # hammingdistancemodulemethod GAGCCTACTAACGGGAT CATCGTAATGACGGCCT
-    # hammingdistancemodulemethod ATC ATT

data/lib/bioroebe/toplevel_methods/infer.rb

@@ -1,66 +0,0 @@
-#!/usr/bin/ruby -w
-# Encoding: UTF-8
-# frozen_string_literal: true
-# =========================================================================== #
-# This file may contain code that can be used to "infer" something.
-#
-# The primary use case is to infer whether a given sequence is DNA,
-# RNA or an aminoacid sequence.
-# =========================================================================== #
-# require 'bioroebe/toplevel_methods/infer.rb'
-# Bioroebe.infer_type_from_this_sequence
-# =========================================================================== #
-module Bioroebe
-
-  # ========================================================================= #
-  # === Bioroebe.infer_type_from_this_sequence
-  #
-  # This method will try to infer the type from a given sequence.
-  #
-  # The three valid return types are the following symbols:
-  #
-  #   :dna
-  #   :rna
-  #   :protein
-  #
-  # Note that this may not work 100% reliably, so do not depend too
-  # much on this method working absolutely perfect.
-  # ========================================================================= # 
-  def self.infer_type_from_this_sequence(
-      i = 'ATGGTACGACAC'
-    )
-    if i.is_a? Array
-      i = i.join
-    end
-    type = :dna # This is the default - DNA.
-    # ======================================================================= #
-    # === :rna
-    # ======================================================================= #
-    if i.include? 'U'
-      type = :rna
-    # ======================================================================= #
-    # === :dna
-    # ======================================================================= #
-    elsif i =~ /^[ATCG]+$/
-      type = :dna 
-    # ======================================================================= #
-    # === :protein
-    # ======================================================================= #
-    else # else simply assume this to be a protein.
-      type = :protein
-    end
-    return type
-  end; self.instance_eval { alias infer_the_type_from_this_sequence infer_type_from_this_sequence } # === Bioroebe.infer_the_type_from_this_sequence
-
-end
-
-if __FILE__ == $PROGRAM_NAME
-  if ARGV.empty?
-    # In this case test this.
-    pp Bioroebe.infer_type_from_this_sequence('ATCGATCATTCGATGCAGTCA')   # => :dna
-    pp Bioroebe.infer_type_from_this_sequence('UCAGUCAGUCAGUCAGUACGUCA') # => :rna
-    pp Bioroebe.infer_type_from_this_sequence('ATGGGVVVIIILLP')          # => :protein
-  else
-    pp Bioroebe.infer_type_from_this_sequence(ARGV)
-  end
-end # rb infer.rb ATCAGCTAGCATCA

data/lib/bioroebe/toplevel_methods/leading_five_prime_and_trailing_three_prime.rb

@@ -1,101 +0,0 @@
-#!/usr/bin/ruby -w
-# Encoding: UTF-8
-# frozen_string_literal: true
-# =========================================================================== #
-# require 'bioroebe/toplevel_methods/leading_five_prime_and_trailing_three_prime.rb'
-# Bioroebe.leading_five_prime(ARGV)
-# Bioroebe.trailing_three_prime(ARGV)
-# =========================================================================== #
-module Bioroebe
-
-  # ========================================================================= #
-  # === Bioroebe.leading_five_prime
-  #
-  # This method will output the leading 5' part of a nucleotide sequence,
-  # like a header. In this context, the most commonly usage case for
-  # this method is to display a leading "5'-" part to a sequence such
-  # as "ATCGATCG".
-  #
-  # The hyphen refers to the '-' character which may be used by this
-  # method. This is optional, though - have a look at the third
-  # argument to this method called `use_hyphen?.
-  # ========================================================================= #
-  def self.leading_five_prime(
-      i                 = '', # The default to '' is important.
-      get_rid_of_spaces = false,
-      use_hyphen        = true # By default this method will use '-' characters.
-    )
-    case get_rid_of_spaces
-    # ======================================================================= #
-    # === :no_spaces
-    # ======================================================================= #
-    when :no_spaces,
-         :get_rid_of_spaces
-      get_rid_of_spaces = true
-    end
-    if i.is_a? Array
-      i = i.join.strip
-    end
-    if use_hyphen
-      _ = "5' - #{i}" # ← This here is the header-tag.
-    else # This variant is a bit simpler and shorter.
-      _ = "5' #{i}" # ← This here is the header-tag.
-    end
-    if get_rid_of_spaces
-      _ = _.dup if _.frozen?
-      _.delete!(' ')
-    end
-    return _
-  end; self.instance_eval { alias five_prime               leading_five_prime } # === Bioroebe.five_prime
-       self.instance_eval { alias leading_5_prime          leading_five_prime } # === Bioroebe.leading_five_prime
-       self.instance_eval { alias leader                   leading_five_prime } # === Bioroebe.leader
-       self.instance_eval { alias lead_five_prime          leading_five_prime } # === Bioroebe.lead_five_prime
-       self.instance_eval { alias return_five_prime_header leading_five_prime } # === Bioroebe.return_five_prime
-       self.instance_eval { alias leading_five             leading_five_prime } # === Bioroebe.return_five
-
-  # ========================================================================= #
-  # === Bioroebe.trailing_three_prime
-  #
-  # This method will output the trailing 3' part, like a header (or rather,
-  # a trailer).
-  # ========================================================================= #
-  def self.trailing_three_prime(
-      i                 = '', # The default to '' is important.
-      get_rid_of_spaces = false,
-      use_hyphen        = true
-    )
-    case get_rid_of_spaces
-    # ======================================================================= #
-    # === :no_spaces
-    # ======================================================================= #
-    when :no_spaces,
-         :get_rid_of_spaces,
-         :eliminate_spaces
-      get_rid_of_spaces = true
-    end
-    if i.is_a? Array
-      i = i.join.strip
-    end
-    if use_hyphen
-      _ = "#{i} - 3'" # ← This here is the header-tag.
-    else # This variant is a bit simpler and shorter.
-      _ = "#{i} 3'"   # ← This here is the header-tag.
-    end
-    _.delete!(' ') if get_rid_of_spaces
-    return _
-  end; self.instance_eval { alias three_prime               trailing_three_prime } # === Bioroebe.three_prime
-       self.instance_eval { alias trailing_3_prime          trailing_three_prime } # === Bioroebe.trailing_three_prime
-       self.instance_eval { alias leader                    trailing_three_prime } # === Bioroebe.leader
-       self.instance_eval { alias lead_three_prime          trailing_three_prime } # === Bioroebe.lead_three_prime
-       self.instance_eval { alias return_three_prime_header trailing_three_prime } # === Bioroebe.return_three_prime
-       self.instance_eval { alias trailing_three            trailing_three_prime } # === Bioroebe.return_three
-
-end
-
-if __FILE__ == $PROGRAM_NAME
-  puts Bioroebe.leading_five_prime(ARGV)
-  puts Bioroebe.trailing_three_prime(ARGV)
-  puts Bioroebe.leading_five_prime(ARGV, :eliminate_spaces)
-  puts Bioroebe.trailing_three_prime(ARGV, :eliminate_spaces)
-end # leadingfiveprime   ATGCT
-    # trailingthreeprime ATGCT