bioroebe 0.10.80 → 0.11.32

data/lib/bioroebe/fasta_and_fastq/parse_fasta/misc.rb

@@ -1,981 +0,0 @@
-#!/usr/bin/ruby -w
-# Encoding: UTF-8
-# frozen_string_literal: true
-# =========================================================================== #
-# === Bioroebe::ParseFasta
-#
-# This class will parse through a local FASTA file and find the
-# proper entries.
-#
-# A FASTA file may have nucleotides or an aminoacid-sequence, so
-# we have to keep this in mind when parsing it.
-#
-# Usage examples:
-#
-#   Bioroebe::ParseFasta.new(ARGV)
-#   Bioroebe.parse_fasta(ARGV)
-#
-# =========================================================================== #
-# require 'bioroebe/fasta_and_fastq/parse_fasta/misc.rb'
-# Bioroebe.parse_fasta
-# Bioroebe.sizeseq
-# =========================================================================== #
-require 'bioroebe/base/commandline_application/commandline_application.rb'
-require 'bioroebe/fasta_and_fastq/parse_fasta/menu.rb'
-require 'bioroebe/fasta_and_fastq/parse_fasta/report.rb'
-
-module Bioroebe
-
-class ParseFasta < ::Bioroebe::CommandlineApplication # === Bioroebe::ParseFasta
-
-  require 'bioroebe/calculate/calculate_gc_content.rb'
-
-  # ========================================================================= #
-  # === show_help                                                  (help tag)
-  #
-  # This method will inform the user how this class may be used from the
-  # commandline.
-  #
-  # Invocation example:
-  #
-  #   pfasta --help
-  #
-  # ========================================================================= #
-  def show_help
-    e
-    eparse '  --size'
-    eparse '  --also-show-the-sequence'
-    eparse '  --header     # show the header as well (normally the '\
-           'header is not shown)'
-    eparse '  --limit=1000 # limit to show only the first 1000 '\
-           'nucleotides; use'
-    eparse '               # any number that you need here'
-    eparse '  --one-line   # show the sequence on one line only, '\
-           'e. g. all newlines'
-    eparse '               # were removed'
-    eparse '  --toprotein  # show the protein sequence as well '\
-           '(assumes DNA or RNA'
-    eparse '               # .fasta file)'
-    e
-  end
-
-  # ========================================================================= #
-  # === show_the_translated_protein_sequence?
-  # ========================================================================= #
-  def show_the_translated_protein_sequence?
-    @internal_hash[:show_the_translated_protein_sequence]
-  end
-
-  # ========================================================================= #
-  # === set_round_to
-  #
-  # This will set to how many decimal numbers we will round to. This is
-  # mostly done for display-purposes, hence why the default is a fairly
-  # low value.
-  # ========================================================================= #
-  def set_round_to(
-      i = :default
-    )
-    case i
-    # ======================================================================= #
-    # === :default
-    #
-    # Since as of April 2021, the new default is 2, for rounding.
-    # ======================================================================= #
-    when :default
-      i = DEFAULT_ROUND_TO
-    end
-    @round_to = i.to_i
-  end
-
-  # ========================================================================= #
-  # === do_process_the_commandline_arguments_that_are_files
-  # ========================================================================= #
-  def do_process_the_commandline_arguments_that_are_files(
-      these_files = commandline_arguments_that_are_files?
-    )
-    unless these_files.is_a? Array
-      these_files = [these_files].flatten.compact
-    end
-    these_files.each {|this_file|
-      set_input_file(this_file)
-      set_data # This will use the default file.
-      split_into_proper_sections
-      report_the_FASTA_header if @show_the_header
-      if @sort_by_size
-        run_sizeseq_comparison
-      else
-        # =================================================================== #
-        # === Handle cases where the input is a protein
-        # =================================================================== #
-        if is_the_sequence_a_polypeptide?
-          if be_verbose?
-            erev "This sequence is assumed to be a #{royalblue('protein')}#{rev}."
-            report_how_many_elements_we_have_found
-          end
-        else # Must be a protein.
-          # =================================================================== #
-          # === Else it must be RNA or DNA
-          # =================================================================== #
-          if be_verbose?
-            erev "This sequence is assumed to "\
-                 "be #{royalblue('DNA')}#{rev} or #{royalblue('RNA')}#{rev}."
-          end
-          calculate_gc_content # GC content makes only sense for nucleotides.
-          report_how_many_elements_we_have_found if be_verbose?
-        end
-        if be_verbose?
-          report_the_nucleotide_composition
-          report_on_how_many_entries_we_did_work
-          if report_the_sequence?
-            do_report_the_sequence
-          end
-        end
-      end
-    }
-  end
-
-  # ========================================================================= #
-  # === sanitize_the_description
-  #
-  # This method will iterate over the description entry and sanitize
-  # it. In this context sanitizing means to add the "length" entry,
-  # and the "type" entry, such as in:
-  #
-  #   " # length=231; type=dna"
-  #
-  # ========================================================================= #
-  def sanitize_the_description
-    @data.map! {|line|
-      if line.start_with?('>') and !line.include?('length=')
-        length = 0
-        if @hash.has_key? line.delete('>')
-          length = @hash[line.delete('>')].size
-        end
-        line << " # length=#{length}; type=dna" # Currently hardcoded to DNA.
-      end
-      line
-    }
-  end
-
-  # ========================================================================= #
-  # === entries?
-  # ========================================================================= #
-  def entries?
-    @data
-  end
-
-  # ========================================================================= #
-  # === we_may_exit
-  # ========================================================================= #
-  def we_may_exit
-    @may_we_exit = true
-  end
-
-  # ========================================================================= #
-  # === output_results
-  # ========================================================================= #
-  def output_results
-    pp @hash
-  end
-
-  # ========================================================================= #
-  # === sanitize_data
-  # ========================================================================= #
-  def sanitize_data(i)
-    if i.is_a? Array
-      i.flatten!
-      i.reject! {|entry| entry.start_with? '#' }
-      i.reject! {|entry| entry.strip.empty? }
-      if i.first and i.first.include? "\r"
-        # =================================================================== #
-        # Some FASTA files include "\r" line endings. We will check first
-        # for the first entry to contain a \r, and if so, we assume the
-        # whole FASTA file may have \r, which then will be removed.
-        # =================================================================== #
-        i.map! {|entry| entry.delete("\r") }
-      end
-    end
-    # ========================================================================= #
-    # === Run through SanitizeNucleotideSequence
-    # ========================================================================= #
-    if @internal_hash[:remove_numbers_from_input]
-      i = Bioroebe::SanitizeNucleotideSequence[i]
-    end
-    i
-  end
-
-  # ========================================================================= #
-  # === current_key?
-  # ========================================================================= #
-  def current_key?
-    @current_key
-  end; alias id?          current_key? # === id?
-       alias sequence_id? current_key? # === sequence_id?
-       alias title        current_key? # === title
-       alias title?       current_key? # === title?
-
-  # ========================================================================= #
-  # === opnn
-  # ========================================================================= #
-  def opnn
-    super(NAMESPACE) if use_opn?
-  end
-  
-  # ========================================================================= #
-  # === use_opn?
-  # ========================================================================= #
-  def use_opn?
-    @use_opn
-  end
-
-  # ========================================================================= #
-  # === calculate_gc_content
-  #
-  # Calculate the gc content through this method, which is called from
-  # within the method run().
-  # ========================================================================= #
-  def calculate_gc_content
-    _ = @hash.values.join.delete(N)
-    if is_polynucleotide? _
-      @hash.each_pair {|key, content|
-        # =================================================================== #
-        # Delegate towards the method Bioroebe.gc_content next, including
-        # to round towards 5 positions:
-        # =================================================================== #
-        gc_content = ::Bioroebe.gc_content(content.upcase, @round_to)
-        gc_content = gc_content.first if gc_content.is_a? Array
-        gc_content = gc_content.to_s
-        minimal_key = key.to_s
-        if minimal_key.include? '|'
-          minimal_key = minimal_key.split('|').last.strip
-        end
-        if be_verbose?
-          _ = minimal_key.strip
-          if _.size > 40 # Shorten the content a bit if it is too long.
-            _ = _[0 .. 40]+' [...]'
-          end
-          erev 'GC content of "'+simp(_)+rev+'" is: '+
-               "#{sfancy(gc_content)}#{rev} %"
-        end
-      }
-    else
-      erev '`'+simp(_)+rev+'` is not a polynucleotide.' if be_verbose?
-    end
-  end
-
-  # ========================================================================= #
-  # === first_value
-  #
-  # This will return the first entry of the Fasta files.
-  # ========================================================================= #
-  def first_value
-    sequences?.first
-  end
-
-  # ========================================================================= #
-  # === nucleotides_or_aminoacids?
-  # ========================================================================= #
-  def nucleotides_or_aminoacids?
-    if is_polynucleotide?
-      'nucleotides'
-    else
-      'aminoacids'
-    end
-  end
-
-  # ========================================================================= #
-  # === is_polynucleotide?
-  # ========================================================================= #
-  def is_polynucleotide?(i = main_sequence?)
-    !is_protein?(i)
-  end; alias is_a_nucleotide? is_polynucleotide? # === is_a_nucleotide?
-
-  # ========================================================================= #
-  # === is_this_sequence_a_polynucleotide_sequence?
-  # ========================================================================= #
-  def is_this_sequence_a_polynucleotide_sequence?
-    !is_protein?
-  end
-
-  # ========================================================================= #
-  # === data?
-  #
-  # This will contain the full content of the (whole) .fasta file, including
-  # the header.
-  # ========================================================================= #
-  def data?
-    @data
-  end; alias input?   data? # === input?
-       alias dataset? data? # === dataset?
-
-  # ========================================================================= #
-  # === hash?
-  # ========================================================================= #
-  def hash?
-    @hash
-  end
-
-  # ========================================================================= #
-  # === sequences?
-  #
-  # This method will obtain all found sequences.
-  # ========================================================================= #
-  def sequences?
-    @hash.values
-  end; alias sequences sequences? # === sequences
-       alias values    sequences? # === values
-
-  # ========================================================================= #
-  # === short_headers?
-  #
-  # The short-headers are like the headers, but if a ' ' token is found
-  # then the line will be truncated towards that first ' '.
-  #
-  # An example is:
-  #
-  #   sp|Q91FT8|234R_IIV6 Uncharacterized protein 234R OS=Invertebrate iridescent virus 6 OX=176652 GN=IIV6-234R PE=4 SV=1
-  #
-  # This will be truncated towards
-  #
-  #   sp|Q91FT8|234R_IIV6
-  #
-  # This could then be used to automatically rename FASTA files, for
-  # instance.
-  # ========================================================================= #
-  def short_headers?
-    headers?.map {|entry|
-      if entry.include? ' '
-        entry = entry.split(' ').first
-      end
-      entry
-    }
-  end
-
-  # ========================================================================= #
-  # === set_data
-  #
-  # This is the setter-method towards @data. It is no longer allowed to
-  # invoke set_input_file() since as of 12.06.2020. This means that
-  # you have to invoke that method prior to calling this method.
-  # ========================================================================= #
-  def set_data(i = @input_file)
-    # ======================================================================= #
-    # The next line attempts to ensure that even an Array can be used
-    # as input to that method.
-    # ======================================================================= #
-    i = [i].flatten.compact.first.to_s.dup
-    if File.exist? i.to_s # First try to read in from a file.
-      if be_verbose?
-        opnn; erev "Will read from the file `#{sfile(i)}#{rev}`."
-      end
-      i = File.readlines(i)
-      if @is_a_genbank_file
-        selected = i.select {|line|
-          line.start_with?('       ') and # such as: "       61 atggggcctg caatggggcc tgcaatgggg cctgca\n"
-          (line.strip =~ /\d+/)
-        }.map {|inner_line|
-          inner_line.strip.delete(' 0123456789').strip.upcase
-        }
-        i = ["> genbank file"]+selected
-      end
-    end
-    if i.nil? or i.empty?
-      i = DEFAULT_FASTA
-      opnn; erev 'No input was provided. Thus a default FASTA '\
-                 'sequence will be used instead.'
-    end
-    i = sanitize_data(i)
-    i = i.split(N) if i.is_a? String
-    @data = i
-  end; alias set_sequence set_data # === set_Sequence
-
-  # ========================================================================= #
-  # === set_be_verbose_and_report_the_sequence
-  # ========================================================================= #
-  def set_be_verbose_and_report_the_sequence
-    set_be_verbose
-    @internal_hash[:report_the_sequence] = true
-  end
-
-  # ========================================================================= #
-  # === condense_the_sequence_onto_a_single_line?
-  # ========================================================================= #
-  def condense_the_sequence_onto_a_single_line?
-    @internal_hash[:condense_the_sequence_onto_a_single_line]
-  end
- 
-  # ========================================================================= #
-  # === return_size_sorted_hash
-  # ========================================================================= #
-  def return_size_sorted_hash(i = @hash)
-    _ = i.sort_by {|key, value| value.size }
-    i = Hash[_]
-    return i
-  end
-
-  # ========================================================================= #
-  # === do_sort_by_size
-  #
-  # This method will sort the hash by size of the sequence. It has been
-  # inspired by the EMBOSS sizeq functionality.
-  #
-  # The output that should be generated might look like this:
-  #
-  #   https://www.bioinformatics.nl/cgi-bin/emboss/help/sizeseq#input.1
-  #
-  # Invocation example:
-  #
-  #   x = Bioroebe::ParseFasta.new('/Depot/j/globins.fasta'); x.do_sort_by_size
-  #
-  # ========================================================================= #
-  def do_sort_by_size
-    # ======================================================================= #
-    # Sort it here first, by the size of the "value", aka the sequence body.
-    # ======================================================================= #
-    @hash = return_size_sorted_hash(@hash)
-    _ = ''.dup
-    @hash.each_pair {|key, sequence|
-      _ << '> ID '+sequence.size.to_s+' AA.; DE: '+key.to_s+
-           ' SQ '+sequence.size.to_s+' AA'+N # ; unknown MW as of yet; '\
-           #'unknown CRC64 as of yet'+N
-      _ << sequence+N+N
-    }
-    e _
-  end; alias run_sizeseq_comparison do_sort_by_size # === run_sizeseq_comparison
-
-  # ========================================================================= #
-  # === n_nucleotides?
-  # ========================================================================= #
-  def n_nucleotides?
-    @hash.values.first.delete("\n").size
-  end; alias return_n_aminoacids n_nucleotides? # === return_n_aminoacids
-       alias size?               n_nucleotides? # === size?
-       alias sequence_size?      n_nucleotides? # === sequence_size?
-
-  # ========================================================================= #
-  # === headers?
-  # ========================================================================= #
-  def headers?
-    @hash.keys
-  end
-
-  # ========================================================================= #
-  # === first_key?
-  #
-  # Obtain the very first entry.
-  # ========================================================================= #
-  def first_key?
-    headers?.first
-  end
-
-  # ========================================================================= #
-  # === header?
-  #
-  # This variant will always return the first entry.
-  # ========================================================================= #
-  def header?
-    headers?.first.to_s
-  end
-
-  # ========================================================================= #
-  # === raw_body?
-  # ========================================================================= #
-  def raw_body?
-    @hash.values.first
-  end
-
-  # ========================================================================= #
-  # === do_show_the_header
-  # ========================================================================= #
-  def do_show_the_header
-    @show_the_header = true
-  end
-
-  # ========================================================================= #
-  # === set_input_file
-  #
-  # This method will be used to keep track of the input-file, from
-  # which we will read the dataset.
-  # ========================================================================= #
-  def set_input_file(i = nil)
-    if i.nil?
-      # ===================================================================== #
-      # First, we try to find a .fasta or .fa file in the current
-      # directory. If we can find it, we will use that instead.
-      # ===================================================================== #
-      unless Dir['*.{fa,fasta}'].empty?
-        file = Dir['*.{fa,fasta}'].first
-        if be_verbose?
-          result = 'A '
-          if file.end_with? '.fasta'
-            result < 'FASTA '
-          end
-          result << 'file was found in this directory ('+sfile(file)+').'
-          opnn; erev result
-          opnn; erev 'We will use it.'
-        end
-        i = file
-      end
-      unless Dir['*.{fa,fasta}'].empty?
-        file = Dir['*.{fa,fasta}'].first
-        if be_verbose?
-          opnn; erev "We have found a file in this "\
-                     "directory (#{sfile(file)}#{rev})."
-          opnn; erev 'We will use it.'
-        end
-        i = file
-      end
-    end
-    if i and File.exist?(i)
-      dataset = File.read(i)
-      if dataset[0 .. ('LOCUS'.size - 1)] == 'LOCUS'
-        @is_a_genbank_file = true
-      end
-    end
-    @input_file = i
-  end; alias set_input_files set_input_file # === set_input_files
-
-  # ========================================================================= #
-  # === save_the_file?
-  # ========================================================================= #
-  def save_the_file?
-    @internal_hash[:save_the_file]
-  end
-
-  # ========================================================================= #
-  # === overwrite_the_original_file?
-  # ========================================================================= #
-  def overwrite_the_original_file?
-    @internal_hash[:overwrite_the_original_file]
-  end
-
-  # ========================================================================= #
-  # === split_into_proper_sections
-  #
-  # Split up into the fasta identifier, and the content.
-  # ========================================================================= #
-  def split_into_proper_sections
-    unless @data.to_s.include? '>'
-      erev 'No ">" character was found in this dataset.'
-      erev 'It is recommended to always have a > identifier '\
-           'for the'
-      erev 'FASTA format (such as in a .fasta or a .fa file).'
-    end if be_verbose? # Ok, the input data includes >. We can proceed.
-    @data.each { |line|
-      # ===================================================================== #
-      # === Handle the leading > FASTA identifier first
-      # ===================================================================== #
-      if line.start_with? '>' # leading identifier.
-        @current_key = line[1..-1].chomp # Select all but the first character.
-        @hash[@current_key] = ''.dup
-      else
-        line.delete!('_')
-        unless @current_key
-          @current_key = 'standard'
-          @hash[@current_key] = ''.dup
-        end
-        # =================================================================== #
-        # === Retain the newlines
-        #
-        # Here we may decide to get rid of newlines, but it is better to
-        # NOT remove the newlines - that way we can simply save the
-        # dataset again.
-        # @hash[@current_key] << no_newlines(line)
-        # =================================================================== #
-        @hash[@current_key] << line
-      end
-    }
-  end
-
-  # ========================================================================= #
-  # ===   save_into_a_fasta_file
-  # ========================================================================= #
-  def save_into_a_fasta_file(
-      be_verbose = be_verbose?
-    )
-    case be_verbose
-    when :be_verbose
-      be_verbose = true
-    end
-    if @data
-      what = @data.join("\n")
-      into = 'standard.fasta'
-      erev 'Saving into '+sfile(into)+rev+'.' if be_verbose
-      write_what_into(what, into)
-      return File.absolute_path(into) # And return the file we saved into.
-    else
-      opnn; erev 'No @data variable exists.'
-    end
-  end; alias do_save_the_file save_into_a_fasta_file # === do_save_the_file
-
-  # ========================================================================= #
-  # === add_length_information_to_the_header
-  # ========================================================================= #
-  def add_length_information_to_the_header
-    _ = header?.strip
-    _ << ' length='+sequence_size?.to_s+';'
-    # ======================================================================= #
-    # Next, designate where to store this file.
-    # ======================================================================= #
-    into = 'new_fasta_file.fasta'
-    if overwrite_the_original_file?
-      into = @input_file
-    end
-    what = ''.dup
-    what << "> "+_+"\n"
-    what << raw_body?
-    if what and into
-      erev 'Storing into `'+sfile(into)+rev+'`.'
-      write_what_into(what, into)
-    end
-  end
-
-  # ========================================================================= #
-  # === simplify_header
-  #
-  # This method can be called to simplify the header. It will save into
-  # a .fasta file at once.
-  # ========================================================================= #
-  def simplify_header
-    _ = header?
-    # ======================================================================= #
-    # Next, simplify the header. We must start with checking for [] first,
-    # because if there are any [] in the FASTA header then we can simplify
-    # stuff at once.
-    # ======================================================================= #
-    if _.include?('[') and _.include?(']')
-      _ = '> '+_.strip.scan(/\[.+\]/).flatten.first.delete('[]')+"\n"
-    elsif _.include? ','
-      _ = _[0 .. (_.index(',') - 1) ].strip
-    end
-    what = nil
-    # ======================================================================= #
-    # Next, designate where to store this file.
-    # ======================================================================= #
-    into = 'new_fasta_file.fasta'
-    if overwrite_the_original_file?
-      into = @input_file
-    end
-    if _.start_with? '>'
-      what = _
-    elsif _.include?('[') and _.include?(']') # For example: [Pan troglodytes]
-      # ===================================================================== #
-      # See rubular at:
-      #
-      #   https://rubular.com/r/aDjI0JwMOUlZzP
-      #
-      # ===================================================================== #
-      what = "> "+_.scan(/\[(.+)\]/).flatten.first.to_s+"\n".dup 
-    elsif _.include? 'Human'
-      _scanned_result = _.scan(/(Human)/)
-      what = "> "+$1.to_s.dup+"\n".dup
-    else
-      erev "Unsure what to do: #{steelblue(_)}"
-    end
-    if what and into
-      what << raw_body?
-      erev 'Storing into `'+sfile(into)+rev+'`.'
-      write_what_into(what, into)
-    end
-  end
-
-  # ========================================================================= #
-  # === sequence
-  #
-  # This method will return the sequence, without any newlines. It is also
-  # called the "body" of a FASTA file.
-  # ========================================================================= #
-  def sequence
-    _ = @hash.values.first
-    _.chomp! if _ and _.end_with?(N)
-    return no_newlines(_)
-  end; alias fasta_sequence      sequence # === fasta_sequence
-       alias sequence?           sequence # === sequence?
-       alias body?               sequence # === body?
-       alias body                sequence # === body?
-       alias naseq               sequence # === naseq
-       alias nucleotide_sequence sequence # === nucleotide_sequence
-       alias return_sequence     sequence # === return_sequence
-       alias content?            sequence # === content?
-
-  # ========================================================================= #
-  # === save
-  #
-  # This method will save our FASTA file.
-  # ========================================================================= #
-  def save
-    if @input_file.nil?
-      erev "The generic file #{sfile('foobar.fasta')}#{rev} "\
-           "will be used."
-      set_input_file('foobar.fasta')
-    end
-    into = @input_file
-    what = @data.join("\n")
-    erev 'Storing into '+sfile(into)+rev+'.'
-    write_what_into(what, into)
-    return into
-  end
-
-  # ========================================================================= #
-  # === []
-  #
-  # This is a simpler query-interface for obtaining the DNA/RNA sequence
-  # of the FASTA file (or aminoacid sequence, if we have a protein at
-  # hand here).
-  #
-  # Using the method sequences? here, which in turn works on @hash, is
-  # ok because Hashes are kept in a sorted manner in ruby since some
-  # time.
-  # ========================================================================= #
-  def [](i)
-    sequences?[i]
-  end
-
-  # ========================================================================= #
-  # === Bioroebe::ParseFasta[]
-  # ========================================================================= #
-  def self.[](i)
-    _ = new(i)
-    _.sequences?
-  end
-
-  # ========================================================================= #
-  # === type?
-  # ========================================================================= #
-  def type?
-    if is_the_sequence_a_polypeptide?
-      :protein
-    elsif is_this_sequence_a_polynucleotide_sequence?
-      :dna_or_rna
-    else
-      :unknown
-    end
-  end
-
-  # ========================================================================= #
-  # === is_the_sequence_a_polypeptide?
-  #
-  # This method can be used to determine whether a given input sequence
-  # is a polypeptide (aka a protein) or whether it is not.
-  #
-  # If this sequence is a polypeptide then this method will return true.
-  # Otherwise false will be returned.
-  # ========================================================================= #
-  def is_the_sequence_a_polypeptide?(
-      i = main_sequence?
-    )
-    return_value = false # Set the default return value here.
-    # ======================================================================= #
-    # Look at the first 120 positions to determine whether this is a protein
-    # or a nucleotide sequence.
-    # ======================================================================= #
-    subsequence = i[0 .. 119] # Must deduct 1 at the end since Arrays in ruby start at 0.
-    # ======================================================================= #
-    # Build a frequency of the characters there.
-    # ======================================================================= #
-    hash = {}
-    hash.default = 0
-    subsequence.chars.each {|character|
-      hash[character] += 1
-    }
-    keys_to_check_for = %w(
-      B D E F H I J K L M O P Q R S V W X Y Z
-    )
-
-    values = hash.select {|key, value|
-      if keys_to_check_for.include? key
-        true
-      else
-        false
-      end
-    }.values.sum
-    if values > 0
-      return_value = true
-    end
-    return return_value
-  end; alias is_protein?   is_the_sequence_a_polypeptide? # === is_protein?
-       alias is_a_protein? is_the_sequence_a_polypeptide? # === is_a_protein?
-
-  # ========================================================================= #
-  # === main_sequence?
-  #
-  # This will always return the first entry.
-  # ========================================================================= #
-  def main_sequence?
-    @hash.values.first
-  end
-
-  # ========================================================================= #
-  # === gc_content?
-  # ========================================================================= #
-  def gc_content?
-    return ::Bioroebe.gc_content(main_sequence?).to_f # Must be a float.
-  end; alias gc_content gc_content? # === gc_content
-
-  # ========================================================================= #
-  # === sequence_object
-  #
-  # This method will return a Sequence object.
-  #
-  # Usage example:
-  #
-  #   x = Bioroebe.parse_fasta 'ls_orchid.fasta'
-  #   y = x.sequence_object # y is now an instance of Bioroebe::Sequence
-  #
-  # ========================================================================= #
-  def sequence_object
-    ::Bioroebe::Sequence.new(main_sequence?)
-  end
-
-end
-
-Fasta = ParseFasta # Add an "alias" constant to class ParseFasta.
-
-# =========================================================================== #
-# === Bioroebe.parse_fasta_quietly
-#
-# As the variant above, but will work quietly.
-# =========================================================================== #
-def self.parse_fasta_quietly(
-    i, use_colours = true
-  )
-  ::Bioroebe.parse_fasta(i, use_colours) { :be_quiet }
-end
-
-# =========================================================================== #
-# === Bioroebe.return_fasta_entry_with_the_highest_gc_content
-#
-# The first argument should be a locally existing FASTA file that
-# contains different sequences.
-#
-# Usage example:
-#
-#   x = Bioroebe.return_fasta_entry_with_the_highest_gc_content('/rosalind_gc.txt')
-#
-# =========================================================================== #
-def self.return_fasta_entry_with_the_highest_gc_content(this_fasta_file)
-  if File.exist? this_fasta_file
-    dataset = File.read(this_fasta_file)
-    dataset = parse_fasta(dataset) { :be_quiet }
-    hash = dataset.hash?
-    hash.transform_values! {|this_value|
-      ::Bioroebe.gc_content(this_value).to_f
-    }
-    return hash.max_by {|key, value| value }
-  else
-    erev "No file exists at #{sfile(this_fasta_file)}#{rev}."
-  end
-end
-
-# =========================================================================== #
-# === Bioroebe.sizeseq
-#
-# This method will "size-sequence compare", typically on a .fasta file.
-# =========================================================================== #
-def self.sizeseq(i)
-  if i.is_a? Array
-    i = i.first
-  end
-  _ = Bioroebe.parse_fasta(i) { :be_quiet }
-  _.do_sort_by_size
-end
-
-# =========================================================================== #
-# === Bioroebe.return_sizeseq
-#
-# This is as Bioroebe.sizeseq(), but it will just return the result,
-# rather than output it.
-# =========================================================================== #
-def self.return_sizeseq(i)
-  if i.is_a? Array
-    i = i.first
-  end
-  _ = Bioroebe.parse_fasta(i) { :be_quiet }
-  hash = _.return_size_sorted_hash
-  result = ''.dup
-  hash.each_pair {|key, sequence|
-    result << '> ID '+sequence.size.to_s+' AA.; DE: '+key.to_s+
-         ' SQ '+sequence.size.to_s+' AA'+N
-    result << sequence+N+N
-  }
-  return result
-end
-
-# =========================================================================== #
-# === Bioroebe.genbank_to_fasta
-#
-# This method will convert from a genbank file, to a .fasta file.
-#
-# Invocation example:
-#
-#   Bioroebe.genbank_to_fasta('/home/x/DATA/PROGRAMMING_LANGUAGES/RUBY/src/bioroebe/lib/bioroebe/data/genbank/sample_file.genbank')
-#
-# =========================================================================== #
-def self.genbank_to_fasta(
-    this_file,
-    be_verbose = :be_verbose
-  )
-  case be_verbose
-  when :be_quiet
-    be_verbose = false
-  end
-  if this_file.is_a? Array
-    this_file = this_file.first
-  end
-  if File.exist? this_file
-    _ = Bioroebe::ParseFasta.new(this_file) { :be_quiet }
-  else
-    _ = Bioroebe::ParseFasta.new(:do_not_run_yet) { :be_quiet }
-    _.set_data # This will use the default file.
-    _.split_into_proper_sections
-  end
-  file_path = _.save_into_a_fasta_file(be_verbose)
-  return file_path
-end
-
-# =========================================================================== #
-# === Bioroebe.parse_fasta_file
-# =========================================================================== #
-def self.parse_fasta_file(
-    i, use_colours = true
-  )
-  use_this_hash = {
-    use_colours: use_colours,
-    be_verbose:  false
-  }
-  ParseFasta.new(i) { use_this_hash }
-end; self.instance_eval { alias fasta_file parse_fasta_file } # === Bioroebe.fasta_file
-
-# =========================================================================== #
-# === Bioroebe.parse_fasta
-#
-# Easier reader-method for .fasta files.
-#
-# The second argument determines whether we will use colours or whether
-# we will not. For now, the default is to not use colours when we use
-# this particular class method.
-#
-# Invocation examples:
-#
-#   x = Bioroebe.parse_fasta('/rosalind_gc.txt')
-#   hash = Bioroebe.parse_fasta('/rosalind_gc.txt').hash?
-#
-# =========================================================================== #
-def self.parse_fasta(
-    i,
-    use_colours = true
-  )
-  use_this_hash = {
-    use_colours: use_colours
-  }
-  if block_given?
-    use_this_hash = {
-      use_colours: use_colours,
-      be_verbose:  yield
-    }
-  end
-  ::Bioroebe::ParseFasta.new(i) { use_this_hash }
-end; self.instance_eval { alias fasta parse_fasta } # === Bioroebe.fasta
-
-end