Class: Bioroebe::DeduceAminoacidSequence

Inherits:
CommandlineApplication show all
Defined in:
lib/bioroebe/aminoacids/deduce_aminoacid_sequence.rb

Overview

Bioroebe::DeduceAminoacidSequence

Constant Summary collapse

DEFAULT_SEQUENCE =
#

DEFAULT_SEQUENCE

This constant specifies a default aminoacid sequence that could be used.

#
'M-K-S-P-S-L-N-A-A-K'

Constants inherited from CommandlineApplication

CommandlineApplication::OLD_VERBOSE_VALUE

Constants included from ColoursForBase

ColoursForBase::ARRAY_HTML_COLOURS_IN_USE

Constants inherited from Base

Base::NAMESPACE

Class Method Summary collapse

Instance Method Summary collapse

Methods inherited from CommandlineApplication

#all_aminoacids?, #append_what_into, #at_home?, #be_silent, #be_verbose?, #cat, #ccliner, #change_directory, #cliner, #codon_table_dataset?, #codon_to_aminoacid, #codons_for?, #colourize_this_dna_sequence, #complement, #cp, #disable_warnings, #download_dir?, #editor?, #enable_warnings, #ensure_that_the_base_directories_exist, #esystem, #extract, #is_this_a_start_codon?, #is_this_a_stop_codon?, #leading_five_prime, #load_bioroebe_yaml_file, #log_directory?, #one_letter_to_long_name, #one_to_three, #only_numbers?, #open_in_browser, #opnerev, #opnn, #pad_with_double_quotes, #pad_with_single_quotes, #partner_nucleotide, #remove_numbers, #remove_trailing_ansii_escape_code, #return_all_possible_start_codons, #return_array_of_one_letter_aminoacids, #return_cheerful_person, #return_chunked_display, #return_ubiquitin_sequence, #runmode?, #set_be_verbose, #set_runmode, #start_codon?, #stop_codons?, #strict_filter_away_invalid_aminoacids, #taxonomy_download_directory?, #three_to_one, #to_rna, #trailing_three_prime, #use_opn?, #verbose_truth, #was_or_were, #without_extname, #write_what_into

Methods included from BaseModule

#absolute_path, #default_file_read, #file_readlines

Methods included from CommandlineArguments

#commandline_arguments?, #commandline_arguments_that_are_files?, #e, #first?, #first_non_hyphen_argument?, #remove_hyphens_from_the_commandline_arguments, #return_commandline_arguments_as_string, #return_commandline_arguments_that_are_not_files, #return_entries_without_two_leading_hyphens, #select_commandline_arguments, #select_entries_starting_with_two_hyphens, #set_commandline_arguments

Methods included from ColoursForBase

#colourize_this_aminoacid_sequence_for_the_commandline, #colourize_this_nucleotide_sequence, #disable_colours, #ecomment, #efancy, #egold, #enable_colours, #eorange, #eparse, #erev, #red, #remove_trailing_escape_part, #return_colour_for_nucleotides, #rev, #sdir, #set_will_we_use_colours, #sfancy, #sfile, #simp, #swarn, #use_colours?, #use_colours_within_the_bioroebe_namespace?

Methods inherited from Base

#append_what_into, #can_base_pair?, #convert_global_env, #delete_file, #directory_to_the_codon_tables?, #is_on_roebe?, #is_palindrome?, #main_encoding?, #mkdir, #move_file, #mv, #no_file_exists_at, #no_newlines, #project_yaml_directory?, #rds, #register_sigint, #return_pwd, #return_the_first_line_of_this_file, #word_wrap, #write_what_into

Methods included from InternalHashModule

#internal_hash?, #reset_the_internal_hash

Methods included from InferTheNamespaceModule

#infer_the_namespace, #namespace?

Constructor Details

#initialize(commandline_arguments = DEFAULT_SEQUENCE, format_how = :dna, run_already = true) ⇒ DeduceAminoacidSequence

#

initialize

#


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# File 'lib/bioroebe/aminoacids/deduce_aminoacid_sequence.rb', line 53

def initialize(
    commandline_arguments = DEFAULT_SEQUENCE,
    format_how            = :dna,
    run_already           = true
  )
  reset
  set_commandline_arguments(
    commandline_arguments
  )
  set_format_how(format_how)
  run if run_already
end

Class Method Details

.[](i = ARGV) ⇒ Object

#

Bioroebe::DeduceAminoacidSequence[]

#


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# File 'lib/bioroebe/aminoacids/deduce_aminoacid_sequence.rb', line 456

def self.[](i = ARGV)
  new(i)
end

Instance Method Details

#aminoacid_sequence? ⇒ Boolean Also known as: input?, array_aminoacid_sequence?, main_array?

#

aminoacid_sequence?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/aminoacids/deduce_aminoacid_sequence.rb', line 382

def aminoacid_sequence?
  @internal_hash[:aminoacid_sequence]
end

#aminoacid_to_possible_codons(this_aminoacid) ⇒ Object Also known as: possible_codons_for_this_aminoacid, show_possible_codons_for_this_aminoacid

#

aminoacid_to_possible_codons

Internally this method depends on class PossibleCodonsForThisAminoacid.

#


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# File 'lib/bioroebe/aminoacids/deduce_aminoacid_sequence.rb', line 374

def aminoacid_to_possible_codons(this_aminoacid)
  return ::Bioroebe.aminoacid_to_possible_codons(this_aminoacid).sort # .sort was added on 25.09.2019
end

#array_all_discovered_codons? ⇒ Boolean Also known as: all_codons?, codons_to_use?, discovered_codons?

#

array_all_discovered_codons?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/aminoacids/deduce_aminoacid_sequence.rb', line 228

def array_all_discovered_codons?
  @internal_hash[:array_all_discovered_codons]
end

#determine_the_aminoacid_sequence(from_this_given_input = first? ) ⇒ Object

#

determine_the_aminoacid_sequence

#


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# File 'lib/bioroebe/aminoacids/deduce_aminoacid_sequence.rb', line 152

def determine_the_aminoacid_sequence(
    from_this_given_input = first?
  )
  set_aminoacid_sequence(from_this_given_input)
end

#display_separator(n_aminoacids = n_aminoacids? ) ⇒ Object

#

display_separator (middle tag)

#


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# File 'lib/bioroebe/aminoacids/deduce_aminoacid_sequence.rb', line 277

def display_separator(
    n_aminoacids = n_aminoacids?
  )
  distance = UNICODE_HORIZONTAL_BAR*5# + '┬'
  e ' '+swarn(
    (
      (distance * n_aminoacids)+'----'
    ).chop
  )
end

#do_show_a_possible_sequence(array = first_row_of_the_codons_to_use? ) ⇒ Object

#

do_show_a_possible_sequence

This will simply show the very first sequence that would code for the given codon at hand.

#


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# File 'lib/bioroebe/aminoacids/deduce_aminoacid_sequence.rb', line 247

def do_show_a_possible_sequence(
    array = first_row_of_the_codons_to_use?
  )
  erev 'One likely possible '+
       colourize_dna_sequence('sequence ')+
       'on the DNA/RNA level '\
       'may thus be:'
  e
  _ = array
  sequence = '  '+_.join('-')
  ruler = ::Bioroebe.ruler_return_as_string_without_colours(sequence.strip.delete('-'))
  ruler = ruler.scan(/.{3}|.+/).join('-')
  n_nucleotides = springgreen(
    ruler.strip.delete('-').size.to_s
  )
  erev '     '+ruler+' # ('+n_nucleotides+rev+' nucleotides)'
  result = colourize_this_dna_sequence(sequence.strip)
  if show_the_rna_sequence?
    result.tr!('T','U')
  end
  erev "  5'-"+result+"-3'"
  e '     '+
      result.delete('-')+
      rev+' (← standalone sequence)'
  e
end

#do_show_the_rna_sequence ⇒ Object

#

do_show_the_rna_sequence

#


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# File 'lib/bioroebe/aminoacids/deduce_aminoacid_sequence.rb', line 145

def do_show_the_rna_sequence
  set_show_the_rna_sequence :rna
end

#first_row_of_the_codons_to_use? ⇒ Boolean

#

first_row_of_the_codons_to_use?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/aminoacids/deduce_aminoacid_sequence.rb', line 237

def first_row_of_the_codons_to_use?
  return codons_to_use?.map {|inner_array| inner_array[0] }.compact
end

#map_each_aminoacid_to_an_array_of_corresponding_codons(_ = aminoacid_sequence? ) ⇒ Object

#

map_each_aminoacid_to_an_array_of_corresponding_codons

#


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# File 'lib/bioroebe/aminoacids/deduce_aminoacid_sequence.rb', line 357

def map_each_aminoacid_to_an_array_of_corresponding_codons(
    _ = aminoacid_sequence?
  )
  array_of_corresponding_codons = []
  _.each_char {|this_aminoacid|
    array = aminoacid_to_possible_codons(this_aminoacid)
    array_of_corresponding_codons << array
  }
  return array_of_corresponding_codons
end

#menu(i = return_commandline_arguments_starting_with_hyphens) ⇒ Object

#

menu (menu tag)

#


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# File 'lib/bioroebe/aminoacids/deduce_aminoacid_sequence.rb', line 316

def menu(
    i = return_commandline_arguments_starting_with_hyphens
  )
  if i.is_a? Array
    i.each {|entry| menu(entry) }
  else
    case i
    # ===================================================================== #
    # === --help
    # ===================================================================== #
    when /^-?-?help$/i
      show_help
      exit
    # ===================================================================== #
    # === --RNA
    #
    # Usage example:
    #
    #   deduce WDENNM --RNA
    #
    # ===================================================================== #
    when /--RNA$/i
      do_show_the_rna_sequence
    end
  end
end

#n_aminoacids? ⇒ Boolean

#

n_aminoacids?

Return the amount (an integer value) of aminoacids.

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/aminoacids/deduce_aminoacid_sequence.rb', line 203

def n_aminoacids?
  aminoacid_sequence?.delete('-').size
end

#report(array_containing_all_discovered_codons = array_all_discovered_codons? ) ⇒ Object

#

report (report tag)

This is the primary method for reporting the codon sequence at hand.

#


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# File 'lib/bioroebe/aminoacids/deduce_aminoacid_sequence.rb', line 428

def report(
    array_containing_all_discovered_codons =
      array_all_discovered_codons?
  )
  show_the_header # This has the long intro-text.
  show_the_aminoacid_sequence_in_steelblue_and_orange_colour
  show_all_possible_codons
  if show_a_possible_sequence?
    do_show_a_possible_sequence
  end
end

#reset ⇒ Object

#

reset (reset tag)

#


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# File 'lib/bioroebe/aminoacids/deduce_aminoacid_sequence.rb', line 69

def reset
  super()
  infer_the_namespace
  # ======================================================================= #
  # === :aminoacid_sequence
  #
  # This will contain the aminoacid sequence.
  # ======================================================================= #
  @internal_hash[:aminoacid_sequence] = nil
  # ======================================================================= #
  # === :show_rna_or_dna
  #
  # This variable keeps track as to whether we will show a DNA sequence
  # or a RNA sequence. This functionality exists mostly due to
  # convenience.
  # ======================================================================= #
  @internal_hash[:show_rna_or_dna] = :dna
  # ======================================================================= #
  # === :show_a_possible_sequence
  # ======================================================================= #
  @internal_hash[:show_a_possible_sequence] = true
  # ======================================================================= #
  # === @left_pad
  # ======================================================================= #
  @left_pad = ' '
  set_show_the_rna_sequence(:no)
end

#reset_the_class ⇒ Object

#

reset_the_class

#


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# File 'lib/bioroebe/aminoacids/deduce_aminoacid_sequence.rb', line 221

def reset_the_class
  @internal_hash[:array_all_discovered_codons] = [] # Reset it to empty again.
end

#run ⇒ Object

#

run (run tag)

#


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# File 'lib/bioroebe/aminoacids/deduce_aminoacid_sequence.rb', line 443

def run
  reset_the_class
  determine_the_aminoacid_sequence
  set_array_all_discovered_codons(
    map_each_aminoacid_to_an_array_of_corresponding_codons
  )
  menu
  report
end

#set_aminoacid_sequence(i = :default) ⇒ Object

#

set_aminoacid_sequence

#


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# File 'lib/bioroebe/aminoacids/deduce_aminoacid_sequence.rb', line 161

def set_aminoacid_sequence(
    i = :default
  )
  case i
  # ======================================================================= #
  # === :default
  # ======================================================================= #
  when :default
    i = DEFAULT_SEQUENCE
  end if i.is_a? Symbol
  if i.is_a? Array
    i = i.join(' ').strip
  end
  i = i.to_s.dup # Have a String past this point.
  if i.empty?
    i = DEFAULT_SEQUENCE
  end
  i.tr!('?','-') if i.include? '?'
  # ======================================================================= #
  # Handle input that has no '-'.
  # ======================================================================= #
  if i.include?('-') and !i[0,3].include?('-')
    # ===================================================================== #
    # Assume input such as: "ARG-ALA-SER-LEU" here.
    # ===================================================================== #
    splitted = i.split('-')
    splitted.map! {|entry|
      three_aminoacid_letter_code_to_one_aminoacid_letter_code(entry.capitalize) # Added .capitalize as of 25.09.2019.
    }
    i = splitted.join
  end
  # ======================================================================= #
  # Finally assign it to the main variable:
  # ======================================================================= #
  @internal_hash[:aminoacid_sequence] = i
end

#set_array_all_discovered_codons(i) ⇒ Object

#

set_array_all_discovered_codons

#


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# File 'lib/bioroebe/aminoacids/deduce_aminoacid_sequence.rb', line 309

def set_array_all_discovered_codons(i)
  @internal_hash[:array_all_discovered_codons] = i
end

#set_format_how(format_how = :default) ⇒ Object

#

set_format_how

#


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# File 'lib/bioroebe/aminoacids/deduce_aminoacid_sequence.rb', line 100

def set_format_how(
    format_how = :default
  )
  case format_how
  # ======================================================================= #
  # === :default
  # ======================================================================= #
  when :default
    format_how = :dna
  end
  @internal_hash[:show_rna_or_dna] = format_how
end

#set_show_the_rna_sequence(i = :rna) ⇒ Object

#

set_show_the_rna_sequence

#


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# File 'lib/bioroebe/aminoacids/deduce_aminoacid_sequence.rb', line 123

def set_show_the_rna_sequence(
    i = :rna
  )
  case i
  when :yes
    i = :rna
  when :no
    i = :dna
  end
  @internal_hash[:show_rna_or_dna] = i
end

#show_a_possible_sequence? ⇒ Boolean

#

show_a_possible_sequence?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/aminoacids/deduce_aminoacid_sequence.rb', line 116

def show_a_possible_sequence?
  @internal_hash[:show_a_possible_sequence]
end

#show_all_possible_codons(n_aminoacids = n_aminoacids?, , codons_to_use = all_codons? ) ⇒ Object

#

show_all_possible_codons

#


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# File 'lib/bioroebe/aminoacids/deduce_aminoacid_sequence.rb', line 391

def show_all_possible_codons(
    n_aminoacids  = n_aminoacids?,
    codons_to_use = all_codons?
  )
  display_separator(n_aminoacids)
  n_aminoacids.times {|index|
    array = codons_to_use.map {|entry| entry[index] }
    unless array.all? {|entry| entry.nil? }
      # =================================================================== #
      # This array may contain some nil values. We will
      # replace all these nil values via '   ' strings.
      # =================================================================== #
      array.map! {|entry|
        entry = ' ' * 3 if entry.nil?
        entry
      }
      if show_the_rna_sequence?
        array.map! {|entry| entry.tr('T','U') }
      end
      e @left_pad+rev+
        array.map {|entry|
          entry.to_s.ljust(3)
        }.join(
          swarn(" #{VERTICAL_UNICODE_BAR} ")+rev
        )
    end
  }
  display_separator(n_aminoacids)
  e # And a newline for prettier output. \o/
end

#show_help ⇒ Object

#

show_help (help tag)

#


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# File 'lib/bioroebe/aminoacids/deduce_aminoacid_sequence.rb', line 346

def show_help
  e 'The following help options are available for this class:'
  e
  ecomment '  --RNA  # show the codon table in RNA rather than DNA'
  ecomment '  --full # show all possible codons'
  e
end

#show_the_aminoacid_sequence_in_steelblue_and_orange_colour(i = aminoacid_sequence? ) ⇒ Object

#

show_the_aminoacid_sequence_in_steelblue_and_orange_colour

#


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# File 'lib/bioroebe/aminoacids/deduce_aminoacid_sequence.rb', line 291

def show_the_aminoacid_sequence_in_steelblue_and_orange_colour(
    i = aminoacid_sequence?
  )
  i = i.join(' ').strip if i.is_a? Array
  i = i.delete('-')
  splitted = i.split(//)
  mapped = splitted.map {|entry|
    steelblue(entry)
  }
  joined = mapped[0 .. -2].join(orange(' --- '))+
           orange(' --- ')+
           steelblue(splitted.last)
  e @left_pad+joined
end

#show_the_header ⇒ Object Also known as: show_header

#

show_the_header

#


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# File 'lib/bioroebe/aminoacids/deduce_aminoacid_sequence.rb', line 210

def show_the_header
  e
  erev 'This amino acid sequence ('+sfancy(n_aminoacids?.to_s)+rev+
       ' aminoacids) has the following possible'
  erev 'codons:'
  e
end

#show_the_rna_sequence? ⇒ Boolean

#

show_the_rna_sequence?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/aminoacids/deduce_aminoacid_sequence.rb', line 138

def show_the_rna_sequence?
  @internal_hash[:show_rna_or_dna] == :rna
end