Class: Bioroebe::ConvertThisCodonToThatAminoacid

Inherits:
CommandlineApplication show all
Defined in:
lib/bioroebe/codons/convert_this_codon_to_that_aminoacid.rb

Overview

Bioroebe::ConvertThisCodonToThatAminoacid

Constant Summary

Constants inherited from CommandlineApplication

Bioroebe::CommandlineApplication::OLD_VERBOSE_VALUE

Constants included from ColoursForBase

Bioroebe::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(i = ARGV, run_already = true, &block) ⇒ ConvertThisCodonToThatAminoacid

#

initialize

#


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# File 'lib/bioroebe/codons/convert_this_codon_to_that_aminoacid.rb', line 60

def initialize(
    i           = ARGV, # This should be an Array.
    run_already = true,
    &block
  )
  reset
  set_commandline_arguments(i)
  # ========================================================================= #
  # === Handle blocks next
  # ========================================================================= #
  if block_given?
    yielded = yield
    case yielded
    # ======================================================================= #
    # === :be_quiet
    # ======================================================================= #
    when :be_quiet
      be_quiet
    end
  end
  run if run_already
end

Class Method Details

.[](i = ARGV) ⇒ Object

#

Bioroebe::ConvertThisCodonToThatAminoacid[]

Usage example:

Bioroebe::ConvertThisCodonToThatAminoacid[]
#


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# File 'lib/bioroebe/codons/convert_this_codon_to_that_aminoacid.rb', line 216

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

Instance Method Details

#

menu (menu tag)

#


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# File 'lib/bioroebe/codons/convert_this_codon_to_that_aminoacid.rb', line 102

def menu(
    i = commandline_arguments_starting_with_a_hyphen?
  )
  if i.is_a? Array
    i.each {|entry| menu(entry) }
  else
    case i # case tag
    # ===================================================================== #
    # === codon_to_aa --with-trailer
    # ===================================================================== #
    when /^-?-?with(-|_)?trailer$/i
      @internal_hash[:with_trailer] = true
    # ===================================================================== #
    # === codon_to_aa --help
    # ===================================================================== #
    when /^-?-?help$/i
      show_help
      exit
    end
  end
end

#report ⇒ Object

#

report (report tag)

#


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# File 'lib/bioroebe/codons/convert_this_codon_to_that_aminoacid.rb', line 204

def report
  e @result if be_verbose?
end

#reset ⇒ Object

#

reset (reset tag)

#


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# File 'lib/bioroebe/codons/convert_this_codon_to_that_aminoacid.rb', line 86

def reset
  super()
  # ======================================================================= #
  # === @internal_hash[:shall_we_replace_stop_codons]
  # ======================================================================= #
  @internal_hash[:shall_we_replace_stop_codons] = :default
  # ======================================================================= #
  # === :with_trailer
  # ======================================================================= #
  @internal_hash[:with_trailer] = false
  set_be_verbose
end

#result? ⇒ Boolean Also known as: sequence?

#

result?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/codons/convert_this_codon_to_that_aminoacid.rb', line 143

def result?
  @result
end

#run ⇒ Object

#

run (run tag)

#


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# File 'lib/bioroebe/codons/convert_this_codon_to_that_aminoacid.rb', line 150

def run
  i = commandline_arguments?
  menu( # Pass all arguments that start with -- next.
    commandline_arguments_starting_with_a_hyphen(i)
  )
  case @internal_hash[:shall_we_replace_stop_codons]
  # ======================================================================= #
  # === :default
  # ======================================================================= #
  when :default
    @internal_hash[:shall_we_replace_stop_codons] = true
  end
  if i.is_a? Array
    i = reject_hyphens(i).join
  end
  i = i.to_s.dup
  i.upcase!
  i.tr!('U','T') # We need DNA here, so U becomes T.
  use_this_codon_table = codon_table_dataset?.dup
  # ======================================================================= #
  # Obtain the dataset from the correct codon_table next.
  # ======================================================================= #
  if i.size < 3
    scanned = i.scan(/./)
  else
    scanned = i.scan(/.../)
  end
  scanned.map! {|potential_codon|
    if use_this_codon_table.has_key? potential_codon
      potential_codon = use_this_codon_table[potential_codon]
    end
    # ===================================================================== #
    # Get rid of stop codons. This works because 'O' is not
    # a valid aminoacid.
    # ===================================================================== #
    if potential_codon.include? 'STOP'
      potential_codon.gsub!(/STOP/, '*') if shall_we_replace_stop_codons
    end
    potential_codon
  }
  result = scanned
  result = result.join if result.is_a? Array
  if with_trailer?
    result = result.dup
    result.prepend("5'-")
    result << "-3'"
  end
  @result = result
  report
end

#show_help ⇒ Object

#

show_help (help tag)

#


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# File 'lib/bioroebe/codons/convert_this_codon_to_that_aminoacid.rb', line 127

def show_help
  e
  e "  --with-trailer # display any result via 5'- and -3' padding"
  e
end

#with_trailer? ⇒ Boolean

#

with_trailer?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/codons/convert_this_codon_to_that_aminoacid.rb', line 136

def with_trailer?
  @internal_hash[:with_trailer]
end