Class: Bioroebe::Compacter

Inherits:
CommandlineApplication show all
Defined in:
lib/bioroebe/utility_scripts/compacter.rb

Overview

Bioroebe::Compacter

Constant Summary collapse

NAMESPACE =
#

NAMESPACE

#
inspect

Constants inherited from CommandlineApplication

Bioroebe::CommandlineApplication::OLD_VERBOSE_VALUE

Constants included from ColoursForBase

Bioroebe::ColoursForBase::ARRAY_HTML_COLOURS_IN_USE

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, #opne, #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, #set_be_verbose, #start_codon?, #stop_codons?, #strict_filter_away_invalid_aminoacids, #taxonomy_download_directory?, #three_to_one, #to_rna, #trailing_three_prime, #use_opn?, #was_or_were, #without_extname, #write_what_into

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, #egold, #enable_colours, #eorange, #eparse, #erev, #red, #remove_trailing_escape_part, #return_colour_for_nucleotides, #rev, #sdir, #set_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?, #file_readlines, #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, #write_what_into

Constructor Details

#initialize(i = nil, run_already = true) ⇒ Compacter

#

initialize

#


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# File 'lib/bioroebe/utility_scripts/compacter.rb', line 32

def initialize(
    i           = nil,
    run_already = true
  )
  register_sigint
  reset
  set_input(i)
  case run_already
  # ======================================================================= #
  # === :do_not_ask_for_user_input
  # ======================================================================= #
  when :do_not_ask_for_user_input
    @ask_for_user_input = false
    run_already = true
  end
  run if run_already
end

Instance Method Details

#input? ⇒ Boolean Also known as: file?

#

input?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/utility_scripts/compacter.rb', line 77

def input?
  @input
end

#reset ⇒ Object

#

reset (reset tag)

#


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# File 'lib/bioroebe/utility_scripts/compacter.rb', line 53

def reset
  super()
  # ======================================================================= #
  # === @namespace
  # ======================================================================= #
  @namespace = NAMESPACE
  # ======================================================================= #
  # === @ask_for_user_input
  # ======================================================================= #
  @ask_for_user_input = true
end

#run ⇒ Object

#

run (run tag)

#


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# File 'lib/bioroebe/utility_scripts/compacter.rb', line 84

def run
  this_file = file?
  if this_file
    if File.exist? this_file
      # =================================================================== #
      # Tell the user which file we will compact next.
      # =================================================================== #
      e "We will now compact the file `#{sfile(this_file)}`."
      dataset = File.read(this_file)
      if dataset.start_with? 'ORIGIN'
        dataset[0,'ORIGIN'.size] = ''
        dataset.lstrip!
      elsif dataset.start_with? '>'
        # ================================================================= #
        # In this case, chop off the first line completely.
        # ================================================================= #
        dataset[0, dataset.index("\n")] = ''
        dataset.lstrip!
      end
      # =================================================================== #
      # Here we tap into class Bioroebe::SanitizeNucleotideSequence
      # =================================================================== #
      require 'bioroebe/nucleotides/sanitize_nucleotide_sequence.rb'
      dataset = Bioroebe::SanitizeNucleotideSequence[dataset]
      if @ask_for_user_input
        e 'We will now store into the same file, but you must'
        e 'type "'+steelblue('y')+'" to confirm, else we cancel:'
        user_input = $stdin.gets.chomp
      else
        user_input = 'yes'
      end
      if user_input.start_with? 'y'
        e "Now storing into the file #{sfile(this_file)}."
        write_what_into(dataset, this_file)
      end
    else
      e "The file `#{sfile(this_file)}` does not exist."
    end
  else
    opnn; e 'Please provide an existing file as input.'
  end
end

#set_input(i = '') ⇒ Object

#

set_input

#


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# File 'lib/bioroebe/utility_scripts/compacter.rb', line 68

def set_input(i = '')
  i = i.first if i.is_a? Array
  i = i.to_s.dup if i
  @input = i
end