Class: Bioroebe::ProfilePattern

Inherits:
CommandlineApplication show all
Defined in:
lib/bioroebe/patterns/profile_pattern.rb

Overview

Bioroebe::ProfilePattern

Constant Summary collapse

PER_POSITION_HASH =
#

PER_POSITION_HASH

This hash can be used to specify the likelihood per position.

#
{
  'A': [  61,  16, 352,   3, 354, 268, 360, 222, 155,  56,  83,  82,  82,  68,  77 ],
  'C': [ 145,  46,   0,  10,   0,   0,   3,   2,  44, 135, 147, 127, 118, 107, 101 ],
  'G': [ 152,  18,   2,   2,   5,   0,  10,  44, 157, 150, 128, 128, 128, 139, 140 ],
  'T': [  31, 309,  35, 374,  30, 121,   6, 121,  33,  48,  31,  52,  61,  75,  71 ]
}

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 = nil, run_already = true) ⇒ ProfilePattern

#

initialize

#


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# File 'lib/bioroebe/patterns/profile_pattern.rb', line 39

def initialize(
    commandline_arguments = nil,
    run_already           = true
  )
  reset
  set_commandline_arguments(
    commandline_arguments
  )
  case run_already
  when :do_not_run_yet
    run_already = false
  end
  run if run_already
end

Class Method Details

.[](i = ARGV) ⇒ Object

#

Bioroebe::ProfilePattern[]

#


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# File 'lib/bioroebe/patterns/profile_pattern.rb', line 172

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

Instance Method Details

#determine_the_dna_sequence_based_on_the_main_hash_profile ⇒ Object

#

determine_the_dna_sequence_based_on_the_main_hash_profile

#


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# File 'lib/bioroebe/patterns/profile_pattern.rb', line 120

def determine_the_dna_sequence_based_on_the_main_hash_profile
  @string = Bioroebe.generate_random_dna_sequence(30, @hash_profiles)
end

#display(i = @string) ⇒ Object Also known as: report

#

display

#


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# File 'lib/bioroebe/patterns/profile_pattern.rb', line 156

def display(i = @string)
  erev i
end

#generate_sequence_based_on_this_profile(i = @per_position_hash) ⇒ Object

#

generate_sequence_based_on_this_profile

#


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# File 'lib/bioroebe/patterns/profile_pattern.rb', line 81

def generate_sequence_based_on_this_profile(
    i = @per_position_hash
  )
  @string = ''.dup
  n_times = i.values.first.size
  n_times.times {|position|
    # ===================================================================== #
    # Determine the max values for the four nucleotides next:
    # ===================================================================== #
    max_value_for_A = i[:A][position]
    max_value_for_C = i[:C][position]
    max_value_for_G = i[:G][position]
    max_value_for_T = i[:T][position]
    sum = max_value_for_A+
          max_value_for_C+
          max_value_for_G+
          max_value_for_T
    match_with_this_number = rand(sum)+1
    case match_with_this_number
    when 1..(max_value_for_A)
      this_nucleotide = 'A'
    when (max_value_for_A)..(max_value_for_A+max_value_for_C)
      this_nucleotide = 'C'
    when (max_value_for_A+max_value_for_C)..(max_value_for_A+max_value_for_C+max_value_for_G)
      this_nucleotide = 'G'
    when (max_value_for_A+max_value_for_C+max_value_for_G)..(max_value_for_A+max_value_for_C+max_value_for_G+max_value_for_T)
      this_nucleotide = 'T'
    else
      e tomato('Value of '+match_with_this_number.to_s+' is not registered.')
    end
    # GTATAAAAGGC
    @string << this_nucleotide
  }
  display @string
end

#menu(i = return_commandline_arguments_starting_with_hyphens) ⇒ Object

#

menu (menu tag)

#


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# File 'lib/bioroebe/patterns/profile_pattern.rb', line 127

def menu(
    i = return_commandline_arguments_starting_with_hyphens
  )
  if i.is_a? Array
    i.each {|entry| menu(entry) }
  else
    case i # case tag
    # ===================================================================== #
    # === --debug
    # ===================================================================== #
    when /^-?-?debug/
      show_debug_information
    end
  end
end

#reset ⇒ Object

#

reset (reset tag)

#


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# File 'lib/bioroebe/patterns/profile_pattern.rb', line 57

def reset
  super()
  # ======================================================================= #
  # === @hash_profiles
  #
  # This Hash can be used to specify a particular profile for each
  # nucleotide position. The default is 25, which  means 25% chance
  # for each individual nucleotide.
  # ======================================================================= #
  @hash_profiles = {
    A: 25,
    T: 25,
    C: 25,
    G: 25
  }
  # ======================================================================= #
  # === @per_position_hash
  # ======================================================================= #
  @per_position_hash = PER_POSITION_HASH
end

#run ⇒ Object

#

run (run tag)

#


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# File 'lib/bioroebe/patterns/profile_pattern.rb', line 163

def run
  menu
  determine_the_dna_sequence_based_on_the_main_hash_profile
  display
end

#show_debug_information ⇒ Object

#

show_debug_information

Right now this will only display the profile in use.

#


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# File 'lib/bioroebe/patterns/profile_pattern.rb', line 148

def show_debug_information
  erev 'The profile in use is:'; print '  '
  pp @hash_profiles
end