Class: Bioroebe::Punnet

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

Overview

Bioroebe::Pathways

Constant Summary collapse

DEFAULT_INPUT =
#

DEFAULT_INPUT

#
'0.7x0.3'
ROUND_TO_THIS =
#

ROUND_TO_THIS

#
4

Constants inherited from CommandlineApplication

CommandlineApplication::OLD_VERBOSE_VALUE

Constants included from ColoursForBase

ColoursForBase::ARRAY_HTML_COLOURS_IN_USE

Constants inherited from Base

Base::NAMESPACE

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 = DEFAULT_INPUT, run_already = true) ⇒ Punnet

#

initialize

#


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# File 'lib/bioroebe/utility_scripts/punnet/punnet.rb', line 35

def initialize(
    i           = DEFAULT_INPUT,
    run_already = true
  )
  reset
  set_input(i)
  run if run_already
end

Instance Method Details

#line(n_times = 31) ⇒ Object

#

line

#


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# File 'lib/bioroebe/utility_scripts/punnet/punnet.rb', line 90

def line(n_times = 31)
  e '-' * n_times
end

#menu(i) ⇒ Object

#

menu

#


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# File 'lib/bioroebe/utility_scripts/punnet/punnet.rb', line 76

def menu(i)
  case i # case tag
  # ======================================================================= #
  # === punnet --help
  # ======================================================================= #
  when /^-?-?help$/i
    show_usage
    exit
  end
end

#report_results ⇒ Object

#

report_results

#


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# File 'lib/bioroebe/utility_scripts/punnet/punnet.rb', line 97

def report_results
  splitted = @input.split('x')
  links  = splitted[0].to_f
  rechts = splitted[1].to_f
  links_value  = (links * links).to_f.round(ROUND_TO_THIS).to_s
  mitte_value  = ((2 * links * rechts) / 2.0).to_s.to_f.round(ROUND_TO_THIS).to_s
  rechts_value = (rechts * rechts).to_f.round(ROUND_TO_THIS).to_s
  erev 'Probabilities for '+simp(@input.to_s)+rev+':'
  e
  erev '   |      A     |     a      |'
  line
  erev ' A |  '+links_value+' (AA) | '+mitte_value+' (Aa)  |'
  erev ' a |  '+mitte_value+' (aA) | '+rechts_value+' (aa)  |'
  line
  erev N+links.to_s
  mitte_value = mitte_value.to_f * 2
  erev mitte_value.round(ROUND_TO_THIS).to_s
  erev rechts
end

#reset ⇒ Object

#

reset (reset tag)

#


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# File 'lib/bioroebe/utility_scripts/punnet/punnet.rb', line 47

def reset
  super()
end

#run ⇒ Object

#

run (run tag)

#


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# File 'lib/bioroebe/utility_scripts/punnet/punnet.rb', line 120

def run
  report_results
end

#set_input(i = DEFAULT_INPUT) ⇒ Object

#

set_input

#


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# File 'lib/bioroebe/utility_scripts/punnet/punnet.rb', line 54

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

#show_usage ⇒ Object

#

show_usage

#


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# File 'lib/bioroebe/utility_scripts/punnet/punnet.rb', line 65

def show_usage
  e 'Simply input commandline options here:'
  e
  e '  0.7 x 0.3'
  e '  punnett 0.7x0.3'
  e
end