Class: Bioroebe::ShowCodonUsage

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

Overview

Bioroebe::ShowCodonUsage

Constant Summary

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?, #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 = nil, run_already = true) ⇒ ShowCodonUsage

#

initialize

#


31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
 
# File 'lib/bioroebe/codons/show_codon_usage.rb', line 31

def initialize(
    i           = nil,
    run_already = true
  )
  reset
  set_input(i)
  # ======================================================================= #
  # === Handle blocks given to this method next
  # ======================================================================= #
  if block_given?
    yielded = yield
    case yielded
    when :be_quiet
      do_not_be_verbose
    end
  end
  run if run_already
end

Class Method Details

.[](i = ARGV) ⇒ Object

#

Bioroebe::ShowCodonUsage[]

#


180
181
182
 
# File 'lib/bioroebe/codons/show_codon_usage.rb', line 180

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

Instance Method Details

#codon_to_aminoacid(i) ⇒ Object

#

codon_to_aminoacid

#


155
156
157
 
# File 'lib/bioroebe/codons/show_codon_usage.rb', line 155

def codon_to_aminoacid(i)
  ::Bioroebe.codon_to_aminoacid(i)
end

#hash? ⇒ Boolean Also known as: result?

#

hash?

This hash will keep the codon-usage.

It may look like this:

{"GTA"=>6,
 "TAC"=>5,
 "ACG"=>4,
 "CGT"=>4,

So it is already sorted properly.

#

Returns:

  • (Boolean) 


173
174
175
 
# File 'lib/bioroebe/codons/show_codon_usage.rb', line 173

def hash?
  @hash
end

#input? ⇒ Boolean Also known as: string?

#

input?

#

Returns:

  • (Boolean) 


69
70
71
 
# File 'lib/bioroebe/codons/show_codon_usage.rb', line 69

def input?
  @input
end

#menu(i = @input) ⇒ Object

#

menu

#


76
77
78
79
80
81
82
83
 
# File 'lib/bioroebe/codons/show_codon_usage.rb', line 76

def menu(i = @input)
  if i and File.file?(i)
    # ===================================================================== #
    # Handle locally existing files next.
    # ===================================================================== #
    @input = File.read(i).strip.delete("\n")
  end
end

#report_the_top_five_codons(from_this_dataset) ⇒ Object

#

report_the_top_five_codons

#


134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
 
# File 'lib/bioroebe/codons/show_codon_usage.rb', line 134

def report_the_top_five_codons(from_this_dataset)
  e
  erev 'The '+mediumpurple('top five codons')+
       rev+' in use, sorted by frequency, are:'
  e
  top_five = from_this_dataset.sort_by {|key, values| values }.reverse[0..4]
  top_five.each {|name_of_codon, how_many_of_them|
    _ = name_of_codon.upcase
    this_codon = codon_to_aminoacid(_).sequence?
    colourized_this_codon = turquoise(this_codon)
    e rev+'  - '+
      teal(_)+
      rev+
      ': '+simp(how_many_of_them.to_s.rjust(2))+
      rev+' ('+colourized_this_codon+rev+')'
  }; e
end

#reset ⇒ Object

#

reset (reset tag)

#


53
54
55
 
# File 'lib/bioroebe/codons/show_codon_usage.rb', line 53

def reset
  super()
end

#run ⇒ Object

#

run (run tag)

#


88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
 
# File 'lib/bioroebe/codons/show_codon_usage.rb', line 88

def run
  menu
  codon_usage = Hash.new(0)
  if string?.empty?
    e rev+'Not found any string. Please "'+simp('assign')+rev+'" one first.'
  else
    string = string?
    _ = string.dup
    # ===================================================================== #
    # Next, obtain the codons in that sequence:
    # ===================================================================== #
    _ = _.scan(/..?.?/) # Grab 3 pairs each here.
    _.each { |this_codon|
      codon_usage[this_codon] += 1
    }
    # ===================================================================== #
    # Sort it next, so that the highest entries come on top. That
    # way we simplify downstream-applications that want to show the
    # result in a sensible manner.
    # ===================================================================== #
    codon_usage = codon_usage.sort_by {|key, value|
      value
    }.reverse
    codon_usage = Hash[*codon_usage.flatten]
    type = 'DNA'
    # ===================================================================== #
    # RNA is supported as well.
    # ===================================================================== #
    if string.include? 'U'
      type = 'RNA'
    end
    if be_verbose?
      erev 'The codon usage of this '+simp(type)+rev+
           ' string ('+sfancy(string.size.to_s)+rev+
           ' nucleotides) is as follows:'
      e
      print '  '; pp codon_usage # Simply report the main Hash in use here.
      report_the_top_five_codons(codon_usage)
    end
    @hash = codon_usage
  end
end

#set_input(i = '') ⇒ Object

#

set_input

#


60
61
62
63
64
 
# File 'lib/bioroebe/codons/show_codon_usage.rb', line 60

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