Class: Bioroebe::ParseFrequencyTable

Inherits:
CommandlineApplication show all
Defined in:
lib/bioroebe/codon_tables/frequencies/parse_frequency_table.rb

Overview

Bioroebe::ParseFrequencyTable

Constant Summary collapse

AUTOMATICALLY_CREATE_A_LOCAL_YAML_FILE_IF_IT_DOES_NOT_YET_EXIST =
#

AUTOMATICALLY_CREATE_A_LOCAL_YAML_FILE_IF_IT_DOES_NOT_YET_EXIST

If this constant is set to true then this class will attempt to create a local .yml file, unless such a file already exists.

That .yml file will include the keys and frequency values associated with these keys, such as: “UUU: 17.7”.

The idea behind this is so that we can simplify the creation of such .yml files, which in turn may then be used to populate a SQL database.

#
true
USE_THIS_REGEX =
#

USE_THIS_REGEX

See here:

https://rubular.com/r/NgSPXJ2f5WG2kq
#
/([A-Z]{3})  ?(\d{1,2}\.\d{0,2})/
DEFAULT_INPUT =
#

DEFAULT_INPUT

This is just sample-data that can be used to test the inner-working of this class.

#
'UUU 17.7(  2478)  UCU 14.2(  1994)  UAU 12.1(  1698)  UGU 10.5(  1473)
UUC 25.9(  3630)  UCC 18.9(  2641)  UAC 18.9(  2640)  UGC 13.8(  1928)
UUA  6.3(   880)  UCA  9.5(  1328)  UAA  0.7(   102)  UGA  1.5(   216)
UUG 13.5(  1892)  UCG  4.9(   684)  UAG  0.5(    64)  UGG 15.3(  2148)

CUU 11.9(  1667)  CCU 13.9(  1947)  CAU  8.7(  1219)  CGU  3.7(   519)
CUC 22.9(  3210)  CCC 20.4(  2860)  CAC 14.8(  2076)  CGC  9.8(  1371)
CUA  6.4(   897)  CCA 13.1(  1838)  CAA 11.6(  1630)  CGA  5.0(   696)
CUG 45.8(  6407)  CCG  6.8(   952)  CAG 30.1(  4212)  CGG 10.7(  1502)

AUU 14.9(  2081)  ACU 11.4(  1594)  AAU 17.0(  2378)  AGU 10.2(  1426)
AUC 24.9(  3483)  ACC 21.6(  3020)  AAC 24.2(  3391)  AGC 18.8(  2630)
AUA  7.4(  1041)  ACA 12.7(  1784)  AAA 23.3(  3255)  AGA 12.0(  1678)
AUG 22.4(  3140)  ACG  8.5(  1186)  AAG 30.7(  4292)  AGG 12.7(  1779)

GUU 10.2(  1421)  GCU 16.5(  2314)  GAU 19.5(  2733)  GGU  9.2(  1293)
GUC 18.3(  2566)  GCC 31.4(  4391)  GAC 26.8(  3758)  GGC 22.5(  3143)
GUA  6.2(   869)  GCA 13.1(  1833)  GAA 27.1(  3800)  GGA 16.0(  2239)
GUG 30.5(  4267)  GCG  8.6(  1207)  GAG 35.8(  5005)  GGG 15.6(  2181)'

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_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

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) ⇒ ParseFrequencyTable

#

initialize

#


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# File 'lib/bioroebe/codon_tables/frequencies/parse_frequency_table.rb', line 84

def initialize(
    i           = ARGV,
    run_already = true
  )
  reset
  set_commandline_arguments(i)
  run if run_already
end

Class Method Details

.[](i = ARGV) ⇒ Object

#

Bioroebe::ParseFrequencyTable[]

#


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# File 'lib/bioroebe/codon_tables/frequencies/parse_frequency_table.rb', line 318

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

Instance Method Details

#determine_whether_we_have_to_download_from_a_remote_url ⇒ Object

#

determine_whether_we_have_to_download_from_a_remote_url

This method will determine whether this class has to download the dataset from a remote URL.

#


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# File 'lib/bioroebe/codon_tables/frequencies/parse_frequency_table.rb', line 192

def determine_whether_we_have_to_download_from_a_remote_url
  first = first?
  if first and first.start_with?('http')
    set_use_this_url(first)
  end
end

#do_store_into_a_local_yaml_file(into = :default) ⇒ Object

#

do_store_into_a_local_yaml_file

#


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# File 'lib/bioroebe/codon_tables/frequencies/parse_frequency_table.rb', line 218

def do_store_into_a_local_yaml_file(
    into = :default
  )
  case into
  when :default
    into = 'default_yaml_file.yml'
  end
  if File.exist? into
    e "Can not store into the local file #{sfile(into)} as such a file "\
      "already exists."
  else
    remote_url = remote_url?
    what = ''.dup
    if remote_url.include? '?species='
      # =================================================================== #
      # Assume an URL such as this one here:
      #
      #   https://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=107243
      #
      # =================================================================== #
      if into.include? 'default_yaml'
        into = remote_url.split('=').last.strip
        # ================================================================= #
        # We can also use a regex on the original dataset to obtain
        # the name of the organism, such as here:
        #
        #   <STRONG><i>Thlaspi caerulescens </i>[gbpln]: 45 CDS's (20416 codons)</STRONG>
        #
        # ================================================================= #
        original_dataset = original_dataset?
        if original_dataset.include? '<STRONG>'
          use_this_regex = /<STRONG><i>(.+) <\/i>/ # See: https://rubular.com/r/o4WJAeRxuvB4kM
          original_dataset =~ use_this_regex
          match = $1.to_s.dup.strip.tr(' ','_')
          into << "_#{match}"
        end
        into << '.yml' unless into.end_with? '.yml'
      end
    end
    if @hash_storing_the_codon_frequencies.empty?
      e 'No dataset was found at the URL `'+sfancy(url?)+'`.'
    else
      # =================================================================== #
      # First create a generic header for that file:
      # =================================================================== #
      what << "#\n"
      what << "# Filename: #{into}\n"
      what << "#\n"
      what << "# The following dataset was obtained from:\n"
      what << "#\n"
      what << "#   #{remote_url}\n"
      what << "#\n"
      what << "#\n"
      @hash_storing_the_codon_frequencies.each_pair {|key, value|
        what << "#{key}: #{value.to_s.rjust(4)}\n"
      }
      e "Saving into the local file at `#{sfile(into)}`."
      write_what_into(what, into)
    end
  end
end

#first? ⇒ Boolean Also known as: input?, original_dataset?

#

first?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/codon_tables/frequencies/parse_frequency_table.rb', line 154

def first?
  @commandline_arguments.first
end

#menu(i = commandline_arguments? ) ⇒ Object

#

menu (menu tag)

#


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# File 'lib/bioroebe/codon_tables/frequencies/parse_frequency_table.rb', line 123

def menu(
    i = commandline_arguments?
  )
  if i.is_a? Array
    i.each {|entry| menu(entry) }
  else
    case i # case tag
    # ===================================================================== #
    # === --random
    #
    # This entry point will try to randomly grab an (any) entry.
    # Thus it will often fail.
    # ===================================================================== #
    when /^-?-?random$/
      i = return_url_from_a_random_entry
      set_url(i)
    end
  end
end

#report_the_frequencies_properly_formatted ⇒ Object

#

report_the_frequencies_properly_formatted

#


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# File 'lib/bioroebe/codon_tables/frequencies/parse_frequency_table.rb', line 202

def report_the_frequencies_properly_formatted
  @hash_storing_the_codon_frequencies.each_pair {|key, value|
    e "#{key}: #{value.to_s.rjust(4)}"
  }
end

#reset ⇒ Object

#

reset (reset tag)

#


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# File 'lib/bioroebe/codon_tables/frequencies/parse_frequency_table.rb', line 96

def reset
  super()
  infer_the_namespace
  # ======================================================================= #
  # === @use_this_url
  #
  # This variable will be nil on startup, so that this class can decide
  # whether to download from a remote URL or not.
  # ======================================================================= #
  @use_this_url = nil
  # ======================================================================= #
  # === @hash_storing_the_codon_frequencies
  # ======================================================================= #
  @hash_storing_the_codon_frequencies = {}
end

#return_url_from_a_random_entry ⇒ Object

#

return_url_from_a_random_entry (random tag)

#


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# File 'lib/bioroebe/codon_tables/frequencies/parse_frequency_table.rb', line 146

def return_url_from_a_random_entry
  'https://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species='+
  (rand(100_000)+1).to_s
end

#run ⇒ Object

#

run (run tag)

#


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# File 'lib/bioroebe/codon_tables/frequencies/parse_frequency_table.rb', line 283

def run
  determine_whether_we_have_to_download_from_a_remote_url
  if @use_this_url and @use_this_url.start_with?('http')
    opnn; e 'Obtaining dataset from the following remote URL:'
    e
    e sfancy("  #{@use_this_url}")
    e
    _ = @use_this_url
    dataset_obtained = URI.open(_).read
    set_first(
      dataset_obtained
    )
  else
    set_first(first?)
  end
  splitted = first?.split("\n").reject {|line| line.to_s.strip.empty? }
  splitted.each {|line|
    # ===================================================================== #
    # This line may look like:
    #
    #   UUC 25.9(  3630)  UCC 18.9(  2641)  UAC 18.9(  2640)  UGC 13.8(  1928)
    #
    # ===================================================================== #
    inner_splitted = line.scan(USE_THIS_REGEX)
    inner_splitted.each {|key, value|
      @hash_storing_the_codon_frequencies[key] = value
    }
  }
  report_the_frequencies_properly_formatted
  do_store_into_a_local_yaml_file if store_locally?
end

#set_commandline_arguments(i) ⇒ Object

#

set_commandline_arguments

#


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# File 'lib/bioroebe/codon_tables/frequencies/parse_frequency_table.rb', line 115

def set_commandline_arguments(i)
  @commandline_arguments = [i].flatten.compact
  menu(@commandline_arguments)
end

#set_first(i) ⇒ Object

#

set_first

#


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# File 'lib/bioroebe/codon_tables/frequencies/parse_frequency_table.rb', line 162

def set_first(i)
  @commandline_arguments[0] = i
end

#set_use_this_url(i = nil) ⇒ Object Also known as: set_url

#

set_use_this_url

#


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# File 'lib/bioroebe/codon_tables/frequencies/parse_frequency_table.rb', line 169

def set_use_this_url(i = nil)
  if i.is_a? Array
    i = i.first
  end
  i = SAMPLE_INPUT if i.nil? # Use default in this case.
  i = i.to_s.dup
  @use_this_url = i
end

#store_locally? ⇒ Boolean

#

store_locally?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/codon_tables/frequencies/parse_frequency_table.rb', line 211

def store_locally?
  AUTOMATICALLY_CREATE_A_LOCAL_YAML_FILE_IF_IT_DOES_NOT_YET_EXIST
end

#use_this_url? ⇒ Boolean Also known as: remote_url?, url?

#

use_this_url?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/codon_tables/frequencies/parse_frequency_table.rb', line 181

def use_this_url?
  @use_this_url
end