Class: Bioroebe::ShowHydrophobicity

Inherits:
CommandlineApplication show all
Defined in:
lib/bioroebe/aminoacids/show_hydrophobicity.rb

Overview

Bioroebe::ShowHydrophobicity

Constant Summary collapse

HYDROPATHY_TABLE = 
YAML.load_file(FILE_HYDROPATHY_TABLE)

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, #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) ⇒ ShowHydrophobicity

#

initialize

#


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# File 'lib/bioroebe/aminoacids/show_hydrophobicity.rb', line 33

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

Class Method Details

.[](i = ARGV) ⇒ Object

#

Bioroebe::ShowHydrophobicity[]

#


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# File 'lib/bioroebe/aminoacids/show_hydrophobicity.rb', line 171

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

Instance Method Details

#input? ⇒ Boolean

#

input?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/aminoacids/show_hydrophobicity.rb', line 90

def input?
  @input
end

#main_table ⇒ Object

#

main_table

This will be a Hash.

#


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# File 'lib/bioroebe/aminoacids/show_hydrophobicity.rb', line 99

def main_table
  HYDROPATHY_TABLE
end

#opnn(i = nil) ⇒ Object

#

opnn

#


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# File 'lib/bioroebe/aminoacids/show_hydrophobicity.rb', line 138

def opnn(i = nil)
  hash = {}
  hash.merge!(namespace: namespace?)
  hash.merge!(i) if i
  super(hash)
end

#report_one_letter_code ⇒ Object

#

report_one_letter_code

#


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# File 'lib/bioroebe/aminoacids/show_hydrophobicity.rb', line 148

def report_one_letter_code
  e
  opnn(trailing_colon: false); e; e
  erev 'The one-letter code of the given input '\
       'of aminoacids is: '
  e
  erev '  '+sfancy(input?.join(', '))
  e
end

#report_sorted_by_most_hydrophobic_aminoacid_first ⇒ Object

#

report_sorted_by_most_hydrophobic_aminoacid_first

#


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# File 'lib/bioroebe/aminoacids/show_hydrophobicity.rb', line 121

def report_sorted_by_most_hydrophobic_aminoacid_first
  erev 'Sorted by hydrophobicity first yields:'
  e
  # ======================================================================= #
  # Take the value from @hash_aminoacids and report things properly,
  # with hydrophobic aminoacid first.
  # ======================================================================= #
  @hash_aminoacids.sort_by {|key, value|
    value
  }.reverse.each {|key, value|
    erev "  #{key}: #{orange(value.to_s.rjust(5))}"
 }
end

#report_translated_hydropathy ⇒ Object

#

report_translated_hydropathy

#


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# File 'lib/bioroebe/aminoacids/show_hydrophobicity.rb', line 106

def report_translated_hydropathy
  values = input?.map {|entry|
    hydrophobicity = main_table[entry]
      @hash_aminoacids[entry] = hydrophobicity
    hydrophobicity
  }
  erev 'Their corresponding hydrophobicity values are:'
  e
  erev "  #{sfancy(values.join(', '))}"
  e
end

#reset ⇒ Object

#

reset (reset tag)

#


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# File 'lib/bioroebe/aminoacids/show_hydrophobicity.rb', line 45

def reset
  super()
  # ======================================================================= #
  # === @hash_aminoacids
  # ======================================================================= #
  @hash_aminoacids = {}
end

#run ⇒ Object

#

run (run tag)

#


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# File 'lib/bioroebe/aminoacids/show_hydrophobicity.rb', line 161

def run
  report_one_letter_code
  report_translated_hydropathy
  report_sorted_by_most_hydrophobic_aminoacid_first
  e # A trailing newline - looks nicer that way.
end

#sanitize_input(i = @input) ⇒ Object

#

sanitize_input

#


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# File 'lib/bioroebe/aminoacids/show_hydrophobicity.rb', line 65

def sanitize_input(
    i = @input
  )
  i.map! {|entry|
    if entry.include? '-'
      entry = entry.split('-').flatten
      entry.map! {|inner_entry|
        # ================================================================= #
        # Find the corresponding first character IF we have entries
        # of size exactly 3.
        # ================================================================= #
        if inner_entry.size == 3
          inner_entry = three_letters_to_one_letter(inner_entry)
        end
        inner_entry
      }
    end
    entry
  }
  i.flatten!
end

#set_input(i = '') ⇒ Object

#

set_input

#


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# File 'lib/bioroebe/aminoacids/show_hydrophobicity.rb', line 56

def set_input(i = '')
  i = [i] unless i.is_a? Array
  @input = i
  sanitize_input
end