Class: Bioroebe::Pathways

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

Overview

Bioroebe::Pathways

Constant Summary collapse

ALL_PATHWAYS =
#

ALL_PATHWAYS

Grab all available pathways and store them in the main constant next.

#
Dir["#{PATHWAYS_DIRECTORY}*.yml"].sort

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(run_already = true) ⇒ Pathways

#

initialize

#


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# File 'lib/bioroebe/utility_scripts/pathways/pathways.rb', line 32

def initialize(
    run_already = true
  )
  reset
  case run_already
  when :dont_run_yet
    run_already = false
  end
  run if run_already
end

Class Method Details

.e(i = '') ⇒ Object

#

Pathways.e

#


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# File 'lib/bioroebe/utility_scripts/pathways/pathways.rb', line 136

def self.e(i = '')
  puts i
end

.erev ⇒ Object

#

Pathways.erev

#


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# File 'lib/bioroebe/utility_scripts/pathways/pathways.rb', line 129

def self.erev
  ::Bioroebe.erev
end

.glycolysis_pathway ⇒ Object

#

Pathways.glycolysis_pathway

This method will return the glycolysis pathway.

#


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# File 'lib/bioroebe/utility_scripts/pathways/pathways.rb', line 55

def self.glycolysis_pathway
  _ = Pathways.new(:dont_run_yet)
  dataset = _.dataset_from_every_pathway
  # ======================================================================= #
  # The second entry is the glycolysis pathway for now.
  # ======================================================================= #
  dataset = dataset[1]
  return dataset
end

.rev ⇒ Object

#

rev

#


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# File 'lib/bioroebe/utility_scripts/pathways/pathways.rb', line 96

def self.rev
  ::Bioroebe.rev
end

.show_all_pathways ⇒ Object

#

Pathways.show_all_pathways

#


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# File 'lib/bioroebe/utility_scripts/pathways/pathways.rb', line 122

def self.show_all_pathways
  Pathways.new
end

.show_this_pathway(pathway) ⇒ Object

#

Bioroebe::Pathways.show_this_pathway

#


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# File 'lib/bioroebe/utility_scripts/pathways/pathways.rb', line 103

def self.show_this_pathway(pathway)
  dataset = YAML.load_file(pathway)
  name_of_pathway = File.basename(pathway).tr('_',' ').
                    gsub(/#{File.extname(pathway)}/, '')
  e rev+'Pathway: '+::Colours.sfancy(name_of_pathway); e
  dataset.each {|entry| e rev+" - #{entry.rjust(2)}" }
  e # Trailing newline.
end

Instance Method Details

#dataset_from_every_pathway ⇒ Object

#

dataset_from_every_pathway

Return the complete dataset.

#


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# File 'lib/bioroebe/utility_scripts/pathways/pathways.rb', line 70

def dataset_from_every_pathway
  ALL_PATHWAYS.map {|pathway|
    YAML.load_file(pathway) if File.exist? pathway
  }
end

#reset ⇒ Object

#

reset (reset tag)

#


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# File 'lib/bioroebe/utility_scripts/pathways/pathways.rb', line 46

def reset
  super()
end

#run ⇒ Object

#

run (run tag)

#


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# File 'lib/bioroebe/utility_scripts/pathways/pathways.rb', line 115

def run
  show_every_pathway
end

#show_every_pathway ⇒ Object

#

show_every_pathway

#


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# File 'lib/bioroebe/utility_scripts/pathways/pathways.rb', line 79

def show_every_pathway
  if ALL_PATHWAYS.empty?
    erev 'No pathways were found. Does the directory exist at '
    erev sdir(PATHWAYS_DIRECTORY)+rev+
         ' and is it not empty?'
  else
    e "#{Pathways.rev}Now showing the available pathways."
    e
    ALL_PATHWAYS.each {|pathway|
      Pathways.show_this_pathway(pathway)
    }
  end
end