Class: Bioroebe::GenomePattern

Inherits:
CommandlineApplication show all
Defined in:
lib/bioroebe/genomes/genome_pattern.rb

Overview

Bioroebe::GenomePattern

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

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 = nil, run_already = true) ⇒ GenomePattern

#

initialize

#


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# File 'lib/bioroebe/genomes/genome_pattern.rb', line 34

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

Instance Method Details

#add_gene(i = :foo) ⇒ Object Also known as: add, <<

#

add_gene

#


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# File 'lib/bioroebe/genomes/genome_pattern.rb', line 88

def add_gene(
    i = :foo
  )
  _ = array_genes?
  unless _.include? i
    if be_verbose?
      opnerev "Now adding the gene `#{sfancy(i.to_s)}#{rev}`."
    end
    _ << i
  end
end

#array_genes? ⇒ Boolean

#

array_genes?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/genomes/genome_pattern.rb', line 81

def array_genes?
  @hash[:array_genes]
end

#cmdline? ⇒ Boolean Also known as: input?

#

cmdline?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/genomes/genome_pattern.rb', line 74

def cmdline?
  @hash[:cmdline]
end

#genome? ⇒ Boolean Also known as: genes?

#

genome?

return an Array of all genes available in said organism.

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/genomes/genome_pattern.rb', line 106

def genome?
  array_genes?
end

#remove_gene(i = :foo, be_verbose = be_verbose? ) ⇒ Object Also known as: remove

#

remove_gene

Use this method to remove a Gene again.

#


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# File 'lib/bioroebe/genomes/genome_pattern.rb', line 129

def remove_gene(
    i = :foo, be_verbose = be_verbose?
  )
  case be_verbose
  when :be_verbose
    be_verbose = true
  end
  _ = array_genes?
  if _.include? i
    if be_verbose
      opnerev "Now removing the gene `#{sfancy(i.to_s)}#{rev}`."
    end
    _.delete i
  end
end

#report ⇒ Object

#

report

#


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# File 'lib/bioroebe/genomes/genome_pattern.rb', line 113

def report
  if genome?.empty?
    opnerev 'We have no genes stored.'
  else
    opnerev 'We have these genes:'
    genes?.each {|entry|
      opnerev "  #{sfancy(entry.to_s)}"
    }
  end
end

#reset ⇒ Object

#

reset (reset tag)

#


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# File 'lib/bioroebe/genomes/genome_pattern.rb', line 46

def reset
  super()
  infer_the_namespace
  # ======================================================================= #
  # === @hash
  # ======================================================================= #
  @hash = {}
  # ======================================================================= #
  # === :array_genes
  # ======================================================================= #
  @hash[:array_genes] = []
  # ======================================================================= #
  # === :be_verbose
  # ======================================================================= #
  set_be_verbose
end

#run ⇒ Object

#

run (run tag)

#


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# File 'lib/bioroebe/genomes/genome_pattern.rb', line 148

def run
end

#set_cmdline(i = '') ⇒ Object

#

set_cmdline

#


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# File 'lib/bioroebe/genomes/genome_pattern.rb', line 66

def set_cmdline(i = '')
  i = [i] unless i.is_a? Array
  @hash[:cmdline] = i
end