Class: Bioroebe::AnalyseGlycosylationPattern

Inherits:
CommandlineApplication show all
Defined in:
lib/bioroebe/patterns/analyse_glycosylation_pattern.rb

Overview

Bioroebe::AnalyseGlycosylationPattern

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?, #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(commandline_arguments = ARGV, run_already = true) ⇒ AnalyseGlycosylationPattern

#

initialize

#


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# File 'lib/bioroebe/patterns/analyse_glycosylation_pattern.rb', line 25

def initialize(
    commandline_arguments = ARGV,
    run_already           = true
  )
  reset
  set_commandline_arguments(
    commandline_arguments
  )
  case run_already
  when :do_not_run_yet
    run_already = false
  end
  run if run_already
end

Class Method Details

.[](i = ARGV) ⇒ Object

#

Bioroebe::AnalyseGlycosylationPattern[]

#


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# File 'lib/bioroebe/patterns/analyse_glycosylation_pattern.rb', line 141

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

Instance Method Details

#could_be(i = :N_linked) ⇒ Object

#

could_be

#


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# File 'lib/bioroebe/patterns/analyse_glycosylation_pattern.rb', line 83

def could_be(i = :N_linked)
  case i
  when :O_linked
    'These could be sites for '+
    steelblue('O-linked glycosylation')+
    rev
  when :N_linked
    'These could be sites for '+
    steelblue('N-linked glycosylation')+
    rev
  end
end

#menu(i = return_commandline_arguments_starting_with_hyphens) ⇒ Object

#

menu (menu tag)

#


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# File 'lib/bioroebe/patterns/analyse_glycosylation_pattern.rb', line 50

def menu(
    i = return_commandline_arguments_starting_with_hyphens
  )
  if i.is_a? Array
    i.each {|entry| menu(entry) }
  else
    case i # case tag
    # ===================================================================== #
    # === --help
    # ===================================================================== #
    when /^-?-?help/
      show_help
    end
  end
end

#report_how_many_asparagines_are_in_this_sequence(i = @sequence) ⇒ Object

#

report_how_many_asparagines_are_in_this_sequence

#


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# File 'lib/bioroebe/patterns/analyse_glycosylation_pattern.rb', line 69

def report_how_many_asparagines_are_in_this_sequence(
    i = @sequence
  )
  erev 'This sequence contains '+
        steelblue(
          i.to_s.count('N').to_s.rjust(2)
        )+rev+
        ' asparagine residues. '+could_be(:N_linked)+
        rev+'.'
end

#report_how_many_serines_are_in_this_sequence(i = @sequence) ⇒ Object

#

report_how_many_serines_are_in_this_sequence

#


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# File 'lib/bioroebe/patterns/analyse_glycosylation_pattern.rb', line 99

def report_how_many_serines_are_in_this_sequence(
    i = @sequence
  )
  erev 'This sequence contains '+
        steelblue(
          i.to_s.count('S').to_s.rjust(2)
        )+rev+
        ' serine residues.     '+could_be(:O_linked)+
        '.'
end

#report_how_many_threonines_are_in_this_sequence(i = @sequence) ⇒ Object

#

report_how_many_threonines_are_in_this_sequence

#


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# File 'lib/bioroebe/patterns/analyse_glycosylation_pattern.rb', line 113

def report_how_many_threonines_are_in_this_sequence(
    i = @sequence
  )
  erev 'This sequence contains '+
        steelblue(
          i.to_s.count('T').to_s.rjust(2)
        )+rev+
       ' threonines residues. '+could_be(:O_linked)+
       '.'
end

#reset ⇒ Object

#

reset (reset tag)

#


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# File 'lib/bioroebe/patterns/analyse_glycosylation_pattern.rb', line 43

def reset
  super()
end

#run ⇒ Object

#

run (run tag)

#


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# File 'lib/bioroebe/patterns/analyse_glycosylation_pattern.rb', line 127

def run
  menu
  @sequence = first_argument?
  erev 'The sequence '
  e  "  #{colourize_nucleotides(@sequence)}"
  erev 'will now be analysed.'
  report_how_many_asparagines_are_in_this_sequence
  report_how_many_serines_are_in_this_sequence
  report_how_many_threonines_are_in_this_sequence
end