Class: Bioroebe::DetermineAntigenicAreas
- Inherits:
-
CommandlineApplication
- Object
- Base
- CommandlineApplication
- Bioroebe::DetermineAntigenicAreas
- Defined in:
- lib/bioroebe/utility_scripts/determine_antigenic_areas/determine_antigenic_areas.rb
Overview
Bioroebe::DetermineAntigenicAreas
Constant Summary collapse
- ARRAY_IMPORTANT_HYDROPHOBIC_RESIDUES =
#
ARRAY_IMPORTANT_HYDROPHOBIC_RESIDUES
#
%w( C L V )
- SAMPLE_INPUT =
#
SAMPLE_INPUT
Use this as example for the input.
#
'MEDEIAALVVDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQS'\ 'KRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMT'\ 'QIMFETFNTPAMYVAIQAVLSLYASGRTTGIVMDSGDGVTHTVPIYEGYALPHAILRLDL'\ 'AGRDLTDYLMKILTERGYSFTTTAEREIVRDIKEKLCYVALDFEQEMGTAASSSSLEKSY'\ 'ELPDGQVITIGNERFRCPEALFQPSFLGMESCGIHETTYNSIMKCDVDIRKDLYANTVLS'\ 'GGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWISKQ'\ 'EYDESGPSIVHRKCF'
Constants inherited from CommandlineApplication
CommandlineApplication::OLD_VERBOSE_VALUE
Constants included from ColoursForBase
ColoursForBase::ARRAY_HTML_COLOURS_IN_USE
Constants inherited from Base
Class Method Summary collapse
-
.[](i = ARGV) ⇒ Object
# === Bioroebe::DetermineAntigenicAreas[] ========================================================================= #.
Instance Method Summary collapse
-
#initialize(i = SAMPLE_INPUT, run_already = true) ⇒ DetermineAntigenicAreas
constructor
# === initialize ========================================================================= #.
-
#input? ⇒ Boolean
# === input? ========================================================================= #.
-
#reset ⇒ Object
# === reset (reset tag) ========================================================================= #.
-
#run ⇒ Object
# === run (run tag) ========================================================================= #.
-
#set_input(i = SAMPLE_INPUT) ⇒ Object
# === set_input ========================================================================= #.
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 = SAMPLE_INPUT, run_already = true) ⇒ DetermineAntigenicAreas
#
initialize
#
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# File 'lib/bioroebe/utility_scripts/determine_antigenic_areas/determine_antigenic_areas.rb', line 59 def initialize( i = SAMPLE_INPUT, run_already = true ) reset set_input(i) run if run_already end |
Class Method Details
.[](i = ARGV) ⇒ Object
#
Bioroebe::DetermineAntigenicAreas[]
#
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# File 'lib/bioroebe/utility_scripts/determine_antigenic_areas/determine_antigenic_areas.rb', line 107 def self.[](i = ARGV) new(i) end |
Instance Method Details
#input? ⇒ Boolean
#
input?
#
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# File 'lib/bioroebe/utility_scripts/determine_antigenic_areas/determine_antigenic_areas.rb', line 88 def input? @input end |
#reset ⇒ Object
#
reset (reset tag)
#
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# File 'lib/bioroebe/utility_scripts/determine_antigenic_areas/determine_antigenic_areas.rb', line 71 def reset super() end |
#run ⇒ Object
#
run (run tag)
#
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# File 'lib/bioroebe/utility_scripts/determine_antigenic_areas/determine_antigenic_areas.rb', line 95 def run erev 'The provided input had '+steelblue(@input.size.to_s)+rev+' entries.' e erev ' n '+lightgreen('C')+rev+':'+@input.count('C').to_s.rjust(3) erev ' n '+lightgreen('L')+rev+':'+@input.count('L').to_s.rjust(3) erev ' n '+lightgreen('V')+rev+':'+@input.count('V').to_s.rjust(3) e end |
#set_input(i = SAMPLE_INPUT) ⇒ Object
#
set_input
#
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# File 'lib/bioroebe/utility_scripts/determine_antigenic_areas/determine_antigenic_areas.rb', line 78 def set_input(i = SAMPLE_INPUT) i = i.first if i.is_a? Array i = SAMPLE_INPUT if i.nil? # Use default in this case. i = i.to_s.dup @input = i end |