Class: Bioroebe::MostLikelyNucleotideSequenceForThisAminoacidSequence
- Inherits:
-
CommandlineApplication
- Object
- Base
- CommandlineApplication
- Bioroebe::MostLikelyNucleotideSequenceForThisAminoacidSequence
- Defined in:
- lib/bioroebe/nucleotides/most_likely_nucleotide_sequence_for_this_aminoacid_sequence.rb
Overview
Bioroebe::MostLikelyNucleotideSequenceForThisAminoacidSequence
Constant Summary
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::MostLikelyNucleotideSequenceForThisAminoacidSequence[] ========================================================================= #.
Instance Method Summary collapse
-
#codon_percentage? ⇒ Boolean
# === codon_percentage? ========================================================================= #.
-
#final_sequence? ⇒ Boolean
(also: #sequence?)
# === final_sequence? ========================================================================= #.
-
#initialize(commandline_arguments = nil, use_this_codon_table = :default, run_already = true) ⇒ MostLikelyNucleotideSequenceForThisAminoacidSequence
constructor
# === initialize ========================================================================= #.
-
#name_of_the_codon_table? ⇒ Boolean
# === name_of_the_codon_table? ========================================================================= #.
-
#reset ⇒ Object
# === reset (reset tag) ========================================================================= #.
-
#run ⇒ Object
# === run (run tag) ========================================================================= #.
-
#set_use_this_codon_table(i) ⇒ Object
# === set_use_this_codon_table ========================================================================= #.
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 = nil, use_this_codon_table = :default, run_already = true) ⇒ MostLikelyNucleotideSequenceForThisAminoacidSequence
#
initialize
#
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# File 'lib/bioroebe/nucleotides/most_likely_nucleotide_sequence_for_this_aminoacid_sequence.rb', line 33 def initialize( commandline_arguments = nil, use_this_codon_table = :default, run_already = true ) reset set_commandline_arguments( commandline_arguments ) # ======================================================================= # # === Handle blocks next # ======================================================================= # if block_given? yielded = yield case yielded when :be_quiet set_be_quiet end end set_use_this_codon_table(use_this_codon_table) run if run_already end |
Class Method Details
.[](i = ARGV) ⇒ Object
#
Bioroebe::MostLikelyNucleotideSequenceForThisAminoacidSequence[]
#
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# File 'lib/bioroebe/nucleotides/most_likely_nucleotide_sequence_for_this_aminoacid_sequence.rb', line 131 def self.[](i = ARGV) new(i) end |
Instance Method Details
#codon_percentage? ⇒ Boolean
#
codon_percentage?
#
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# File 'lib/bioroebe/nucleotides/most_likely_nucleotide_sequence_for_this_aminoacid_sequence.rb', line 85 def codon_percentage? @internal_hash[:codon_percentage] end |
#final_sequence? ⇒ Boolean Also known as: sequence?
#
final_sequence?
#
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# File 'lib/bioroebe/nucleotides/most_likely_nucleotide_sequence_for_this_aminoacid_sequence.rb', line 124 def final_sequence? @internal_hash[:final_sequence] end |
#name_of_the_codon_table? ⇒ Boolean
#
name_of_the_codon_table?
#
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# File 'lib/bioroebe/nucleotides/most_likely_nucleotide_sequence_for_this_aminoacid_sequence.rb', line 78 def name_of_the_codon_table? codon_percentage?.name_of_the_codon_table? end |
#reset ⇒ Object
#
reset (reset tag)
#
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# File 'lib/bioroebe/nucleotides/most_likely_nucleotide_sequence_for_this_aminoacid_sequence.rb', line 59 def reset super() infer_the_namespace # ======================================================================= # # === :codon_percentage # ======================================================================= # @internal_hash[:codon_percentage] = Bioroebe::CodonPercentage.new end |
#run ⇒ Object
#
run (run tag)
#
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# File 'lib/bioroebe/nucleotides/most_likely_nucleotide_sequence_for_this_aminoacid_sequence.rb', line 92 def run _ = first?.delete('-').split(//) erev 'The aminoacid sequence '+steelblue(_.join)+rev+ ' is best represented by:' if be_verbose? codon_percentage = codon_percentage? all_codons = ::Bioroebe.possible_codons_for_these_aminoacids(_) final_sequence = ''.dup all_codons.each {|array_codons| max_value = array_codons.map {|this_codon| codon_percentage[this_codon] } # ===================================================================== # # Next we build a sorted Hash representing these frequencies: # ===================================================================== # max_element = array_codons.zip(max_value). max_by {|key, value| value }.first # This will give us: "ATC" from ["ATC", 20.8] final_sequence << max_element } @internal_hash[:final_sequence] = final_sequence if be_verbose? e e " 5'-#{colourize_nucleotide_sequence(final_sequence)}-3'" e erev 'This assumes the codon table '+ steelblue(name_of_the_codon_table?)+ rev+'.' end end |
#set_use_this_codon_table(i) ⇒ Object
#
set_use_this_codon_table
#
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# File 'lib/bioroebe/nucleotides/most_likely_nucleotide_sequence_for_this_aminoacid_sequence.rb', line 71 def set_use_this_codon_table(i) @internal_hash[:codon_percentage].set_use_this_codon_table(i) end |