Class: Bioroebe::AnalyseLocalDataset
- Inherits:
-
CommandlineApplication
- Object
- Base
- CommandlineApplication
- Bioroebe::AnalyseLocalDataset
- Defined in:
- lib/bioroebe/utility_scripts/analyse_local_dataset.rb
Overview
Bioroebe::AnalyseLocalDataset
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::AnalyseLocalDataset[] ========================================================================= #.
Instance Method Summary collapse
-
#analyse_the_working_directory ⇒ Object
# === analyse_the_working_directory ========================================================================= #.
-
#determine_the_working_directory ⇒ Object
# === determine_the_working_directory ========================================================================= #.
-
#file_or_files(i) ⇒ Object
# === file_or_files ========================================================================= #.
-
#initialize(i = nil, run_already = true) ⇒ AnalyseLocalDataset
constructor
# === initialize ========================================================================= #.
-
#reset ⇒ Object
# === reset ========================================================================= #.
-
#run ⇒ Object
# === run ========================================================================= #.
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) ⇒ AnalyseLocalDataset
#
initialize
#
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# File 'lib/bioroebe/utility_scripts/analyse_local_dataset.rb', line 27 def initialize( i = nil, run_already = true ) reset set_commandline_arguments(i) run if run_already end |
Class Method Details
.[](i = ARGV) ⇒ Object
#
Bioroebe::AnalyseLocalDataset[]
#
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# File 'lib/bioroebe/utility_scripts/analyse_local_dataset.rb', line 111 def self.[](i = ARGV) new(i) end |
Instance Method Details
#analyse_the_working_directory ⇒ Object
#
analyse_the_working_directory
#
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# File 'lib/bioroebe/utility_scripts/analyse_local_dataset.rb', line 68 def analyse_the_working_directory pdb_directory = "#{@working_directory}pdb/" # ======================================================================= # # Check for a directory with .pdb files next: # ======================================================================= # if File.directory? pdb_directory pdb_files = Dir["#{pdb_directory}*.pdb"] unless pdb_files.empty? erev 'The directory '+sdir(pdb_directory)+ rev+' contains '+steelblue( pdb_files.size.to_s )+rev+' .pdb '+ file_or_files(pdb_files.size)+'.' end end # ======================================================================= # # Check for a directory with .fasta files next: # ======================================================================= # fasta_directory = @working_directory+'fasta/' if File.directory? fasta_directory fasta_files = Dir["#{fasta_directory}*.fasta"] fasta_files << Dir["#{fasta_directory}*.fa"] fasta_files.flatten! unless fasta_files.empty? erev 'The directory '+sdir(fasta_directory)+ rev+' contains '+steelblue( fasta_files.size.to_s )+rev+' .fasta '+file_or_files(fasta_files.size)+'.' end end end |
#determine_the_working_directory ⇒ Object
#
determine_the_working_directory
#
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# File 'lib/bioroebe/utility_scripts/analyse_local_dataset.rb', line 50 def determine_the_working_directory @working_directory = log_dir? end |
#file_or_files(i) ⇒ Object
#
file_or_files
#
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# File 'lib/bioroebe/utility_scripts/analyse_local_dataset.rb', line 57 def file_or_files(i) if i > 1 'files' else 'file' end end |
#reset ⇒ Object
#
reset
#
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# File 'lib/bioroebe/utility_scripts/analyse_local_dataset.rb', line 39 def reset super() # ======================================================================= # # === @working_directory # ======================================================================= # @working_directory = return_pwd end |
#run ⇒ Object
#
run
#
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# File 'lib/bioroebe/utility_scripts/analyse_local_dataset.rb', line 103 def run determine_the_working_directory analyse_the_working_directory end |