Class: Bioroebe::AnalyseLocalDataset

Inherits:
CommandlineApplication show all
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

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, #opne, #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, #set_be_verbose, #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 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_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?, #file_readlines, #infer_the_namespace, #is_on_roebe?, #is_palindrome?, #main_encoding?, #mkdir, #move_file, #mv, #namespace?, #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

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) ⇒ Object

#

Bioroebe::AnalyseLocalDataset[]

#

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# File 'lib/bioroebe/utility_scripts/analyse_local_dataset.rb', line 111

def self.[](i)
  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