Class: Bioroebe::CommandlineApplication

Inherits:
Base
  • Object
show all
Includes:
ColoursForBase, CommandlineArguments
Defined in:
lib/bioroebe/base/commandline_application/opn.rb,
lib/bioroebe/base/commandline_application/misc.rb,
lib/bioroebe/base/commandline_application/extract.rb,
lib/bioroebe/base/commandline_application/warnings.rb,
lib/bioroebe/base/commandline_application/directory.rb,
lib/bioroebe/base/commandline_application/aminoacids.rb,
lib/bioroebe/base/commandline_application/write_what_into.rb,
lib/bioroebe/base/commandline_application/commandline_application.rb

Overview

Bioroebe::CommandlineApplication

Direct Known Subclasses

AdvancedDotplot, AlignOpenReadingFrames, Alignment, AlphaHelix, AminoacidSubstitution, AnalyseGlycosylationPattern, AnalyseLocalDataset, AutocorrectTheNameOfThisFastaFile, BiolangParser, BlosumParser, CalculateGCContent, CalculateMeltingTemperature, CalculateThePositionSpecificScoringMatrix, Cell, CheckForMismatches, CodonPercentage, CompactFastaFile, Compacter, Compseq, ConsensusSequence, ConvertAminoacidToDNA, CountAmountOfAminoacids, CountAmountOfNucleotides, CreateAnnotationFormat, CreateBatchEntrezFile, CreateRandomAminoacids, DeduceAminoacidSequence, DetermineMissingNucleotidesPercentage, DetermineOptimalCodons, Digestion, DisplayAminoacidTable, DisplayHowManyFastaEntriesAreInThisDirectory, DisplayOpenReadingFrames, DnaToAminoacidSequence, DotAlignment, DownloadFasta, DownloadFilesFromRebase, DownloadTaxonomyDatabase, ElectronMicroscopy::CoordinateAnalyzer, ElectronMicroscopy::FixPosFile, ElectronMicroscopy::FlipY, ElectronMicroscopy::GenerateEm2emFile, ElectronMicroscopy::ParseCoordinates, ElectronMicroscopy::ReadFileXMD, ElectronMicroscopy::SimpleStarFileGenerator, FastaDefline, FastaToYaml, FastqFormatExplainer, FetchFastaSequenceFromPdb, FindGene, FindLongestSubstring, FindLongestSubstringViaLCSalgorithm, GenbankFlatFileFormatGenerator, GenbankParser, GenomePattern, GenomeRetriever, HammingDistance, HelixWheel, LengthModifier, Levensthein, MatplotlibGenerator, MirrorRepeat, MostLikelyNucleotideSequenceForThisAminoacidSequence, MoveFileToItsCorrectLocation, Palindrome2DStructure, PalindromeFinder, PalindromeGenerator, ParseEMBL, ParseFasta, ParseFastq, ParseFrequencyTable, ParsePdbFile, ParseTaxonomy, ParsemmCIFFile, Parser::GFF, Pathways, Permutations, PhredQualityScoreTable, PossibleCodonsForThisAminoacid, ProfilePattern, Quiz::ThreeLetterToAminoacid, RGG_Scanner, RNALfoldWrapper, ReportSecondaryStructuresFromThisPdbFile, RestrictionEnzyme, Ruler, ScanForRepeat, Shell, ShowCodonTables, ShowCodonUsage, ShowFastaHeaders, ShowFastaStatistics, ShowHydrophobicity, ShowOrf, ShowThisCodonTable, ShowThisDNASequence, SimpleStringComparer, SimplifyFastaHeader, SplitThisFastaFileIntoChromosomes, StrideParser, Taxonomy::Chart, Taxonomy::Info, Taxonomy::Interactive, Taxonomy::Node, Taxonomy::ParseFasta, UsefulFormulas

Constant Summary collapse

OLD_VERBOSE_VALUE =
#

OLD_VERBOSE_VALUE

Keep an old reference to the VERBOSE flag.

#
$VERBOSE

Constants included from ColoursForBase

Bioroebe::ColoursForBase::ARRAY_HTML_COLOURS_IN_USE

Constants inherited from Base

Base::NAMESPACE

Instance Method Summary collapse

Methods included from CommandlineArguments

#commandline_arguments?, #commandline_arguments_that_are_files?, #e, #first?, #first_non_hyphen_argument?, #remove_hyphens_from_the_commandline_arguments, #reset, #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

#can_base_pair?, #convert_global_env, #delete_file, #directory_to_the_codon_tables?, #file_readlines, #infer_the_namespace, #initialize, #is_on_roebe?, #is_palindrome?, #main_encoding?, #mkdir, #move_file, #mv, #namespace?, #no_file_exists_at, #no_newlines, #project_yaml_directory?, #rds, #register_sigint, #reset, #return_pwd, #return_the_first_line_of_this_file, #word_wrap

Constructor Details

This class inherits a constructor from Bioroebe::Base

Instance Method Details

#all_aminoacids? ⇒ Boolean

#

all_aminoacids?

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/base/commandline_application/aminoacids.rb', line 29

def all_aminoacids?
  ::Bioroebe.all_aminoacids?
end

#append_what_into(what, into) ⇒ Object

#

append_what_into

#

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# File 'lib/bioroebe/base/commandline_application/write_what_into.rb', line 25

def append_what_into(what, into)
  ::Bioroebe.append_what_into(what, into)
end

#at_home? ⇒ Boolean Also known as: is_roebe?

#

at_home?

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/base/commandline_application/misc.rb', line 259

def at_home?
  if ENV['IS_ROEBE']
    true
  else
    false
  end
end

#be_silent ⇒ Object Also known as: be_quiet, set_be_silent, set_be_quiet, do_not_be_verbose

#

be_silent

#

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# File 'lib/bioroebe/base/commandline_application/misc.rb', line 342

def be_silent
  @be_verbose = false
end

#be_verbose? ⇒ Boolean Also known as: verbose?

#

be_verbose?

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/base/commandline_application/misc.rb', line 335

def be_verbose?
  @be_verbose
end

#cat(i) ⇒ Object

#

cat

#

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# File 'lib/bioroebe/base/commandline_application/misc.rb', line 162

def cat(i)
  ::Bioroebe.cat(i)
end

#ccliner(n_times = :default_n_times) ⇒ Object

#

ccliner

#

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# File 'lib/bioroebe/base/commandline_application/misc.rb', line 366

def ccliner(
    n_times = :default_n_times
  )
  ee rev; cliner(:default_token, n_times)
end

#change_directory(i = '$HOME') ⇒ Object Also known as: cd

#

change_directory (cd tag)

Use this to change the directory. The first argument should be the target directory in question.

The second argument means that this method will be verbose.

#

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# File 'lib/bioroebe/base/commandline_application/directory.rb', line 20

def change_directory(
    i = '$HOME'
  )
  # ======================================================================= #
  # The verbose-flag set next is used to also report the current directory.
  # ======================================================================= #
  case i
  when ':home', :home
    i = :home_directory
  end
  ::Bioroebe.change_directory(i, :be_verbose)
end

#cliner(use_this_token = :default_token, how_many_times = :default_n_times, &block) ⇒ Object

#

cliner (cliner tag)

#

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# File 'lib/bioroebe/base/commandline_application/misc.rb', line 376

def cliner(
    use_this_token = :default_token,
    how_many_times = :default_n_times,
    &block
  )
  case how_many_times
  # ======================================================================= #
  # === :default_n_times
  # ======================================================================= #
  when :default_n_times
    how_many_times = 80
  end
  ::Bioroebe.cliner(
    use_this_token,
    how_many_times,
    &block
  )
end

#codon_table_dataset? ⇒ Boolean

#

codon_table_dataset?

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/base/commandline_application/misc.rb', line 46

def codon_table_dataset?
  ::Bioroebe.codon_table_dataset?
end

#codon_to_aminoacid(i) ⇒ Object Also known as: nucleotides_to_aminoacid, codons_to_aminoacid

#

codon_to_aminoacid

#

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# File 'lib/bioroebe/base/commandline_application/misc.rb', line 169

def codon_to_aminoacid(i)
  unless Bioroebe.respond_to? :codon_to_aminoacid
    require 'bioroebe/conversions/dna_to_aminoacid_sequence.rb'
  end
  ::Bioroebe.codon_to_aminoacid(i)
end

#codons_for?(i) ⇒ Boolean

#

codons_for?

See documentation for Bioroebe.codons_for? in the file codons.rb, so it belongs to the above require statement.

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/base/commandline_application/misc.rb', line 91

def codons_for?(i)
  ::Bioroebe.codons_for?(i)
end

#colourize_this_dna_sequence(i) ⇒ Object Also known as: colourize_dna_sequence, colourize_nucleotides, colourize_nucleotide_sequence

#

colourize_this_dna_sequence

This method can be used to colourize a DNA sequence.

#

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# File 'lib/bioroebe/base/commandline_application/misc.rb', line 420

def colourize_this_dna_sequence(i)
  if i.is_a? ::Bioroebe::Sequence
    i = i.to_s
  end
  _ = ''.dup
  if use_colours?
    _ << remove_trailing_escape_code(
      ::Colours.send(USE_THIS_COLOUR_FOR_DNA)
    )
  end
  _ << i
  _ << rev if use_colours?
end

#complement(i) ⇒ Object Also known as: return_the_complementary_nucleotide_sequence_to, complementary_dna_strand, complementary_dna_sequence

#

complement (complement tag)

Usage example:

x = Bioroebe::Sequence.new('ATGGCA').complement # => "TACCGT"
#

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# File 'lib/bioroebe/base/commandline_application/misc.rb', line 291

def complement(i)
  ::Bioroebe.complement(i)
end

#cp(from, to = return_pwd) ⇒ Object Also known as: copy

#

cp (cp tag, copy tag)

Copy some files via this method here.

#

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# File 'lib/bioroebe/base/commandline_application/misc.rb', line 249

def cp(
    from, to = return_pwd
  )
  e "Now copying #{sfile(from.to_s)} to #{sfile(to.to_s)}."
  FileUtils.cp(from.to_s, to.to_s)
end

#disable_warnings ⇒ Object

#

disable_warnings

#

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# File 'lib/bioroebe/base/commandline_application/warnings.rb', line 23

def disable_warnings
  $VERBOSE = nil
end

#download_dir? ⇒ Boolean

#

download_dir?

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/base/commandline_application/misc.rb', line 278

def download_dir?
  ::Bioroebe.download_dir?
end

#editor? ⇒ Boolean

#

editor?

Which editor we will use.

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/base/commandline_application/misc.rb', line 240

def editor?
  Bioroebe.editor?
end

#enable_warnings ⇒ Object

#

enable_warnings

#

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# File 'lib/bioroebe/base/commandline_application/warnings.rb', line 30

def enable_warnings
  $VERBOSE = OLD_VERBOSE_VALUE
end

#ensure_that_the_base_directories_exist ⇒ Object

#

ensure_that_the_base_directory_exists

Common functionality to ensure that the necessary base directories exist on the target computer system.

#

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# File 'lib/bioroebe/base/commandline_application/misc.rb', line 57

def ensure_that_the_base_directories_exist
  ::Bioroebe.ensure_that_the_base_directories_exist
end

#esystem(i) ⇒ Object

#

esystem

Run an external program - and output the result.

#

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# File 'lib/bioroebe/base/commandline_application/misc.rb', line 302

def esystem(i)
  ::Bioroebe.esystem(i)
end

#extract(i) ⇒ Object

#

extract (extract tag)

This method can be used to extract an archive, via a hardcoded call to “tar”.

#

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# File 'lib/bioroebe/base/commandline_application/extract.rb', line 17

def extract(i)
  require 'bioroebe/toplevel_methods/extract.rb'
  ::Bioroebe.extract(i)
end

#is_this_a_start_codon?(i) ⇒ Boolean

#

is_this_a_start_codon?

Note that the method-call defind in this method will return the start codon as a DNA variant, so the given input should be in the form of DNA rather than RNA.

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/base/commandline_application/misc.rb', line 144

def is_this_a_start_codon?(i)
  ::Bioroebe.start_codons?.include? i
end

#is_this_a_stop_codon?(i) ⇒ Boolean

#

is_this_a_stop_codon?

Query method to determine whether the given input is a stop codon or whether it is not.

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/base/commandline_application/misc.rb', line 154

def is_this_a_stop_codon?(i)
  ::Bioroebe.stop_codons?.include? i
end

#leading_five_prime(i = '', get_rid_of_spaces = false, use_hyphen = false) ⇒ Object

#

leading_five_prime

The first argument should be the input sequence; or, alternatively, if you only need the “5' ” header then you can omit it altogether.

#

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# File 'lib/bioroebe/base/commandline_application/misc.rb', line 355

def leading_five_prime(
    i                 = '',
    get_rid_of_spaces = false,
    use_hyphen        = false
  )
  ::Bioroebe.leading_five_prime(i, get_rid_of_spaces, use_hyphen)
end

#load_bioroebe_yaml_file(i = :agarose) ⇒ Object

#

load_bioroebe_yaml_file

This method can be used to more easily load up a yaml file residing in the main yaml/ directory of Bioroebe.

If a Symbol is passed as input, then this will be assumed to correspond to some existing yaml file there.

#

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# File 'lib/bioroebe/base/commandline_application/misc.rb', line 454

def load_bioroebe_yaml_file(
    i = :agarose
  )
  case i # case tag
  when :agarose
    i = 'agarose/agarose_concentrations.yml'
  end
  # ======================================================================= #
  # Aggregate it together with the BIOROEBE_YAML constant.
  # ======================================================================= #
  this_file = "#{yaml_directory?}#{i}"
  if File.exist? this_file
    return YAML.load_file(this_file)
  else
    nil
  end
end

#log_directory? ⇒ Boolean Also known as: log_dir?

#

log_directory?

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/base/commandline_application/misc.rb', line 309

def log_directory?
  ::Bioroebe.log_directory?
end

#one_letter_to_long_name(one_letter_code) ⇒ Object

#

one_letter_to_long_name

The purpose of this method is really simple:

  • Take the one-letter abbreviation of an amino acid, and find the corresponding long name of the aminoacid.

#

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# File 'lib/bioroebe/base/commandline_application/misc.rb', line 229

def one_letter_to_long_name(one_letter_code)
  inverted = AMINO_ACIDS_LONG_NAME_TO_ONE_LETTER.invert
  inverted[one_letter_code.upcase]
end

#one_to_three(i) ⇒ Object

#

one_to_three

#

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# File 'lib/bioroebe/base/commandline_application/misc.rb', line 18

def one_to_three(i)
  ::Bioroebe.one_to_three(i)
end

#only_numbers?(i) ⇒ Boolean

#

only_numbers?

This method will return true if the input consists of only numbers. Otherwise, false will be returned.

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/base/commandline_application/misc.rb', line 193

def only_numbers?(i)
  i = i.to_s
  i =~ /^\d+$/
end

#open_in_browser(this_url) ⇒ Object Also known as: open_in_browser_tab

#

open_in_browser

#

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# File 'lib/bioroebe/base/commandline_application/misc.rb', line 488

def open_in_browser(this_url)
  ::Bioroebe.open_in_browser(this_url)
end

#opne(i = '') ⇒ Object

#

opne

#

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# File 'lib/bioroebe/base/commandline_application/opn.rb', line 43

def opne(i = '')
  opnn; erev i
end

#opnn(i = namespace?, , &block) ⇒ Object

#

opnn

#

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# File 'lib/bioroebe/base/commandline_application/opn.rb', line 28

def opnn(
    i = namespace?,
    &block
  )
  if use_opn?
    if i.is_a? String
      i = { namespace: i }
    end
    Opn.opn(i, &block)
  end
end

#pad_with_double_quotes(i) ⇒ Object

#

pad_with_double_quotes

Pad the input with “” quotes.

#

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# File 'lib/bioroebe/base/commandline_application/misc.rb', line 203

def pad_with_double_quotes(i)
  return "\"#{i}\""
end

#pad_with_single_quotes(i) ⇒ Object

#

pad_with_single_quotes

Pad the input with '' quotes, unless it has them already.

#

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# File 'lib/bioroebe/base/commandline_application/misc.rb', line 212

def pad_with_single_quotes(i)
  _ = ''.dup
  _ << "'"
  _ << i.to_s.delete("'")
  _ << "'"
  return _
end

#partner_nucleotide(i) ⇒ Object Also known as: return_dna_match

#

partner_nucleotide

#

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# File 'lib/bioroebe/base/commandline_application/misc.rb', line 73

def partner_nucleotide(i)
  ::Bioroebe.partner_nucleotide(i)
end

#remove_numbers(i) ⇒ Object

#

remove_numbers

This method will chop off numbers.

#

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# File 'lib/bioroebe/base/commandline_application/misc.rb', line 441

def remove_numbers(i)
  return i.delete('[0-9]')
end

#remove_trailing_ansii_escape_code(i) ⇒ Object

#

remove_trailing_ansii_escape_code

#

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# File 'lib/bioroebe/base/commandline_application/misc.rb', line 270

def remove_trailing_ansii_escape_code(i)
  return ::Colours.remove_trailing_ansii_escape_code(i) if use_colours?
  i
end

#return_all_possible_start_codons ⇒ Object

#

return_all_possible_start_codons

This method will return all possible start codons. The code itself is defined in the file “bioroebe/codons/start_codons.rb”, so the method here is grouped with the above .rb file (the require statement above here).

#

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# File 'lib/bioroebe/base/commandline_application/misc.rb', line 133

def return_all_possible_start_codons
  ::Bioroebe.start_codons?
end

#return_array_of_one_letter_aminoacids ⇒ Object

#

return_array_of_one_letter_aminoacids

This method will return a sorted Array of the one-letter aminoacids.

Specifically, this may look like this:

["A","C","D","E","F","G","H","I","K","L","M","N",
 "O","P","Q","R","S","T","U","V","W","Y"]
#

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# File 'lib/bioroebe/base/commandline_application/aminoacids.rb', line 22

def return_array_of_one_letter_aminoacids
  AMINO_ACIDS_LONG_NAME_TO_ONE_LETTER.values.sort
end

#return_cheerful_person ⇒ Object Also known as: cheerful_person

#

return_cheerful_person

#

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# File 'lib/bioroebe/base/commandline_application/misc.rb', line 106

def return_cheerful_person
  '\\o/'
end

#return_chunked_display(i) ⇒ Object

#

return_chunked_display

#

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# File 'lib/bioroebe/base/commandline_application/misc.rb', line 99

def return_chunked_display(i)
  ::Bioroebe.chunked_display(i)
end

#return_ubiquitin_sequence(i) ⇒ Object

#

return_ubiquitin_sequence

#

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# File 'lib/bioroebe/base/commandline_application/misc.rb', line 328

def return_ubiquitin_sequence(i)
  ::Bioroebe.return_ubiquitin_sequence(i)
end

#set_be_verbose(i = true) ⇒ Object

#

set_be_verbose

#

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# File 'lib/bioroebe/base/commandline_application/misc.rb', line 398

def set_be_verbose(i = true)
  case i
  # ======================================================================= #
  # === :be_verbose
  # ======================================================================= #
  when :be_verbose,
       :default
    i = true
  # ======================================================================= #
  # === :be_quiet
  # ======================================================================= #
  when :be_quiet
    i = false
  end
  @be_verbose = i
end

#start_codon? ⇒ Boolean

#

start_codon?

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/base/commandline_application/misc.rb', line 121

def start_codon?
  ::Bioroebe.start_codon?
end

#stop_codons?(i) ⇒ Boolean

#

stop_codons?

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/base/commandline_application/misc.rb', line 38

def stop_codons?(i)
  ::Bioroebe.stop_codons?(i)
end

#strict_filter_away_invalid_aminoacids(i) ⇒ Object

#

strict_filter_away_invalid_aminoacids

#

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# File 'lib/bioroebe/base/commandline_application/misc.rb', line 65

def strict_filter_away_invalid_aminoacids(i)
  ::Bioroebe.strict_filter_away_invalid_aminoacids(i)
end

#taxonomy_download_directory? ⇒ Boolean

#

taxonomy_download_directory?

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/base/commandline_application/misc.rb', line 81

def taxonomy_download_directory?
  ::Bioroebe.taxonomy_download_directory?
end

#three_to_one(i) ⇒ Object Also known as: three_aminoacid_letter_code_to_one_aminoacid_letter_code, three_letters_to_one_letter

#

three_to_one

This method will “convert” from the three-letter amino acid code to the one-letter amino acid code. So, for instance, “Lys” will become “L”.

#

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# File 'lib/bioroebe/base/commandline_application/misc.rb', line 479

def three_to_one(i)
  ::Bioroebe.three_to_one(i)
end

#to_rna(i) ⇒ Object

#

to_rna

#

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# File 'lib/bioroebe/base/commandline_application/misc.rb', line 113

def to_rna(i)
  i.tr('T','U')
end

#trailing_three_prime(i = '', get_rid_of_spaces = false, use_hyphen = false) ⇒ Object

#

trailing_three_prime

#

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# File 'lib/bioroebe/base/commandline_application/misc.rb', line 26

def trailing_three_prime(
    i                 = '',
    get_rid_of_spaces = false,
    use_hyphen        = false
  )
  ::Bioroebe.trailing_three_prime(i, get_rid_of_spaces, use_hyphen)
end

#use_opn? ⇒ Boolean

#

use_opn?

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/base/commandline_application/opn.rb', line 21

def use_opn?
  ::Bioroebe.use_opn?
end

#verbose_truth(i) ⇒ Object

#

verbose_truth

Delegate towards the module Bioroebe::VerboseTruth here.

#

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# File 'lib/bioroebe/base/commandline_application/misc.rb', line 498

def verbose_truth(i)
  ::Bioroebe::VerboseTruth[i]
end

#was_or_were(i = 1) ⇒ Object

#

was_or_were

#

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# File 'lib/bioroebe/base/commandline_application/misc.rb', line 316

def was_or_were(i = 1)
  if i == 1
    'was'
  else
    'were'
  end
end

#without_extname(i) ⇒ Object

#

without_extname

This method will return a filename without the extname.

#

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# File 'lib/bioroebe/base/commandline_application/misc.rb', line 182

def without_extname(i)
  _ = File.extname(i)
  return i.gsub(/#{_}/, '')
end

#write_what_into(what, into) ⇒ Object Also known as: save_file

#

write_what_into

This method can be used to write into a (local) file.

#

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# File 'lib/bioroebe/base/commandline_application/write_what_into.rb', line 18

def write_what_into(what, into)
  ::Bioroebe.write_what_into(what, into)
end