Class: Bioroebe::Shell::Help

Inherits:
CommandlineApplication show all
Defined in:
lib/bioroebe/shell/help/class.rb

Constant Summary collapse

N_LEFT_PADDING =
#

N_LEFT_PADDING

How many space characters to pad to the left. Currently 4 ‘ ’ space tokens.

#
4
DEFAULT_MIDDLE_PADDING =
#

DEFAULT_MIDDLE_PADDING

#
25
RAW_TITLE =
#

RAW_TITLE

#
'BioShell Help Options:'
TITLE =
#

TITLE

This constant specifies the title that we will use for the bioshell help options. Since as of November 2023 this constant is not as important anymore, as we return the title dynamically, via RAW_TITLE.

#
"#{::Bioroebe.rev}#{RAW_TITLE}"

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, #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(use_colours = true, run_already = true) ⇒ Help

#

initialize

The first argument determines whether we will use colours or not.

We can either use KDE Konsole colours, or the regular colours.

#


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# File 'lib/bioroebe/shell/help/class.rb', line 52

def initialize(
    use_colours = true,
    run_already = true
  )
  reset
  set_use_colours(use_colours)
  # ======================================================================= #
  # === Handle blocks next
  #
  # The user may pass in a block, which usually means that the user
  # wants to display only some subcommands.
  # ======================================================================= #
  if block_given?
    yielded = yield
    if yielded
      unless yielded.empty?
        # ================================================================= #
        # @what_to_show can limit to show only some help-options.
        # ================================================================= #
        @what_to_show = yielded
        @what_to_show = @what_to_show.first if @what_to_show.is_a? Array
        if @what_to_show == '?'
          _  = "#{rev}You can provide an argument such as \"a\" "\
               "or \"b\" and we will#{N}".dup
          _ << 'feedback all help options that start with '\
               'this letter.'+N+N
          _ << 'Example:'+N+N
          _ << '  help a'+N+N
          show_help(_)
          return
        end
      end
    end
  end
  case run_already
  # ======================================================================= #
  # === :do_not_run_yet
  # ======================================================================= #
  when :do_not_run_yet
    run_already = false
  end
  run if run_already
end

Class Method Details

.[](i = ARGV) ⇒ Object

#

Bioroebe::Shell::Help[]

#


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# File 'lib/bioroebe/shell/help/class.rb', line 484

def self.[](i = ARGV)
  new(i)
end

Instance Method Details

#add(i = '', append_this = nil) ⇒ Object

#

add (add tag)

#


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# File 'lib/bioroebe/shell/help/class.rb', line 371

def add(
    i           = '',
    append_this = nil
  )
  original_append_this = nil
  original_append_this = append_this.dup if append_this
  # ======================================================================= #
  # Handle subcommands next.
  # ======================================================================= #
  unless @what_to_show == :everything
    # ===================================================================== #
    # Note that @what_to_show can be 'a' but also 'a-d', so
    # we must check whether it has a '-' token.
    # ===================================================================== #
    _ = @what_to_show # Keep track of what to show here.
    if _.include? '-' # Check for a "range"-like input here.
      splitted       = _.split('-')
      start_position = splitted.first
      end_position   = splitted.last
      range = (start_position .. end_position).to_a
      unless range.any? {|entry| i.delete('(').strip.start_with? entry }
        return
      end
    else
      unless i.delete('(').strip.start_with? _
        return # ^^^ We exclude all entries that do NOT start with this character.
      end
    end
  end unless i.include? TITLE
  # ======================================================================= #
  # === Handle input that includes ()
  # ======================================================================= #
  if i.include? '(' # Assume that we must parse it.
    # ===================================================================== #
    # First pad it.
    # ===================================================================== #
    regex_to_use = /^(\(.+?\)\w*)/ # See: http://rubular.com/r/AbZ0fGRTvd
    splitted = i.split(regex_to_use).reject(&:empty?)
    splitted[0] = splitted[0].ljust(middle_padding?)
    # ===================================================================== #
    # If the second half is too long, we will insert a newline
    # ===================================================================== #
    if splitted[1].size > 75
      splitted[1] = splitted[1].gsub(/(.{1,75})(\s+|$)/,
                                     "\\1\n#{left_padding?} #{expanded_middle_padding?}").rstrip
    end
    i = splitted.join
    if use_colours?
      i.gsub!(regex_to_use, burlywood('\\1')+rev)
    end
    i.prepend(@left_padding)
  end
  # ======================================================================= #
  # Next, colourize the input if the user requested it so.
  # ======================================================================= #
  if append_this
    if append_this.is_a?(Hash)
      if append_this.has_key? :colourize
        # ================================================================= #
        # Use Konsole colours next.
        # ================================================================= #
        append_this = append_this.delete(:colourize)
        append_this = slateblue(append_this) if @use_colours
        i << append_this
      end
    end
    unless i.end_with? ' '
      append_this = append_this.dup if append_this.frozen?
      append_this.prepend(' ')
    end
    if use_colours?
      i << sfancy(append_this)
    else
      i << append_this
    end unless original_append_this.is_a? Hash
  end
  @_ << i+N # This is mostly just an append-action. We will add a newline too.
end

#build_help_string ⇒ Object

#

build_help_string

Called from within the run() method.

#


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# File 'lib/bioroebe/shell/help/class.rb', line 164

def build_help_string
  # ======================================================================= #
  # Add the title first
  # ======================================================================= #
  add "#{title?}#{N}" # Add a newline to start with.
  # ======================================================================= #
  # a tag
  # ======================================================================= #
  add '(aasequence?) to show the amino acid sequence assigned'
  add '(align) to align two difference sequences to one another, '\
      'such as in "align 1 3"'
  add '(align_ORFS) to align all ORFs in the given main DNA sequence'
  add '(analyze_sequence) to analyze the main sequence for '\
      'special sequences'
  add '(aminoacid?) to show the long name of an aminoacid. '\
      'Usage: aminoacid? K'
  add '(ana)lyze to analyze a given aminoacid string. Will '\
      'show percentage of DNA used (if you use dna_analyze).'
  add '(aminoacids?) to show information about the aminoacids'
  add
  # ======================================================================= #
  # === b tag
  # ======================================================================= #
  add '(b)losum ','show blosum matrix (use e. g. "blosum62" to '\
      'show the values for this blosum)'
  add '(backtrack) translate into the most likely '\
      'DNA sequence, from the given aminoacid sequence'
  add '(bparse) to show all available genomes in the bio_lang file'
  add
  # ======================================================================= #
  # === c tag
  # ======================================================================= #
  add '(cat) to display the content of a file'
  add '(chop) to chop off some nucleotides from the end'
  add '(CpG?) to show which CpG islands may exist'
  add '(codon) to translate a RNA Codon into the proper Aminoacids'
  add '(codon?) similar to the above ^^^ but limited to only one '\
      'input-codon at a time'
  add '(codon_usage) to show the codon usage of your '\
      'DNA string'
  add '(codontable) to show the codon table'
  add '(codontables) to show all registered codon tables'
  add '(cola) to colourize a given aminoacid'
  add '(compact) to compact a FASTA (.fa / .fasta) file, '\
      'into a single line in the file'
  add '(complement) to find the complementary sequence of a '\
      'DNA strand'
  add '(cscheme) to colourize the nucleotides in the main '\
      'nucleotide colour scheme'
  add
  # ======================================================================= #
  # === d tag
  # ======================================================================= #
  add '(discover_all_palindromes) to discover all palindromes (min: 4, max: 10)'
  add
  # ======================================================================= #
  # === f tag
  # ======================================================================= #
  add '(files?) to get an overview where some various '\
      'important files are kept locally'
  add '(fasta) to parse some ', 'FASTA data'
  add '(find) to find a subsequence. Example: find ATG'
  add '(fr)ameshift to ', 'perform a frameshift (add '\
      'argument like 1, 2, 3)'
  add '(first) change the first nucleotide to another one'
  add '(find_gene) to find a gene in the given sequence'
  add
  # ======================================================================= #
  # === g tag
  # ======================================================================= #
  add '(gc_content) to calculate the GC content of a sequence '\
      'sequence (They will cut at that sequence. "rest?" '\
      'is an alias.)'
  add '(gff3?) to read and handle .gff or .gff3 files, through the '\
      'parser Bioroebe::Parser::GFF'
  add
  # ======================================================================= #
  # === h tag
  # ======================================================================= #
  add '(h)istory to show the ', 'input history'
  add
  # ======================================================================= #
  # === l tag
  # ======================================================================= #
  add '(load) to load the main string from a file'
  add '(list) age to list the age of different organisms'
  add '(ll) to get a listing of local files and directories'
  add
  # ======================================================================= #
  # === m tag
  # ======================================================================= #
  add '(ma)ss_weight to calculate weight of a Protein (Input must '+
      'be Aminoacids)'
  add '(mmasse) to display the molecular mass of an Aminoacid'
  add '(mt) ', 'to calculate the melting temperature'
  add '(multi_line) ',
      'to assign a FASTA file with several lines'
  add
  # ======================================================================= #
  # === n tag
  # ======================================================================= #
  add '(nucleotides_table?) to show the molecular mass of '\
      'the Nucleotides'
  add
  # ======================================================================= #
  # === o tag
  # ======================================================================= #
  add '(orf?) ','to seek for ORFs in our target sequence'
  if ::Bioroebe.is_on_roebe? # Only relevant for my home system.
    add '(open) to open all my relevant files in an editor'
  end
  add
  # ======================================================================= #
  # === p tag
  # ======================================================================= #
  add '(palindrome) to generate a Palindrome. Input the length of the '\
      'palindrome which should be an even number such as "6" or "12".'
  add '(parse_fasta) to parse a fasta file. pfasta is an '\
      'alias. If input is omitted, we try to '\
      'find a fasta file in the working directory.'
  add '(pathways) to show metabolic pathways'
  add '(phosphorylation_sites?) to find phosphorylation sites '\
      'in the aminoacid sequence'
  add '(pitch) to show how long an alpha helix is (optionally '\
      'pass the amount of aminoacids into it)'
  add '(print_table) to print a useful mnemo-table'
  add '(pun)net ', 'show a punnet square'
  add '(pub)med to ', 'visit pubmed'
  add
  # ======================================================================= #
  # === q tag
  # ======================================================================= #
  add '(q) to exit/quit' # should always be last.
  e
  # ======================================================================= #
  # === r tag
  # ======================================================================= #
  add '(ra)ndom to generate random DNA or random '\
      'Aminoacids (the latter when given two arguments)'
  add '(rest)riction sites to show some restriction sites'
  add '(rest) <sequence> to find restriction sites within a given'
  add '(replay) to replay (or save) input-history' 
  add '(reverse) to simply display the reversed main DNA sequence '\
      'presently in use'
  add '(reverse!) to not only display the reversed main DNA sequence '\
      'presently in use, but to also assign it as the new DNA sequence'
  # ======================================================================= #
  # === s tag
  # ======================================================================= #
  add '(save) to save the main string to a file'
  add '(seq)uence to assign a DNA sequence to use '
  add '(sscompare) to ', 'compare two different strings, '\
      'with + and . characters - or | rather than +'
  add '(shuffle) to re-arrange the nucleotide string'
  add '(shine) to search for a ', colourize: 'Shine-Dalgarno Sequence'
  add '(sub)string to find the longest common substring of two strings'
  add '(shorten_aminoacid) to shorten a 3 letter Aminoacid to '\
      '1 letter'
  add '(showorf) will show all ORFs in the given DNA sequence'
  add '(split) to split the sequence into chunks of n size, such as: split 3'
  add '(stop?) will show all STOP codons in the given '\
      'sequence'
  add
  # ======================================================================= #
  # === t tag
  # ======================================================================= #
  add '(tata?, TATA?) to find a TATA consensus sequence'
  add '(dna_translate) to give out the complementary '\
      'DNA sequence. Example: dna_translate GCATCTGCATTCGA' # This line belongs to dna_translate
  add '(to_protein) convert a DNA sequence to an Amino Acid Sequence.'
  add '(taxonomy) to list some taxonomy thingies'
  add '(to_rna) convert', 'DNA to RNA'
  add '(to_dna) convert', 'RNA to DNA'
  add '(t)ranslate to translate aminoacids into their long '\
      'form (i.e. A -> Alanin)'
  add
  # ======================================================================= #
  # === u tag
  # ======================================================================= #
  add '(upcase) to upcase the main sequence'
  add '(uncola) to uncolourize an amino acid again'
  add
  add 'Note that you can also simply input the name of an amino acid '\
      'and we will'
  add 'feedback its -R group.'
  add
  # ======================================================================= #
  # === Special instructions
  # ======================================================================= #
  add 'You can add and remove nucleotides in a simple manner, via +3 '\
      'or -3, too.'
end

#expanded_middle_padding? ⇒ Boolean

#

expanded_middle_padding?

As middle_padding but returns a String with the properly padded format.

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/shell/help/class.rb', line 141

def expanded_middle_padding?
  ' ' * middle_padding?
end

#left_padding? ⇒ Boolean

#

left_padding?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/shell/help/class.rb', line 148

def left_padding?
  @left_padding
end

#middle_padding? ⇒ Boolean

#

middle_padding?

How much to pad in the middle.

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/shell/help/class.rb', line 124

def middle_padding?
  @middle_padding
end

#reset ⇒ Object

#

reset

#


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# File 'lib/bioroebe/shell/help/class.rb', line 99

def reset
  super()
  # ======================================================================= #
  # === @_
  # ======================================================================= #
  @_ = ''.dup # This is the output/result string.
  # ======================================================================= #
  # === @middle_padding
  # ======================================================================= #
  @middle_padding = DEFAULT_MIDDLE_PADDING # Must be a number.
  # ======================================================================= #
  # === @left_padding
  # ======================================================================= #
  @left_padding = ' ' * N_LEFT_PADDING # This one will be prepended to the displayed input.
  # ======================================================================= #
  # === @what_to_show
  # ======================================================================= #
  @what_to_show = :everything
end

#result? ⇒ Boolean

#

result?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/shell/help/class.rb', line 453

def result?
  @_
end

#run ⇒ Object

#

run

#


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# File 'lib/bioroebe/shell/help/class.rb', line 476

def run
  build_help_string
  show_help
end

#set_use_colours(i = true) ⇒ Object

#

set_use_colours

#


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# File 'lib/bioroebe/shell/help/class.rb', line 460

def set_use_colours(
    i = true
  )
  case i
  # ======================================================================= #
  # === :do_not_use_colours
  # ======================================================================= #
  when :do_not_use_colours
    i = false
  end
  set_will_we_use_colours(i)
end

#show_help(display_this = @_) ⇒ Object Also known as: display_result

#

show_help

This method will show the help subsection for the BioShell.

#


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# File 'lib/bioroebe/shell/help/class.rb', line 362

def show_help(
    display_this = @_
  )
  e "#{display_this}#{N}"
end

#title? ⇒ Boolean

#

title?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/shell/help/class.rb', line 131

def title?
  RAW_TITLE
end

#use_konsole? ⇒ Boolean

#

use_konsole?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/shell/help/class.rb', line 155

def use_konsole?
  true
end