Class: Bioroebe::BlosumParser

Inherits:
CommandlineApplication show all
Defined in:
lib/bioroebe/parsers/blosum_parser.rb

Overview

Bioroebe::BlosumParser

Constant Summary collapse

VERTICAL_LINE =
#

VERTICAL_LINE

#
"｜"

Constants inherited from CommandlineApplication

CommandlineApplication::OLD_VERBOSE_VALUE

Constants included from ColoursForBase

ColoursForBase::ARRAY_HTML_COLOURS_IN_USE

Constants inherited from Base

Bioroebe::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(i = '', run_already = true) ⇒ BlosumParser

#

initialize

The first argument should be the blosum file that we wish to use.

#


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# File 'lib/bioroebe/parsers/blosum_parser.rb', line 33

def initialize(
    i           = '',
    run_already = true
  )
  reset
  set_blosum_file_to_use(i)
  if block_given?
    case yield
    # ===================================================================== #
    # === :be_quiet
    # ===================================================================== #
    when :be_quiet
      set_be_quiet
    end
  end
  run if run_already
end

Class Method Details

.return_as_2D_table(i = :blosum62) ⇒ Object

#

Bioroebe::BlosumParser.return_as_2D_table

#


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# File 'lib/bioroebe/parsers/blosum_parser.rb', line 140

def self.return_as_2D_table(i = :blosum62)
  @result = ''.dup
  if i.is_a? Array
    i = i.first # Only support the first element of an Array.
  end
  _ = Bioroebe::BlosumParser.new(i) { :be_quiet }
  hash = _.hash?
  @result << i.to_s.capitalize+N
  @result << N
  array = %w( A R N D C Q E G H I L K M F P S T W Y V B J Z X * )
  @result << '   '
  array.each {|entry| @result << "#{entry.to_s.rjust(3, ' ')}" }
  @result << N
  @result << '―'* 80
  @result << N
  array.each_with_index {|entry, index|
    @result << "#{entry} #{VERTICAL_LINE}"
    array.each_with_index {|inner_entry, inner_index|
      key_to_use = entry+inner_entry
      if hash.has_key? key_to_use
        match = hash[key_to_use]
        @result << "#{match.to_s.rjust(3, ' ')}"
      else
        @result << "No key found for #{key_to_use}."
      end
    }
    @result << N
  }
  @result << '―'* 80
  @result << N
  return @result
end

.show_as_2D_table(i = :blosum62) ⇒ Object

#

Bioroebe::BlosumParser.show_as_2D_table

#


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# File 'lib/bioroebe/parsers/blosum_parser.rb', line 133

def self.show_as_2D_table(i = :blosum62)
  print Bioroebe::BlosumParser.return_as_2D_table(i)
end

Instance Method Details

#check_if_the_file_exists ⇒ Object

#

check_if_the_file_exists

#


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# File 'lib/bioroebe/parsers/blosum_parser.rb', line 96

def check_if_the_file_exists
  _ = @blosum_file_to_use.to_s
  if File.exist? _
    # Pass through - all is fine.
  else
    erev "The file at `#{sfile(_)}#{rev}` does not exist."
  end
end

#dataset? ⇒ Boolean Also known as: data?, hash, hash?

#

dataset?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/parsers/blosum_parser.rb', line 108

def dataset?
  @hash
end

#reset ⇒ Object

#

reset

#


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# File 'lib/bioroebe/parsers/blosum_parser.rb', line 54

def reset
  super()
  infer_the_namespace
  # ======================================================================= #
  # === @hash
  # ======================================================================= #
  @hash = {} # Initialize our main Hash here.
end

#run ⇒ Object

#

run

#


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# File 'lib/bioroebe/parsers/blosum_parser.rb', line 176

def run
  check_if_the_file_exists
  if File.exist? @blosum_file_to_use
    dataset = File.readlines(@blosum_file_to_use).map {|entry|
      entry.strip
    }
    # ======================================================================= #
    # === Eliminate comments from the file
    #
    # Next, we get rid of all rows that start with '#' character, as
    # we assume these to be comments.
    # ======================================================================= #
    dataset.reject! {|line| line.start_with?('#') or line.empty? }
    # ======================================================================= #
    # First, we obtain the headers in the proper order.
    # ======================================================================= #
    headers = dataset.shift.split(' ')
    # ======================================================================= #
    # Next we can iterate over the remaining dataset - the first entry will
    # be one part of the key in the hash.
    # ======================================================================= #
    dataset.each {|line|
      splitted = line.split(' ')
      which_aminoacid = splitted.shift # Get the first entry.
      splitted.each_with_index {|the_score, index|
        key = which_aminoacid + headers[index]
        @hash[key] = the_score.to_i
      }
    }
  end
end

#save_into_a_yaml_file(blosum_file_to_use = @blosum_file_to_use) ⇒ Object

#

save_into_a_yaml_file

This method can be used to store the main @hash into a yaml file.

#


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# File 'lib/bioroebe/parsers/blosum_parser.rb', line 119

def save_into_a_yaml_file(
    blosum_file_to_use = @blosum_file_to_use
  )
  what = YAML.dump(@hash)
  into = log_dir?+File.basename(blosum_file_to_use)
  erev "Storing the (expanded) hash from the blosum file at"
  erev "#{sfile(blosum_file_to_use)}"
  erev "into the file #{sfile(into)}`."
  write_what_into(what, into)
end

#set_blosum_file_to_use(i) ⇒ Object

#

set_blosum_file_to_use

This method is used to determine the main BLOSUM-file to use, which is typically a .yaml file.

#


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# File 'lib/bioroebe/parsers/blosum_parser.rb', line 69

def set_blosum_file_to_use(i)
  i = i.first if i.is_a? Array
  if i.is_a? Symbol
    i = i.to_s
  end
  if i and i.include?('-')
    i.delete!('-')
  end
  if i.is_a?(String)
    i = i.dup
    # i.downcase! # This has been eliminated at 17.08.2021, because it
                  # may contain the full path. On Linux paths are
                  # case sensitive.
    unless i.end_with?('.yml')
      # =================================================================== #
      # In this case we have to modify the input a little bit.
      # =================================================================== #
      i = ::Bioroebe.blosum_directory?+
          i.to_s.dup+'.yml'
    end
  end
  @blosum_file_to_use = i
end