bioroebe 0.12.24 → 0.13.31

data/lib/bioroebe/constants/misc.rb

@@ -1,209 +0,0 @@
-#!/usr/bin/ruby -w
-# Encoding: UTF-8
-# frozen_string_literal: true
-# =========================================================================== #
-# require 'bioroebe/constants/misc.rb'
-# =========================================================================== #
-module Bioroebe
-
-  require 'bioroebe/constants/aminoacids_and_proteins.rb'
-  require 'bioroebe/constants/roebe.rb' # ← Necessary due to the RUBY_SRC constant.
-
-  # ========================================================================= #
-  # === array_failsave_requires
-  #
-  # Next we do some failsafe requires for the Bioroebe::Shell component
-  # specifically.
-  # ========================================================================= #
-  array_failsave_requires = %w(
-    convert_global_env
-  )
-  array_failsave_requires.each {|project|
-    begin
-      require project
-    rescue LoadError; end # Silent rescue.
-  }
-
-  # ========================================================================= #
-  # === E_BOX
-  #
-  # This constant was disabled in December 2020. It may have to be moved
-  # to .rb files that depend on it, if we still actually need it. If
-  # not then this comment will be removed at a later point anyway.
-  # ========================================================================= #
-  # E_BOX = 'CACGTG' # The "E Box".
-
-  # ========================================================================= #
-  # === BE_VERBOSE
-  # ========================================================================= #
-  BE_VERBOSE = true
-
-  # ========================================================================= #
-  # === TOKEN                                                     (TOKEN tag)
-  # ========================================================================= #
-  TOKEN = '|'
-
-  # ========================================================================= #
-  # === VALID_WAYS_TO_EXIT
-  #
-  # All ways to exit will be recorded here.
-  #
-  # If you need to use more ways, simply append to this Array.
-  #
-  # This constant may have to be moved into the bio-shell part eventually.
-  # ========================================================================= #
-  VALID_WAYS_TO_EXIT = %w(
-    quit q exit qq :q qt
-    bye
-    rda
-    r2
-    tq
-    sq
-    exit_program
-    exitprogram
-  )
-
-  # ========================================================================= #
-  # === NAMES_ENTRIES
-  #
-  # This used to belong to the Taxonomy submodule.
-  # ========================================================================= #
-  NAMES_ENTRIES = 'names.sql'
-
-  # ========================================================================= #
-  # === NODES_ENTRIES
-  #
-  # This used to belong to the Taxonomy submodule.
-  # ========================================================================= #
-  NODES_ENTRIES = 'nodes.sql'
-
-  # ========================================================================= #
-  # === FASTA_ENTRIES
-  #
-  # This used to belong to the Taxonomy submodule.
-  # ========================================================================= #
-  FASTA_ENTRIES = 'fasta.sql'
-
-  # ========================================================================= #
-  # === SHALL_WE_LOG_LAST_UPDATE
-  #
-  # This constant exists specifically for the taxonomy-component of
-  # the Bioroebe project.
-  # ========================================================================= #
-  SHALL_WE_LOG_LAST_UPDATE = true
-
-  require 'bioroebe/toplevel_methods/log_directory.rb'
-  # ========================================================================= #
-  # === TAXONOMY_NCBI_DATABASE_LAST_UPDATE_LOG_FILE
-  #
-  # This constant is used specifically for the taxonomy-component of the
-  # Bioroebe project.
-  # ========================================================================= #
-  TAXONOMY_NCBI_DATABASE_LAST_UPDATE_LOG_FILE =
-    "#{::Bioroebe.log_dir?}taxonomy_ncbi_database_last_update.log"
-
-  # ========================================================================= #
-  # === NAME_OF_BIO_SHELL
-  #
-  # This constant can be used as the default prompt for the bioshell
-  # component.
-  # ========================================================================= #
-  NAME_OF_BIO_SHELL = 'BIO SHELL> '
-
-  # ========================================================================= #
-  # === DEFAULT_DNA_SEQUENCE
-  #
-  # This is a default "test" DNA sequence, in the sense that it can be
-  # used to quickly test functionality within the bioroebe project.
-  #
-  # It was added in May 2020, but it may be that we have to remove
-  # it at a later time, or move it into a separate .yml file. For
-  # the time being, though, it will reside here.
-  # ========================================================================= #
-  DEFAULT_DNA_SEQUENCE =
-    'CGGCCCGATTTGGGTTTCGGAGCGATCGAAATACCAGCACTACCATGAATTCTAT'\
-    'ATGGCTGCCGTTCACAGCCTTAATTTTAGGCTTTCCACCTGATCACTCTTTAATC'\
-    'TCCATTGTTTCTGGTACGCAGAAATTGACGCTTCCCATTCATTCACGGCTAAAAT'\
-    'CAAGGATTCCACCAGAATCGCGGGCCGCGTGGGTGCGCCGTCGACCTCCTCGGCC'\
-    'AAATAAGAACGGGCAGGTAAGAGACTAGGGTACTCAAGAT'
-
-  # ========================================================================= #
-  # === DEFAULT_LENGTH_FOR_DNA
-  #
-  # How long our DNA-generated strings should be by default.
-  #
-  # This may be used by some scripts, so it provides a default value
-  # for use in these scripts.
-  #
-  # 150 nucleotides are the current default.
-  # ========================================================================= #
-  DEFAULT_LENGTH_FOR_DNA = 150
-
-  require 'bioroebe/constants/tabulator.rb'
-  # ========================================================================= #
-  # === FIELD_TERMINATOR
-  # ========================================================================= #
-  FIELD_TERMINATOR = "#{TABULATOR}|#{TABULATOR}"
-    MAIN_DELIMITER = DELIMITER = FIELD_TERMINATOR # An alias to the above.
-
-  # ========================================================================= #
-  # === BIOROEBE_AT_HOME
-  # ========================================================================= #
-  BIOROEBE_AT_HOME = "#{RUBY_SRC}bioroebe/lib/bioroebe/"
-
-  # ========================================================================= #
-  # === LOCALHOST
-  # ========================================================================= #
-  LOCALHOST = 'http://localhost/'
-
-  # ========================================================================= #
-  # === PATH_TO_THE_RELION_BINARY
-  #
-  # This constant can be set to determine where relion resides. It is
-  # mostly an ad-hoc constant.
-  # ========================================================================= #
-  PATH_TO_THE_RELION_BINARY =
-    '/opt/RELION/relion-1.3/bin/relion'
-
-  # ========================================================================= #
-  # === ARRAY_REGISTERED_ACTIONS
-  #
-  # ARRAY_REGISTERED_ACTIONS becomes @registered_actions.
-  # ========================================================================= #
-  ARRAY_REGISTERED_ACTIONS = %w(
-    to_rna
-    to_dna
-    rest
-    pubmed
-    blosum
-    restriction
-    translate
-    quit
-    shorten_aminoacid
-  )
-
-  # ========================================================================= #
-  # === FILE_BIO_LANG
-  # ========================================================================= #
-  FILE_BIO_LANG =
-    "#{USERS_X}data/personal/yaml/bio_lang/bio_lang.md"
-
-  # ========================================================================= #
-  # === AC_ELEMENT
-  # ========================================================================= #
-  # AC_ELEMENT = 4_565 # n nucleotides found in the AC zea mais element.
-
-  # ========================================================================= #
-  # === BIOSHELL_FILE
-  # ========================================================================= #
-  BIOSHELL_FILE = ConvertGlobalEnv[
-    '$BIORUBY/shell/shell.rb'
-  ] if Object.const_defined?(:ConvertGlobalEnv)
-
-end
-
-if __FILE__ == $PROGRAM_NAME
- pp Bioroebe::DEFAULT_DNA_SEQUENCE
- puts "The log file for the taxonomy-component is at: "\
-      "#{Bioroebe::TAXONOMY_NCBI_DATABASE_LAST_UPDATE_LOG_FILE}"  
-end

data/lib/bioroebe/constants/newline.rb

@@ -1,14 +0,0 @@
-#!/usr/bin/ruby -w
-# Encoding: UTF-8
-# frozen_string_literal: true
-# =========================================================================== #
-# require 'bioroebe/constants/newline.rb
-# =========================================================================== #
-module Bioroebe
-
-  # ========================================================================= #
-  # === N
-  # ========================================================================= #
-  N = "\n"
-
-end

data/lib/bioroebe/constants/nucleotides.rb

@@ -1,121 +0,0 @@
-#!/usr/bin/ruby -w
-# Encoding: UTF-8
-# frozen_string_literal: true
-# =========================================================================== #
-# require 'bioroebe/constants/nucleotides.rb'
-# =========================================================================== #
-module Bioroebe
-
-  # ========================================================================= #
-  # === Bioroebe::STOP_CODONS
-  #
-  # The STOP codons that can be found in Humans, in RNA format.
-  # ========================================================================= #
-  STOP_CODONS = %w(
-    UAA UAG UGA
-  )
-
-  # ========================================================================= #
-  # === Bioroebe::RNA_NUCLEOTIDES
-  #
-  # This will refer to an Array including all four RNA nucleotides,
-  # that is A, U, G and C.
-  # ========================================================================= #
-  RNA_NUCLEOTIDES = %w( A U G C )
-    ALLOWED_RNA_NUCLEOTIDES = RNA_NUCLEOTIDES # === ALLOWED_RNA_NUCLEOTIDES
-
-  # ========================================================================= #
-  # === Bioroebe::POSSIBLE_RNA_NUCLEOTIDES
-  #
-  # This is a bit different to RNA_NUCLEOTIDES in that N is also a part
-  # of it. It is not entirely clear whether this array here is kept,
-  # though.
-  # ========================================================================= #
-  POSSIBLE_RNA_NUCLEOTIDES = %w(
-    A U G C N
-  )
-
-  # ========================================================================= #
-  # === Bioroebe::DNA_NUCLEOTIDES
-  #
-  # This is the variant without N.
-  # ========================================================================= #
-  DNA_NUCLEOTIDES = %w( A T G C )
-
-  # ========================================================================= #
-  # === Bioroebe::HASH_DNA_NUCLEOTIDES
-  #
-  # Since as of 20.04.2014, Uracil is also part of this Hash. While this
-  # is, strictly speaking, not absolutely correct, it does simplify some
-  # downstream code. However had, this may possibly be re-evaluated in 
-  # the future.
-  #
-  # This Hash may be helpful when the user wishes to find a complement to
-  # a nucleotide. There is a method that does the same, but this Hash
-  # should be faster than a method call, so use it in particular if 
-  # you need to focus more on speed.
-  # ========================================================================= #
-  HASH_DNA_NUCLEOTIDES = {
-    'A' => 'T',
-    'T' => 'A',
-    'G' => 'C',
-    'C' => 'G',
-    'U' => 'A'
-  }
-
-  # ========================================================================= #
-  # === Bioroebe.this_nucleotide_pairs_with?
-  # ========================================================================= #
-  def self.this_nucleotide_pairs_with?(i)
-    HASH_DNA_NUCLEOTIDES[i.to_s.upcase]
-  end
-
-  # ========================================================================= #
-  # === POSSIBLE_DNA_NUCLEOTIDES
-  #
-  # This constant will keep all possible DNA nucleotides.
-  #
-  # N is also a valid entry, 'Yarrowia_lipolytica_genome.fa' includes it.
-  # However had, 
-  #
-  # Only these sequences are allowed in DNA.
-  #
-  # To scope to this, do:
-  #
-  #   Bioroebe::POSSIBLE_DNA_NUCLEOTIDES
-  #
-  # ========================================================================= #
-  POSSIBLE_DNA_NUCLEOTIDES = %w(
-    A T G C N
-  ); ARRAY_VALID_DNA_SEQUENCES = POSSIBLE_DNA_NUCLEOTIDES # === ARRAY_VALID_DNA_SEQUENCES
-
-  # ========================================================================= #
-  # === Bioroebe.return_random_nucleotide
-  #
-  # This method will randomly return either 'A', 'T', 'C' or 'G'.
-  # ========================================================================= #
-  def self.return_random_nucleotide
-    (POSSIBLE_DNA_NUCLEOTIDES - ['N']).sample # This constant holds A T G and C.
-  end; self.instance_eval { alias random_nucleotide return_random_nucleotide } # === Bioroebe.random_nucleotide
-
-  # ========================================================================= #
-  # === Bioroebe.allowed_dna_nucleotides?
-  #
-  # This will return an Array with valid DNA nucleotides.
-  # ========================================================================= #
-  def self.allowed_dna_nucleotides?
-    ALLOWED_DNA_NUCLEOTIDES
-  end; self.instance_eval { alias dna? allowed_dna_nucleotides? } # === Bioroebe.dna?
-
-  # ========================================================================= #
-  # === Bioroebe.return_DNA_nucleotides
-  # ========================================================================= #
-  def self.return_DNA_nucleotides
-    return DNA_NUCLEOTIDES
-  end
-
-end
-
-if __FILE__ == $PROGRAM_NAME
-  pp Bioroebe.allowed_dna_nucleotides?
-end

data/lib/bioroebe/constants/regex.rb

@@ -1,28 +0,0 @@
-#!/usr/bin/ruby -w
-# Encoding: UTF-8
-# frozen_string_literal: true
-# =========================================================================== #
-# This file will store only regex-constants.
-# =========================================================================== #
-# require 'bioroebe/constants/regex.rb'
-# =========================================================================== #
-module Bioroebe
-
-  # ========================================================================= #
-  # === REGEX_FOR_N_GLYCOSYLATION_PATTERN
-  #
-  # See rubular at:
-  #
-  #   https://rubular.com/r/D95Cq7oR5x
-  #
-  # ========================================================================= #
-  REGEX_FOR_N_GLYCOSYLATION_PATTERN =
-    /(?=(N[^P][ST][^P]))/
-
-  # ========================================================================= #
-  # === REGEX_PROSITE_FOR_ANY_AMINOACID
-  # ========================================================================= #
-  REGEX_PROSITE_FOR_ANY_AMINOACID =
-    /x\((\d+)\)/
-
-end

data/lib/bioroebe/constants/roebe.rb

@@ -1,38 +0,0 @@
-#!/usr/bin/ruby -w
-# Encoding: UTF-8
-# frozen_string_literal: true
-# =========================================================================== #
-# This file contains data particular to my home setup, the system I use
-# at home. It is thus not hugely relevant to other people, but
-# simplifies the job for me whenever I work on bio-related stuff in
-# general.
-# =========================================================================== #
-# require 'bioroebe/constants/roebe.rb'
-# =========================================================================== #
-module Bioroebe
-
-  # ========================================================================= #
-  # === EMAIL
-  #
-  # My email address - not too terribly useful for other people,
-  # but nonetheless it may be useful to display it, in particular
-  # for GUI-related components of the bioroebe-project and simple
-  # feedback in the long run.
-  # ========================================================================= #
-  EMAIL = 'shevy@inbox.lt'
-
-  # ========================================================================= #
-  # === USERS_X
-  # ========================================================================= #
-  USERS_X = '/home/x/'
-
-  # ========================================================================= #
-  # === RUBY_SRC
-  #
-  # This constant is only useful on my home directory. Most other users
-  # will not need it, ever.
-  # ========================================================================= #
-  RUBY_SRC =
-    "#{USERS_X}programming/ruby/src/"
-
-end

data/lib/bioroebe/constants/row_terminator.rb

@@ -1,16 +0,0 @@
-#!/usr/bin/ruby -w
-# Encoding: UTF-8
-# frozen_string_literal: true
-# =========================================================================== #
-# require 'bioroebe/constants/row_terminator.rb'
-# =========================================================================== #
-module Bioroebe
-
-  # ========================================================================= #
-  # === Bioroebe::ROW_TERMINATOR
-  #
-  # This constant is not often in use, though.
-  # ========================================================================= #
-  ROW_TERMINATOR = "\t|\n"
-
-end

data/lib/bioroebe/constants/tabulator.rb

@@ -1,14 +0,0 @@
-#!/usr/bin/ruby -w
-# Encoding: UTF-8
-# frozen_string_literal: true
-# =========================================================================== #
-# require 'bioroebe/constants/tabulator.rb'
-# =========================================================================== #
-module Bioroebe
-
-  # ========================================================================= #
-  # === TABULATOR
-  # ========================================================================= #
-  TABULATOR = "\t"
-
-end

data/lib/bioroebe/constants/unicode.rb

@@ -1,12 +0,0 @@
-#!/usr/bin/ruby -w
-# Encoding: UTF-8
-# frozen_string_literal: true
-# =========================================================================== #
-module Bioroebe
-
-  # ========================================================================= #
-  # === UNICODE_HORIZONTAL_BAR
-  # ========================================================================= #
-  UNICODE_HORIZONTAL_BAR = '―'
-
-end

data/lib/bioroebe/constants/urls.rb

@@ -1,50 +0,0 @@
-#!/usr/bin/ruby -w
-# Encoding: UTF-8
-# frozen_string_literal: true
-# =========================================================================== #
-# This file may contain some handy remote URLs, as constants; we could
-# also use local "URLs", although this is probably no longer necessary.
-# =========================================================================== #
-# require 'bioroebe/constants/urls.rb'
-# =========================================================================== #
-module Bioroebe
-
-  # ========================================================================= #
-  # === FTP_NCBI_TAXONOMY_DATABASE
-  #
-  # This constant refers to the taxonomy-database from NCBI. This is the
-  # file that can be downloaded from the NCBI homepage (actually, the
-  # ftp-listing).
-  #
-  # Take note that this database, in .tar.gz format, is about 50 MB in 
-  # size or even larger these days. So only download it if you really 
-  # need it locally.
-  # ========================================================================= #
-  FTP_NCBI_TAXONOMY_DATABASE =
-    'ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz'
-
-  # ========================================================================= #
-  # === URL_TO_TAXONOMY_ARCHIVE
-  #
-  # An "alias" to the above ^^^ constant.
-  # ========================================================================= #
-  URL_TO_TAXONOMY_ARCHIVE = FTP_NCBI_TAXONOMY_DATABASE
-
-  # ========================================================================= #
-  # === NCBI_NUCCORE
-  # ========================================================================= #
-  NCBI_NUCCORE =
-    'https://www.ncbi.nlm.nih.gov/nuccore/'
-
-  # ========================================================================= #
-  # === NCBI_GENE
-  # ========================================================================= #
-  NCBI_GENE =
-    'https://www.ncbi.nlm.nih.gov/gene/'
-
-end
-
-if __FILE__ == $PROGRAM_NAME
-  _ = "wget #{Bioroebe::FTP_NCBI_TAXONOMY_DATABASE}"
-  puts _; system _
-end

data/lib/bioroebe/gui/gtk

@@ -1 +0,0 @@
-gtk3

data/lib/bioroebe/gui/gtk3/README.md

@@ -1,2 +0,0 @@
-The file at bioroebe/gui/gtk3/controller/controller.rb is the general entry 
-point for the ruby-gtk3 widgets in this project.