bioroebe 0.10.80 → 0.11.12

data/lib/bioroebe/shell/constants.rb

@@ -1,166 +0,0 @@
-#!/usr/bin/ruby -w
-# Encoding: UTF-8
-# frozen_string_literal: true
-# =========================================================================== #
-# require 'bioroebe/shell/constants.rb'
-# =========================================================================== #
-module Bioroebe # === Bioroebe::Shell
-
-class Shell < ::Bioroebe::CommandlineApplication
-
-  # ========================================================================= #
-  # Right now we will only add the chemistry_paradise gem, if it is available.
-  # ========================================================================= #
-  array_failsave_requires = %w(
-    chemistry_paradise
-  )
-  array_failsave_requires.each {|project|
-    begin
-      require project
-    rescue LoadError; end # Silent rescue.
-  }
-
-  # ========================================================================= #
-  # === NAMESPACE
-  # ========================================================================= #
-  NAMESPACE = inspect
-
-  # ========================================================================= #
-  # === TRUNCATE_AT_N_ELEMENTS
-  #
-  # If we display nucleotide strings, then by default, these may be very
-  # long. So the following constant will act as a threshold.
-  # ========================================================================= #
-  TRUNCATE_AT_N_ELEMENTS = 2000
-
-  # ========================================================================= #
-  # === 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
-  )
-
-  # ========================================================================= #
-  # === DEFAULT_PADDING
-  # ========================================================================= #
-  DEFAULT_PADDING = '  ' # This is left-padding.
-
-  # ========================================================================= #
-  # === MAIN_EDITOR
-  #
-  # Which editor to use.
-  # ========================================================================= #
-  if ENV['IS_ROEBE']
-    MAIN_EDITOR = 'bluefish'
-  else # else assume that we may be on windows. 
-    MAIN_EDITOR = 'notepad++.exe'
-  end; MY_EDITOR = MAIN_EDITOR # === MY_EDITOR
-
-  # ========================================================================= #
-  # === HOME_DIRECTORY_OF_USER_X
-  #
-  # Hardcoded path - only useful on my home setup, though.
-  # ========================================================================= #
-  HOME_DIRECTORY_OF_USER_X = '/home/x/'
-
-  # ========================================================================= #
-  # === RUBY_SRC
-  #
-  # Hardcoded. This is only useful on my home system.
-  # ========================================================================= #
-  if ENV['RSRC']
-    RUBY_SRC = "#{ENV['RSRC']}/"
-  else
-    RUBY_SRC = "#{HOME_DIRECTORY_OF_USER_X}programming/ruby/src/"
-  end
-
-  # ========================================================================= #
-  # === RUBY_BIOROEBE
-  #
-  # This allows a user to designate another home directory.
-  # ========================================================================= #
-  if ENV['RUBY_BIOROEBE']
-    BIOROEBE = ENV['RUBY_BIOROEBE'].to_s
-  else
-    BIOROEBE = ENV['HOME']
-  end
-
-  # ========================================================================= #
-  # === BIOSHELL_SAVE_FILE
-  #
-  # Designate the default location for the save-file, a markdown file.
-  # ========================================================================= #
-  if Dir.exist? ::Bioroebe.log_dir?
-    BIOSHELL_SAVE_FILE = "#{::Bioroebe.log_dir?}shell_file.md"
-  else
-    BIOSHELL_SAVE_FILE = '/home/Temp/bioroebe/shell_file.md'
-  end
-
-  # ========================================================================= #
-  # === HOME_DIR
-  #
-  # This probably is not used a lot anymore these days.
-  # ========================================================================= #
-  if RUBY_SRC # This is valid at home.
-    HOME_DIR = "#{ENV['RSRC']}/bioroebe/lib/bioroebe/"
-  else
-    begin
-      home_dir = File.expand_path('~')
-    rescue Exception
-      home_dir = '/root/'
-    end
-    HOME_DIR = home_dir+'.gem/gems/bioroebe-'+
-               Bioroebe.version?.to_s+'/lib/bioroebe/'
-  end
-
-  require 'bioroebe/project/project.rb'
-  # ========================================================================= #
-  # === FILE_USE_SILENT_STARTUP
-  # ========================================================================= #
-  FILE_USE_SILENT_STARTUP = 
-    "#{::Bioroebe.project_base_directory?}shell/configuration/use_silent_startup.yml"
-
-  # ========================================================================= #
-  # === SHALL_WE_DEBUG
-  # ========================================================================= #
-  SHALL_WE_DEBUG = false
-
-  _ = ::Bioroebe.project_yaml_directory?+
-      'default_dna_input.yml' # cat $RUBY_BIO/YAML/default_dna_input.yml
-  # ========================================================================= #
-  # === DEFAULT_DNA_INPUT_YAML_FILE
-  # ========================================================================= #
-  DEFAULT_DNA_INPUT_YAML_FILE = YAML.load_file(_) if File.exist? _
-
-  require 'bioroebe/toplevel_methods/log_directory.rb' # ← Required for: Bioroebe.store_here?
-  # ========================================================================= #
-  # === store_here?
-  #
-  # Where to store output generated by BioRoebe. Should point to a
-  # locally existing directory.
-  # ========================================================================= #
-  def store_here?
-    ::Bioroebe.store_here?
-  end
-
-  # ========================================================================= #
-  # === show_log_dir
-  # ========================================================================= #
-  def show_log_dir
-    e ::Bioroebe.log_dir?
-  end
-
-end; end

data/lib/bioroebe/shell/download.rb

@@ -1,335 +0,0 @@
-#!/usr/bin/ruby -w
-# Encoding: UTF-8
-# frozen_string_literal: true
-# =========================================================================== #
-# require 'bioroebe/shell/download.rb'
-# =========================================================================== #
-require 'bioroebe/base/commandline_application/commandline_application.rb'
-
-module Bioroebe
-
-class Shell < ::Bioroebe::CommandlineApplication
-
-  require 'bioroebe/toplevel_methods/map_ncbi_entry_to_eutils_id.rb'
-
-  # ========================================================================= #
-  # === wget                                                       (wget tag)
-  #
-  # Simply use wget to download remote files.
-  # ========================================================================= #
-  def wget(i)
-    if i.is_a? Array
-      i.each {|entry| wget(entry) }
-    else
-      unless i.start_with? 'wget '
-        i = "wget #{i}"
-      end
-      esystem i
-    end
-  end
-
-  # ========================================================================= #
-  # === download                                               (download tag)
-  #
-  # General download handler. Some sequences will be changed, such
-  # as lambda (for the phage called lambda), to the corresponding
-  # entry at NCBI. 
-  # ========================================================================= #
-  def download(i)
-    if i.is_a? Array
-      i.each {|entry| download(entry) }
-    else
-      case i.to_s
-      # ===================================================================== #
-      # === The lambda phage sequence
-      #
-      # Download the lambda-sequence, via:
-      #
-      #   download lambda
-      #
-      # ===================================================================== #
-      when 'lambda',
-           /^-?-?lambda(_|-)?genome$/i
-        i = ::Bioroebe.map_ncbi_entry_to_eutils_id('NC_001416.1.fasta')+
-            '.fasta'
-      # ===================================================================== #
-      # === Download the cytochrome c sequence (of humans)
-      #
-      # This should be equivalent to:
-      #
-      #   https://www.ncbi.nlm.nih.gov/protein/XP_011521207.1?report=fasta
-      #
-      # ===================================================================== #
-      when /cytochrome_c_protein_sequence/
-        return Bioroebe::Ncbi.efetch_by_url('NP_061820.1')
-      # ===================================================================== #
-      # === P1
-      # ===================================================================== #
-      when 'P1'
-        i = ::Bioroebe.map_ncbi_entry_to_eutils_id('NC_005856.1.fasta')+
-            '.fasta'
-      # ===================================================================== #
-      # === P2
-      #
-      # The P2 phage, from E. coli, a temperate phage.
-      # ===================================================================== #
-      when 'P2'
-        i = ::Bioroebe.map_ncbi_entry_to_eutils_id('NC_041848.1.fasta')+
-            '.fasta'
-      # ===================================================================== #
-      # === T12
-      #
-      # This is the Streptococcus phage T12.
-      # ===================================================================== #
-      when 'T12'
-        i = ::Bioroebe.map_ncbi_entry_to_eutils_id('NC_028700.1.fasta')+
-            '.fasta'
-      # ===================================================================== #
-      # === T2
-      #
-      # This is the phage T2.
-      # ===================================================================== #
-      when 'T2'
-        i = ::Bioroebe.map_ncbi_entry_to_eutils_id('AP018813.1.fasta')+
-            '.fasta'
-      # ===================================================================== #
-      # === T4
-      #
-      # This is the phage T4.
-      # ===================================================================== #
-      when 'T4'
-        i = ::Bioroebe.map_ncbi_entry_to_eutils_id('NC_000866.4.fasta')+
-            '.fasta'
-      # ===================================================================== #
-      # === T6
-      #
-      # This is the phage T6.
-      # ===================================================================== #
-      when 'T6'
-        i = ::Bioroebe.map_ncbi_entry_to_eutils_id('MH550421.1.fasta')+
-            '.fasta'
-      # ===================================================================== #
-      # === rhinovirus
-      # ===================================================================== #
-      when /^-?-?rhinovirus/i
-        i = ::Bioroebe.map_ncbi_entry_to_eutils_id('NC_038311')+
-            '.fasta'
-      # ===================================================================== #
-      # === Handle .pdb files here
-      # ===================================================================== #
-      when /\.pdb$/
-        cd :download_directory
-        wget i
-        register_this_download(i)
-        parse_this_pdb_file(File.basename(i))
-      end
-      # ===================================================================== #
-      # === Handle Fasta files next
-      # ===================================================================== #
-      if i.end_with? '.fa' or i.end_with? '.fasta'
-        i = i.dup if i.frozen?
-        unless File.exist? i
-          _ = Bioroebe::Ncbi.efetch_by_url(
-               i.delete_suffix('.fasta')
-             )
-          if File.exist? _
-            erev "The file is now available at `#{sfile(_)}`."
-          end
-        else
-          # ================================================================= #
-          # The above download_fasta() makes use of NCBI. We need to rewrite
-          # this eventually. For now, we will do another, simpler approach
-          # here.
-          # ================================================================= #
-          what = URI.open(i).read
-          into = log_dir?+File.basename(i)
-          erev "Storing into `#{sfile(into)}#{rev}`."
-          write_what_into(what, into)
-          return into # This will also return the local path.
-        end
-      else
-        # erev 'Unsure what to do with '+sfancy(i)
-        esystem "wget #{i}"
-      end
-    end
-  end
-
-  require 'bioroebe/fasta_and_fastq/download_fasta.rb'
-  # ========================================================================= #
-  # === download_fasta
-  #
-  # Use this to download a fasta sequence.
-  # ========================================================================= #
-  def download_fasta(i = nil)
-    if i.is_a? Array
-      i.each {|entry|
-        download_fasta(entry)
-      }
-    else
-      # ===================================================================== #
-      # Delegate to a special class here.
-      # ===================================================================== #
-      stored_here = ::Bioroebe.download_fasta(i) # bl $BIOROEBE/download_fasta.rb
-      if stored_here
-        if File.exist? stored_here
-          assign_sequence(stored_here)
-        end
-        return stored_here
-      else
-        e crimson('No result could be found for ')+sfancy(i)+rev
-      end
-    end
-  end
-
-  # ========================================================================= #
-  # === register_this_download
-  #
-  # Simply register all downloads - we may use this information at some
-  # later point.
-  #
-  # The entries here typically are HTTP or HTTPS-URLs.
-  # ========================================================================= #
-  def register_this_download(i)
-    @internal_hash[:array_all_downloads] << i
-  end
-
-  # ========================================================================= #
-  # === set_download_directory
-  # ========================================================================= #
-  def set_download_directory(
-      i = ::Bioroebe.log_dir?
-    )
-    i = i.to_s
-    erev "Setting the download directory to #{simp(i)}#{rev} next:"
-    ::Bioroebe.set_log_dir(i)
-  end
-
-  # ========================================================================= #
-  # === download_this_pdb_file
-  #
-  # Use this method to download a .pdb file.
-  #
-  # There seem to be at least two major methods how to use the PDB
-  # database:
-  #
-  #   (1) http://www.rcsb.org/pdb/files/3O30.pdb
-  #   (2) http://www.rcsb.org/pdb/explore.do?structureId=1QRI
-  #
-  # The files/ URI seems to redirect you directly to the .pdb
-  # file in question, so I think it is the preferred way.
-  # However had, the explore.do query gives additional
-  # information.
-  #
-  # Other useful URLs are:
-  #
-  #   http://www.rcsb.org/pdb/explore.do?structureId=1ZAA
-  #   http://dx.doi.org/10.2210/pdb1gi5/pdb
-  #
-  # Usage example:
-  #
-  #   download_this_pdb_file http://www.rcsb.org/pdb/files/3O30.pdb
-  #
-  # ========================================================================= #
-  def download_this_pdb_file(
-      i = '3O30'
-    )
-    i = ['3O30'] if i.nil? # If nil, use a default value.
-    if i.is_a? Array
-      i = ['3O30'] if i.empty?
-      i.each {|entry| download_this_pdb_file(entry) }
-    else
-      i = i.to_s.dup
-      unless i.end_with? '.pdb'
-        i << '.pdb'
-      end
-      unless i.start_with? 'http://www.rcsb.org/pdb/files/'
-        i[0,0] = 'https://www.rcsb.org/pdb/files/'
-      end
-      target_dir = download_dir?
-      cd target_dir
-      # ===================================================================== #
-      # http://www.rcsb.org/pdb/files/3O30.pdb
-      # ===================================================================== #
-      download_this = "#{i.to_s}"
-      erev "Checking for the availability of "\
-           "#{olivedrab(download_this)}#{rev} next ..."
-      if does_this_remote_file_exist?(download_this)
-        erev 'Next downloading '+sfancy(download_this)+
-             rev+' into '+sfancy(target_dir)+'.'
-        esystem "wget #{download_this}" # We will just use wget for now.
-        _ = ::Bioroebe.pdb_directory?
-        if File.directory? _
-          new_target = _+File.basename(download_this)
-          erev 'Moving into '+sfancy(new_target)+rev+', where '\
-               '.pdb files are kept by default.'
-          mv(
-            target_dir+File.basename(download_this),
-            new_target
-          )
-        end
-        register_this_download(download_this)
-      else
-        erev "The remote file at #{sfile(download_this)} does not exist."
-        erev 'Hence, we can not download it.'
-      end
-    end
-  end
-
-  # ========================================================================= #
-  # === does_this_remote_file_exist?
-  #
-  # This method determines, based on wget, whether a remote file
-  # exists or whether it does not.
-  # ========================================================================= #
-  def does_this_remote_file_exist?(i)
-    remote_file_exists = false
-    # ======================================================================= #
-    # Use wget --spider to check if the remote file exists.
-    # ======================================================================= #
-    _ = "wget --spider -v #{i} 2>&1"
-    result = `#{_}`
-    if result.include?('Remote file exists') or # Yes, the remote file exists.
-       result =~ /File '.+' exists./
-      remote_file_exists = true
-    end
-    if result.include? '/404'
-      remote_file_exists = false
-    end
-    return remote_file_exists
-  end
-
-  # ========================================================================= #
-  # === handle_pdb_files
-  #
-  # This method will either show more information about .pdb files or
-  # it will simply attempt to download the .pdb file in question.
-  # ========================================================================= #
-  def handle_pdb_files(i)
-    if i.nil? or i.empty?
-      # In this case, we show some info.
-      cliner
-      erev '.pdb files are files in the "Protein Data Bank" format.'
-      e
-      erev 'It is a standard for files containing atomic coordinates.'
-      e
-      erev 'Each line in a .pdb file is called a "record".'
-      e
-      erev 'You can pass an ID (a number) and we will attempt to download '\
-           'that .pdb file.'
-      e
-      erev 'Example:'
-      e
-      erev '  pdb 333'
-      e
-      erev 'More information can be seen here:'
-      e
-      efancy '  https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/pdbintro.html'
-      e
-      print rev
-      cliner
-    else
-      download_this_pdb_file(i)
-    end
-  end
-
-end; end

data/lib/bioroebe/shell/enable_and_disable.rb

@@ -1,158 +0,0 @@
-#!/usr/bin/ruby -w
-# Encoding: UTF-8
-# frozen_string_literal: true
-# =========================================================================== #
-# require 'bioroebe/shell/enable_and_disable.rb'
-# =========================================================================== #
-# Note that the method disable_colours() can be found in the file
-# colours.rb
-# =========================================================================== #
-require 'bioroebe/base/commandline_application/commandline_application.rb'
-
-module Bioroebe
-
-class Shell < ::Bioroebe::CommandlineApplication
-
-  # ========================================================================= #
-  # === enable                                                   (enable tag)
-  #
-  # Enable-functionality can be passed through this method here.
-  #
-  # Invocation example from within the bioshell:
-  #
-  #   enable colours
-  #
-  # ========================================================================= #
-  def enable(i)
-    if i.is_a? Array
-      i = i.join.strip
-    end
-    case i.to_s # case tag
-    # ======================================================================= #
-    # === enable cd_aliases
-    #
-    # This variant will be verbose.
-    # ======================================================================= #
-    when /^-?-?cd(-|_)?aliases$/
-      erev 'class '+
-           steelblue('Rcfiles::DirectoryAliases')+rev+' will be '\
-           'enabled next, allowing'
-      erev 'you to navigate the local filesystem '\
-           'more easily so.'
-      ::Bioroebe::Configuration.do_use_expand_cd_aliases
-    # ======================================================================= #
-    # === use colours
-    # ======================================================================= #
-    when /^colou?rs$/
-      enable_colours
-    # ======================================================================= #
-    # === use xsel
-    # ======================================================================= #
-    when 'xsel'
-      enable_xsel
-    end
-  end; alias use enable # === use (use tag)
-
-  # ========================================================================= #
-  # === enable_configuration
-  # ========================================================================= #
-  def enable_configuration
-    config_dir = ::Bioroebe.project_yaml_directory?+
-                 '/configuration/'
-    unless Object.const_defined?(:Roebe) and
-           Roebe.const_defined?(:Configuration)
-      begin
-        require 'roebe/configuration/class/configuration.rb'
-      rescue LoadError; end
-    end
-    if Object.const_defined?(:Roebe) and
-       Roebe.const_defined?(:Configuration)
-      # ===================================================================== #
-      # === Initialize @config
-      # ===================================================================== #
-      @config = ::Roebe::Configuration.new(config_dir, :do_not_run_yet)
-      @config.be_verbose if @config.respond_to? :be_verbose
-      @config.run
-    else
-      @config = nil
-    end
-  end
-
-  # ========================================================================= #
-  # === disable                                                 (disable tag)
-  # ========================================================================= #
-  def disable(i)
-    if i.is_a? Array
-      i = i.join(' ').strip
-    end
-    case i.to_s # case tag
-    # ======================================================================= #
-    # === disable :cd_aliases
-    # ======================================================================= #
-    when /^-?-?cd(-|_)?aliases$/i
-      erev 'We will no longer use class Rcfiles::DirectoryAliases'
-      ::Bioroebe::Configuration.do_not_use_expand_cd_aliases
-    # ======================================================================= #
-    # === truncate
-    # ======================================================================= #
-    when /^truncate$/i
-      disable_truncate
-    # ======================================================================= #
-    # === prompt
-    # ======================================================================= #
-    when 'prompt'
-      set_prompt :empty # This means to use an empty prompt.
-    # ======================================================================= #
-    # === padding
-    # ======================================================================= #
-    when 'padding'
-      set_padding 0, :be_verbose
-    # ======================================================================= #
-    # === disable colours
-    # ======================================================================= #
-    when 'colours',
-         'colors',
-         /^col/
-      disable_colours
-    # ======================================================================= #
-    # === disable xsel
-    # ======================================================================= #
-    when 'xsel'
-      disable_xsel
-    else
-      erev "No such disable-action could be found (#{sfancy(i)}#{rev})"
-    end
-  end
-
-  # ========================================================================= #
-  # === disable_truncate
-  # ========================================================================= #
-  def disable_truncate
-    do_not_truncate
-  end
-
-  # ========================================================================= #
-  # === disable_xsel
-  # ========================================================================= #
-  def disable_xsel
-    if use_xsel?
-      e 'Now disabling xsel.'
-      @internal_hash[:use_xsel] = false
-    else
-      e 'xsel is already disabled.'
-    end
-  end
-
-  # ========================================================================= #
-  # === enable_xsel
-  # ========================================================================= #
-  def enable_xsel
-    if @internal_hash[:use_xsel]
-      e 'xsel is already enabled.'
-    else
-      e 'Now enabling xsel.'
-      @internal_hash[:use_xsel] = true
-    end
-  end
-
-end; end