Class: Bioroebe::MoveFileToItsCorrectLocation

Inherits:
CommandlineApplication show all
Defined in:
lib/bioroebe/utility_scripts/move_file_to_its_correct_location.rb

Constant Summary

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(i = nil, run_already = true) ⇒ MoveFileToItsCorrectLocation

#

initialize

#


31
32
33
34
35
36
37
38
 
# File 'lib/bioroebe/utility_scripts/move_file_to_its_correct_location.rb', line 31

def initialize(
    i           = nil,
    run_already = true
  )
  reset
  set_commandline_arguments(i)
  run if run_already
end

Class Method Details

.[](i = ARGV) ⇒ Object

#

Bioroebe::MoveFileToItsCorrectLocation[]

#


131
132
133
 
# File 'lib/bioroebe/utility_scripts/move_file_to_its_correct_location.rb', line 131

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

Instance Method Details

#move_this_file_to_its_correct_location(i) ⇒ Object

#

move_this_file_to_its_correct_location

This method will move the file to its correct location.

#


60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
 
# File 'lib/bioroebe/utility_scripts/move_file_to_its_correct_location.rb', line 60

def move_this_file_to_its_correct_location(i)
  # ======================================================================= #
  # === Handle .pdb files first
  # ======================================================================= #
  if i.end_with? '.pdb'
    target = "#{log_dir?}pdb/"
    verbose_move_file(i, target)
  # ======================================================================= #
  # === Next handle .fasta or .fa files
  # ======================================================================= #
  elsif i.end_with?('.fasta') or i.end_with?('.fa')
    target = "#{log_dir?}fasta/"
    verbose_move_file(i, target)
  else
    # ===================================================================== #
    # Else do a generic-move action.
    # ===================================================================== #
    target = log_dir?
    verbose_move_file(i, target)
  end
end

#reset ⇒ Object

#

reset

#


43
44
45
46
47
48
49
50
51
52
53
 
# File 'lib/bioroebe/utility_scripts/move_file_to_its_correct_location.rb', line 43

def reset
  super()
  infer_the_namespace
  # ======================================================================= #
  # === @try_to_relocate_the_file_to_an_appropriate_subdirectory
  #
  # This variable can be used to relocate the downloaded .pdb file
  # to a correct subdirectory.
  # ======================================================================= #
  @try_to_relocate_the_file_to_an_appropriate_subdirectory = true
end

#run ⇒ Object

#

run

#


105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
 
# File 'lib/bioroebe/utility_scripts/move_file_to_its_correct_location.rb', line 105

def run
  commandline_arguments?.each {|entry|
    if File.exist?(entry) and !entry.start_with?('--')
      file_extension = File.extname(entry)
      case file_extension
      # =================================================================== #
      # === .fasta
      # =================================================================== #
      when '.fasta',
           '.fa'
        move_this_file_to_its_correct_location(entry)
      # =================================================================== #
      # === .pdb
      # =================================================================== #
      when '.pdb'
        move_this_file_to_its_correct_location(entry)
      else
        move_this_file_to_its_correct_location(entry)
      end
    end
  } if @try_to_relocate_the_file_to_an_appropriate_subdirectory
end

#verbose_move_file(i, target) ⇒ Object

#

verbose_move_file

#


85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
 
# File 'lib/bioroebe/utility_scripts/move_file_to_its_correct_location.rb', line 85

def verbose_move_file(i, target)
  unless File.directory? target
    ::Bioroebe.ensure_that_the_base_directories_exist
  end
  # ======================================================================= #
  # We will only move if it is not already at the target location.
  # ======================================================================= #
  full_target = File.absolute_path(
    target+File.basename(i)
  )
  unless File.exist?(full_target)
    erev 'Moving the file '+sfile(i)+rev+' to '+
         steelblue(full_target)+rev+' next.'
    move_file(i, full_target)
  end
end