Class: Bioroebe::Compacter
Overview
Constant Summary
Bioroebe::CommandlineApplication::OLD_VERBOSE_VALUE
Bioroebe::ColoursForBase::ARRAY_HTML_COLOURS_IN_USE
Constants inherited
from Base
Base::NAMESPACE
Class Method Summary
collapse
-
.[](i = ARGV) ⇒ Object
# === Bioroebe::Compacter[] ========================================================================= #.
Instance Method Summary
collapse
#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
#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
#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
#internal_hash?, #reset_the_internal_hash
#infer_the_namespace, #namespace?
Constructor Details
#initialize(commandline_arguments = nil, run_already = true, &block) ⇒ Compacter
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
|
# File 'lib/bioroebe/utility_scripts/compacter/compacter.rb', line 29
def initialize(
commandline_arguments = nil,
run_already = true,
&block
)
register_sigint
reset
set_commandline_arguments(
commandline_arguments
)
if block_given?
yielded = yield
case yielded
when :do_not_ask_for_user_input
@internal_hash[:ask_for_user_input] = false
end
end
run if run_already
end
|
Class Method Details
.[](i = ARGV) ⇒ Object
#
Bioroebe::Compacter[]
#
231
232
233
|
# File 'lib/bioroebe/utility_scripts/compacter/compacter.rb', line 231
def self.[](i = ARGV)
new(i)
end
|
Instance Method Details
149
150
151
|
# File 'lib/bioroebe/utility_scripts/compacter/compacter.rb', line 149
def ask_for_user_input?
@internal_hash[:ask_for_user_input]
end
|
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
|
# File 'lib/bioroebe/utility_scripts/compacter/compacter.rb', line 156
def consider_working_through_the_input_files
_ = @internal_hash[:work_on_these_files]
if _.empty?
opne 'Please provide at the least ony locally existing file as'
opne 'input to this class.'
else
perform_these_actions_on_each_file = perform_these_actions_on_each_file?
_.each {|this_file|
if File.exist? this_file
opne "#{rev}Working to compact the following file next: "\
"`#{sfile(this_file)}#{rev}`." if be_verbose?
dataset = default_readlines(this_file)
if dataset.first
first = dataset.first
if first.start_with? 'ORIGIN'
dataset[0][0,'ORIGIN'.size] = ''
dataset[0].lstrip!
elsif first.start_with? '>'
dataset[0][0, first.index("\n")] = ''
dataset[0].lstrip!
end
end
if perform_these_actions_on_each_file.include? :strip_newlines
dataset.map! {|entry| entry.strip }
end
if perform_these_actions_on_each_file.include? :remove_numbers
dataset.map! {|entry| entry.delete('[0-9]') }
end
if perform_these_actions_on_each_file.include? :upcase_the_sequence
dataset.map! {|entry| entry.upcase }
end
if perform_these_actions_on_each_file.include? :eliminate_spaces
dataset.map! {|entry| entry.delete(' ') }
end
dataset = Bioroebe::SanitizeNucleotideSequence[dataset] { :do_not_remove_newlines }
if ask_for_user_input?
opne 'We will now store into the same file, but you must'
opne 'type "'+steelblue('y')+'" to confirm, else we cancel:'
user_input = $stdin.gets.chomp
else
user_input = 'yes'
end
if user_input.start_with? 'y'
opne "Now storing into the file `#{sfile(this_file)}`." if be_verbose?
write_what_into(dataset, this_file)
end
end }
end
end
|
131
132
133
134
135
136
137
|
# File 'lib/bioroebe/utility_scripts/compacter/compacter.rb', line 131
def determine_the_input_files
commandline_arguments?.each {|this_entry|
if File.file?(this_entry)
@internal_hash[:work_on_these_files] << this_entry
end
}
end
|
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
|
# File 'lib/bioroebe/utility_scripts/compacter/compacter.rb', line 87
def (
i = commandline_arguments?
)
if i.is_a? Array
i.each {|entry| (entry) }
else
case i when /-?-?retain(-|_)?newlines/
@internal_hash[:perform_these_actions_on_each_file].reject! {|entry|
entry == :strip_newlines
}
when /help/
show_help
exit
end
end
end
|
142
143
144
|
# File 'lib/bioroebe/utility_scripts/compacter/compacter.rb', line 142
def perform_these_actions_on_each_file?
@internal_hash[:perform_these_actions_on_each_file]
end
|
#reset ⇒ Object
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
|
# File 'lib/bioroebe/utility_scripts/compacter/compacter.rb', line 58
def reset
super()
infer_the_namespace
@internal_hash[:work_on_these_files] = []
@internal_hash[:ask_for_user_input] = true
@internal_hash[:perform_these_actions_on_each_file] = [
:strip_newlines,
:remove_numbers,
:upcase_the_sequence,
:eliminate_spaces
]
end
|
#run ⇒ Object
222
223
224
225
226
|
# File 'lib/bioroebe/utility_scripts/compacter/compacter.rb', line 222
def run
determine_the_input_files
consider_working_through_the_input_files
end
|
#show_help ⇒ Object
120
121
122
123
124
125
126
|
# File 'lib/bioroebe/utility_scripts/compacter/compacter.rb', line 120
def show_help
opnn { :no_trailing }
e
e
e ' --retain-newlines # retain newlines, aka do not dump into a single line'
e
end
|