Class: Bioroebe::RGG_Scanner
Overview
Constant Summary
CommandlineApplication::OLD_VERBOSE_VALUE
ColoursForBase::ARRAY_HTML_COLOURS_IN_USE
Constants inherited
from Base
Base::NAMESPACE
Class Method Summary
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-
.[](i = '') ⇒ Object
# === Bioroebe::RGG_Scanner[] ========================================================================= #.
Instance Method Summary
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#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) ⇒ RGG_Scanner
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# File 'lib/bioroebe/patterns/rgg_scanner.rb', line 30
def initialize(
commandline_arguments = nil,
run_already = true
)
reset
set_commandline_arguments(
commandline_arguments
)
run if run_already
end
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Class Method Details
.[](i = '') ⇒ Object
#
Bioroebe::RGG_Scanner[]
#
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# File 'lib/bioroebe/patterns/rgg_scanner.rb', line 145
def self.[](i = '')
new(i)
end
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Instance Method Details
#indices? ⇒ Boolean
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# File 'lib/bioroebe/patterns/rgg_scanner.rb', line 58
def indices?
@result
end
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#indices_as_string?(this_array = @result) ⇒ Boolean
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# File 'lib/bioroebe/patterns/rgg_scanner.rb', line 98
def indices_as_string?(
this_array = @result
)
_ = ''.dup
this_array.each {|a,b|
_ << b.to_s+', '
}
_.strip!
_.chop! if _.end_with? ','
return _
end
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#report(array = @result) ⇒ Object
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# File 'lib/bioroebe/patterns/rgg_scanner.rb', line 65
def report(
array = @result
)
sequence = sequence?
if array.empty?
e 'No result for '+orange('RGG')+' has been found.'
else
e
e sequence.gsub(/RGG/, slateblue('RGG')+rev)
e
report_how_many_rgg_motifs_were_found_in_that_sequence
e
erev 'The indices for the starting positions are at:'
e
e slateblue(' '+indices_as_string?(array))
e
end
end
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#report_how_many_rgg_motifs_were_found_in_that_sequence ⇒ Object
#
report_how_many_rgg_motifs_were_found_in_that_sequence
#
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# File 'lib/bioroebe/patterns/rgg_scanner.rb', line 90
def report_how_many_rgg_motifs_were_found_in_that_sequence
erev 'A total of '+slateblue(@result.size.to_s)+rev+' potential RGG '\
'motifs were found in this sequence.'
end
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#reset ⇒ Object
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# File 'lib/bioroebe/patterns/rgg_scanner.rb', line 44
def reset
super()
end
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#run ⇒ Object
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# File 'lib/bioroebe/patterns/rgg_scanner.rb', line 137
def run
scan_for_rgg_sequences
report
end
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#scan_for_rgg_sequences ⇒ Object
#
scan_for_rgg_sequences
#
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# File 'lib/bioroebe/patterns/rgg_scanner.rb', line 120
def scan_for_rgg_sequences
_ = sequence?
array = []
_.scan(/RGG/) {|subsequence|
array << [
subsequence, Regexp.last_match.offset(0).first
]
}
set_result(array)
end
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#sequence? ⇒ Boolean
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# File 'lib/bioroebe/patterns/rgg_scanner.rb', line 51
def sequence?
commandline_arguments?.join(' ').strip.delete(' ')
end
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#set_result(i) ⇒ Object
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# File 'lib/bioroebe/patterns/rgg_scanner.rb', line 113
def set_result(i)
@result = i
end
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