Class: Bioroebe::ShowHydrophobicity
Overview
Bioroebe::ShowHydrophobicity
Constant Summary
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- HYDROPATHY_TABLE =
YAML.load_file(FILE_HYDROPATHY_TABLE)
CommandlineApplication::OLD_VERBOSE_VALUE
ColoursForBase::ARRAY_HTML_COLOURS_IN_USE
Constants inherited
from Base
Base::NAMESPACE
Class Method Summary
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-
.[](i = ARGV) ⇒ Object
# === Bioroebe::ShowHydrophobicity[] ========================================================================= #.
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, #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(i = nil, run_already = true) ⇒ ShowHydrophobicity
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# File 'lib/bioroebe/aminoacids/show_hydrophobicity.rb', line 33
def initialize(
i = nil,
run_already = true
)
reset
set_input(i)
run if run_already
end
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Class Method Details
.[](i = ARGV) ⇒ Object
#
Bioroebe::ShowHydrophobicity[]
#
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# File 'lib/bioroebe/aminoacids/show_hydrophobicity.rb', line 171
def self.[](i = ARGV)
new(i)
end
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Instance Method Details
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# File 'lib/bioroebe/aminoacids/show_hydrophobicity.rb', line 90
def input?
@input
end
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#main_table ⇒ Object
#
main_table
This will be a Hash.
#
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# File 'lib/bioroebe/aminoacids/show_hydrophobicity.rb', line 99
def main_table
HYDROPATHY_TABLE
end
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#opnn(i = nil) ⇒ Object
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# File 'lib/bioroebe/aminoacids/show_hydrophobicity.rb', line 138
def opnn(i = nil)
hash = {}
hash.merge!(namespace: namespace?)
hash.merge!(i) if i
super(hash)
end
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#report_one_letter_code ⇒ Object
#
report_one_letter_code
#
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# File 'lib/bioroebe/aminoacids/show_hydrophobicity.rb', line 148
def report_one_letter_code
e
opnn(trailing_colon: false); e; e
erev 'The one-letter code of the given input '\
'of aminoacids is: '
e
erev ' '+sfancy(input?.join(', '))
e
end
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#report_sorted_by_most_hydrophobic_aminoacid_first ⇒ Object
#
report_sorted_by_most_hydrophobic_aminoacid_first
#
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# File 'lib/bioroebe/aminoacids/show_hydrophobicity.rb', line 121
def report_sorted_by_most_hydrophobic_aminoacid_first
erev 'Sorted by hydrophobicity first yields:'
e
@hash_aminoacids.sort_by {|key, value|
value
}.reverse.each {|key, value|
erev " #{key}: #{orange(value.to_s.rjust(5))}"
}
end
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#report_translated_hydropathy ⇒ Object
#
report_translated_hydropathy
#
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# File 'lib/bioroebe/aminoacids/show_hydrophobicity.rb', line 106
def report_translated_hydropathy
values = input?.map {|entry|
hydrophobicity = main_table[entry]
@hash_aminoacids[entry] = hydrophobicity
hydrophobicity
}
erev 'Their corresponding hydrophobicity values are:'
e
erev " #{sfancy(values.join(', '))}"
e
end
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#reset ⇒ Object
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# File 'lib/bioroebe/aminoacids/show_hydrophobicity.rb', line 45
def reset
super()
@hash_aminoacids = {}
end
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#run ⇒ Object
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# File 'lib/bioroebe/aminoacids/show_hydrophobicity.rb', line 161
def run
report_one_letter_code
report_translated_hydropathy
report_sorted_by_most_hydrophobic_aminoacid_first
e end
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# File 'lib/bioroebe/aminoacids/show_hydrophobicity.rb', line 65
def sanitize_input(
i = @input
)
i.map! {|entry|
if entry.include? '-'
entry = entry.split('-').flatten
entry.map! {|inner_entry|
if inner_entry.size == 3
inner_entry = three_letters_to_one_letter(inner_entry)
end
inner_entry
}
end
entry
}
i.flatten!
end
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# File 'lib/bioroebe/aminoacids/show_hydrophobicity.rb', line 56
def set_input(i = '')
i = [i] unless i.is_a? Array
@input = i
sanitize_input
end
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