Module: Bioroebe::Colourize
- Defined in:
- lib/bioroebe/colours/colourize_related_code.rb
Overview
Bioroebe::Colourize
Class Method Summary collapse
-
.colourize_TAA_stop_codon(i = '', use_this_colour = :lightgreen) ⇒ Object
# === Bioroebe::Colourize.colourize_TAA_stop_codon ========================================================================= #.
-
.colourize_TAG_stop_codon(i = '', use_this_colour = :lightblue) ⇒ Object
# === Bioroebe::Colourize.colourize_TAG_stop_codon ========================================================================= #.
-
.colourize_TGA_stop_codon(i = '', use_this_colour = :olivedrab) ⇒ Object
# === Bioroebe::Colourize.colourize_TGA_stop_codon ========================================================================= #.
-
.colourize_this_FASTA_sequence(i = ARGV) ⇒ Object
# === Bioroebe::Colourize.colourize_this_FASTA_sequence ========================================================================= #.
-
.colourize_TUG_start_codon(i = '', use_this_colour = :mediumslateblue) ⇒ Object
# === Bioroebe::Colourize.colourize_TUG_start_codon ========================================================================= #.
-
.generate_HTML_page_via_this_input(i) ⇒ Object
# === Bioroebe::Colourize.generate_HTML_page_via_this_input.
-
.return_default_CSS_rules_to_use ⇒ Object
# === Bioroebe::Colourize.return_default_CSS_rules_to_use ========================================================================= #.
Class Method Details
.colourize_TAA_stop_codon(i = '', use_this_colour = :lightgreen) ⇒ Object
#
Bioroebe::Colourize.colourize_TAA_stop_codon
#
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# File 'lib/bioroebe/colours/colourize_related_code.rb', line 120 def self.colourize_TAA_stop_codon( i = '', use_this_colour = :lightgreen ) return i.gsub( /(TA\n?A)/, '<span class="'+use_this_colour.to_s+'">\1</span>' ) end |
.colourize_TAG_stop_codon(i = '', use_this_colour = :lightblue) ⇒ Object
#
Bioroebe::Colourize.colourize_TAG_stop_codon
#
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# File 'lib/bioroebe/colours/colourize_related_code.rb', line 107 def self.colourize_TAG_stop_codon( i = '', use_this_colour = :lightblue ) return i.gsub( /(TA\n?G)/, '<span class="'+use_this_colour.to_s+'">\1</span>' ) end |
.colourize_TGA_stop_codon(i = '', use_this_colour = :olivedrab) ⇒ Object
#
Bioroebe::Colourize.colourize_TGA_stop_codon
#
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# File 'lib/bioroebe/colours/colourize_related_code.rb', line 133 def self.colourize_TGA_stop_codon( i = '', use_this_colour = :olivedrab ) return i.gsub( /(TG\n?A)/, '<span class="'+use_this_colour.to_s+'">\1</span>' ) end |
.colourize_this_FASTA_sequence(i = ARGV) ⇒ Object
#
Bioroebe::Colourize.colourize_this_FASTA_sequence
#
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# File 'lib/bioroebe/colours/colourize_related_code.rb', line 82 def self.colourize_this_FASTA_sequence( i = ARGV ) if i.is_a? Array i = i.join(' ').strip end if i and File.file?(i) # unless Bioroebe.const_defined?(:ParseFasta) # require 'bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb' # end # i = Bioroebe::ParseFasta.new(i) { :be_quiet }.sequence? i = File.readlines(i).reject {|line| line.start_with?('#','>') }.join("\n") end result = colourize_TUG_start_codon(i) result = colourize_TAG_stop_codon(result) result = colourize_TAA_stop_codon(result) result = colourize_TGA_stop_codon(result) return result end |
.colourize_TUG_start_codon(i = '', use_this_colour = :mediumslateblue) ⇒ Object
#
Bioroebe::Colourize.colourize_TUG_start_codon
#
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# File 'lib/bioroebe/colours/colourize_related_code.rb', line 146 def self.colourize_TUG_start_codon( i = '', use_this_colour = :mediumslateblue ) return i.gsub( /(TU\n?G)/, '<span class="'+use_this_colour.to_s+'">\1</span>' ) end |
.generate_HTML_page_via_this_input(i) ⇒ Object
#
Bioroebe::Colourize.generate_HTML_page_via_this_input
This method will generate a .html page, using the default colourization rules defined in this file here.
#
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# File 'lib/bioroebe/colours/colourize_related_code.rb', line 26 def self.generate_HTML_page_via_this_input(i) require 'bioroebe/toplevel_methods/toplevel_methods.rb' if i.is_a? Array i = i.join(' ').strip end what = "<!DOCTYPE html>\n<html lang=\"en\"><head>"\ "<title>Colourized FASTA Sequence</title><style>\n".dup what << "#{return_default_CSS_rules_to_use}\n\n" what << "</style>\n</head>\n<body>\n" result = colourize_this_FASTA_sequence(i) what << "#{result}</body></html>\n" # ======================================================================= # # The name of the generated file is determined by the input # argument given. # ======================================================================= # into = File.basename(i).delete_suffix(File.extname(i))+ '.html' if File.exist? into e 'Can not store into an already existing file.' else e 'Storing into the file '+::Bioroebe.sfile(into)+' next.' ::Bioroebe.write_what_into(what, into) end end |
.return_default_CSS_rules_to_use ⇒ Object
#
Bioroebe::Colourize.return_default_CSS_rules_to_use
#
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# File 'lib/bioroebe/colours/colourize_related_code.rb', line 54 def self.return_default_CSS_rules_to_use return '.lightgreen { color: lightgreen; } .lightblue { color: lightblue; } .mediumslateblue { color: lightblue; } .olivedrab { color: olivedrab; } body { background-color: black; color: white; font-family: monospace; font-size: 2em; }' end |