Class: Bioroebe::SanitizeCodonFrequency

Inherits:
Base
  • Object
show all
Defined in:
lib/bioroebe/codons/sanitize_codon_frequency.rb

Overview

Bioroebe::SanitizeCodonFrequency

Constant Summary collapse

TEST_STRING =
#

TEST_STRING

This string can be used as our default test-data.

#
'# UUU 26.1(170666)  UCU 23.5(153557)  UAU 18.8(122728)  UGU  8.1( 52903)
# UUC 18.4(120510)  UCC 14.2( 92923)  UAC 14.8( 96596)  UGC  4.8( 31095)
# UUA 26.2(170884)  UCA 18.7(122028)  UAA  1.1(  6913)  UGA  0.7(  4447)
# UUG 27.2(177573)  UCG  8.6( 55951)  UAG  0.5(  3312)  UGG 10.4( 67789)
# 
# CUU 12.3( 80076)  CCU 13.5( 88263)  CAU 13.6( 89007)  CGU  6.4( 41791)
# CUC  5.4( 35545)  CCC  6.8( 44309)  CAC  7.8( 50785)  CGC  2.6( 16993)
# CUA 13.4( 87619)  CCA 18.3(119641)  CAA 27.3(178251)  CGA  3.0( 19562)
# CUG 10.5( 68494)  CCG  5.3( 34597)  CAG 12.1( 79121)  CGG  1.7( 11351)
# 
# AUU 30.1(196893)  ACU 20.3(132522)  AAU 35.7(233124)  AGU 14.2( 92466)
# AUC 17.2(112176)  ACC 12.7( 83207)  AAC 24.8(162199)  AGC  9.8( 63726)
# AUA 17.8(116254)  ACA 17.8(116084)  AAA 41.9(273618)  AGA 21.3(139081)
# AUG 20.9(136805)  ACG  8.0( 52045)  AAG 30.8(201361)  AGG  9.2( 60289)
# 
# GUU 22.1(144243)  GCU 21.2(138358)  GAU 37.6(245641)  GGU 23.9(156109)
# GUC 11.8( 76947)  GCC 12.6( 82357)  GAC 20.2(132048)  GGC  9.8( 63903)
# GUA 11.8( 76927)  GCA 16.2(105910)  GAA 45.6(297944)  GGA 10.9( 71216)
# GUG 10.8( 70337)  GCG  6.2( 40358)  GAG 19.2(125717)  GGG  6.0( 39359)
'

Constants inherited from Base

Base::NAMESPACE

Constants included from ColoursForBase

ColoursForBase::ARRAY_HTML_COLOURS_IN_USE

Class Method Summary collapse

Instance Method Summary collapse

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 BaseModule

#absolute_path, #default_file_read, #file_readlines

Methods included from InternalHashModule

#internal_hash?, #reset_the_internal_hash

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 included from InferTheNamespaceModule

#infer_the_namespace, #namespace?

Constructor Details

#initialize(i = TEST_STRING, run_already = true) ⇒ SanitizeCodonFrequency

#

initialize

#


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# File 'lib/bioroebe/codons/sanitize_codon_frequency.rb', line 57

def initialize(
    i           = TEST_STRING,
    run_already = true
  )
  reset
  set_input(i)
  run if run_already
end

Class Method Details

.[](i = '') ⇒ Object

#

Bioroebe::SanitizeCodonFrequency[]

#


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# File 'lib/bioroebe/codons/sanitize_codon_frequency.rb', line 136

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

Instance Method Details

#input? ⇒ Boolean

#

input?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/codons/sanitize_codon_frequency.rb', line 86

def input?
  @input
end

#report_result(i = input?) ) ⇒ Object

#

report_result

#


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# File 'lib/bioroebe/codons/sanitize_codon_frequency.rb', line 93

def report_result(i = input?)
  i.each {|entry|
    splitted = entry.split(' ')
    splitted[1] = splitted[1].rjust(4)
    entry = splitted.join(' ')
    e entry
  } if i
end

#reset ⇒ Object

#

reset (reset tag)

#


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# File 'lib/bioroebe/codons/sanitize_codon_frequency.rb', line 69

def reset
  super()
end

#run ⇒ Object

#

run (run tag)

#


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# File 'lib/bioroebe/codons/sanitize_codon_frequency.rb', line 128

def run
  sanitize_input
  report_result
end

#sanitize_input ⇒ Object

#

sanitize_input

#


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# File 'lib/bioroebe/codons/sanitize_codon_frequency.rb', line 105

def sanitize_input
  @input = input?.split(N)
  input?.map! {|entry| entry.delete('#') } # Get rid '#' next.
  input?.map!(&:strip)
  input?.reject!(&:empty?)
  input?.map! {|entry| entry.split(')') }
  input?.flatten!
  input?.map!(&:strip)
  input?.map! {|entry|
    if entry.include? '('
      entry = entry[0..(entry.index('(')-1)]
    end
    entry.squeeze! ' '
    if entry.include? ' '
      entry.gsub!(/ /,': ')
    end
    entry
  }
end

#set_input(i = TEST_STRING) ⇒ Object

#

set_input

#


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# File 'lib/bioroebe/codons/sanitize_codon_frequency.rb', line 76

def set_input(i = TEST_STRING)
  i = i.first if i.is_a? Array
  i = TEST_STRING if i.nil?
  i = i.to_s.dup
  @input = i
end