bioroebe 0.10.80

data/lib/bioroebe/yaml/viruses/ecoli_phages.yml

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+# =========================================================================== #
+# === ecoli_phages.yml
+#
+# title: The T-Phages of E. coli (virulent dsDNA bacteriophages)
+# =========================================================================== #
+# This file will contain some information about the T-Phages of E. coli.
+#
+# It is mostly meant for demonstration-purposes only, not meant to be
+# an exhaustive listing per se.
+#
+# This also allows us to quickly "test" some phages/viruses, in principle.
+# =========================================================================== #
+# phages = YAML.load_file('ecoli_phages.yml')
+# =========================================================================== #
+
+T1:
+ plaque_size: medium
+ head: 50 nm
+ tail: 150x15
+ latent_period: 13 minutes
+ burst_size: 180
+
+T2:
+ plaque_size: small
+ head: 65x80 nm
+ tail: 120x20
+ latent_period: 21 minutes
+ burst_size: 120
+
+T3:
+ plaque_size: large
+ head: 45 nm
+ tail: invisible
+ latent_period: 13 minutes
+ burst_size: 300
+
+T4:
+ plaque_size: small
+ head: 65x80 nm
+ tail: 120x20
+ latent_period: 23,5 minutes
+ burst_size: 300
+
+T5:
+ plaque_size: small
+ head: 100 nm
+ tail: tiny
+ latent_period: 40 minutes
+ burst_size: 300
+
+T6:
+ plaque_size: small
+ head: 65x80 nm
+ tail: 120x20
+ latent_period: 25,5 minutes
+ burst_size: 200-300
+
+T7:
+ plaque_size: large
+ head: 45 nm
+ tail: invisible
+ latent_period: 13 minutes
+ burst_size: 300

data/lib/bioroebe/yaml/viruses/viruses.yml

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+poliovirus:
+ genome: (+)ssRNA
+ n_bp: 7500 # Has about 7500 nucleotides
+ first_isolated: 1909
+ binds_to: CD155 
+ wikipedia: https://en.wikipedia.org/wiki/Poliovirus

data/lib/bioroebe.rb

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+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+require 'bioroebe/requires/require_the_bioroebe_project.rb'

data/spec/testing_toplevel_method_editor.rb

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+require 'colours'
+require 'bioroebe/toplevel_methods/editor.rb'
+
+describe(Bioroebe) {
+  context Colours.yellow('→')+
+          Colours.steelblue(
+          ' when testing the Bioroebe.editor? method') do 
+
+    it(Colours.steelblue('should return a single word')) { 
+      if ENV['IS_ROEBE']
+        result = 'bluefish'
+        expect(result).to eq 'bluefish'
+      else # else assume that we may be on windows. 
+        result = 'notepad++.exe'
+        expect(result).to eq 'notepad++.exe'
+      end 
+    }
+
+  end
+}

data/spec/testing_toplevel_method_url.rb

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+require 'colours'
+require 'bioroebe/toplevel_methods/url.rb'
+
+describe(Bioroebe) {
+  context Colours.yellow('→')+
+          Colours.steelblue(
+          ' when testing the Bioroebe.try_to_pass_through_beautiful_url() method') do 
+
+    it(Colours.steelblue('should return another string')) { 
+      result = Bioroebe.try_to_pass_through_beautiful_url('hardware') 
+      expect(result).to eq 'http://localhost/DATA/PC/HARDWARE/my_hardware.cgi'
+    }
+
+  end
+}

data/spec/testing_toplevel_method_verbose.rb

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+require 'colours'
+require 'bioroebe/toplevel_methods/verbose.rb'
+
+describe(Bioroebe) {
+  context Colours.yellow('→')+
+          Colours.steelblue(
+          ' when testing the Bioroebe.be_verbose? method') do 
+
+    it(Colours.steelblue('should return true, by default')) { 
+      expect(Bioroebe.be_verbose?).to eq true
+    }
+  end
+}

data/test/advanced_svg_example.rb

@@ -0,0 +1,307 @@
+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+#
+# An example that loads data and renders different features
+# from a .gff file.
+#
+# Will select any features in ['gene', 'mRNA','cDNA_match',
+# 'microarray_probe', 'insertion','deletion','substitution',
+# 'transposable_element_insertion_site'] andrender these
+# =========================================================================== #
+require 'bioroebe'
+require 'bioroebe/shell/constants.rb'
+
+page = Bioroebe::SVG::Page.new(
+  :width => 800, 
+  :height => 200, 
+  :number_of_intervals => 10,
+  :background_color => '#F8F8F8'
+)
+
+# =========================================================================== #
+# === new_gene_track_on
+# =========================================================================== #
+def new_gene_track_on(i = page)
+  i.add_track(
+    :glyph => :directed,
+    :height => 15,
+    :name => 'Genes', 
+    :label => true, 
+    :stroke => :green,
+    :fill_color => :green_white_h
+  )
+end
+
+# =========================================================================== #
+# === new_mRNA_track_on page
+# =========================================================================== #
+def new_mRNA_track_on page
+  page.add_track(
+    :glyph => :transcript,
+    :name => 'mRNA', 
+    :height => 15,    
+    :label => true,
+    :exon_stroke => :black,
+    :exon_stroke_width => 1, 
+    :exon_fill_color => :blue,
+    :utr_fill_color => :purple,
+    :utr_stroke => :black,
+    :utr_stroke_width => 1,
+    :gap_marker => 'angled',
+    :line_color => :black,
+    :style => "fill-opacity:0.4;"
+  )
+end
+
+# === new_te_insertion_site_track_on page
+def new_te_insertion_site_track_on page
+  page.add_track(
+    :glyph => :circle,
+    :name => "TE Insertions", 
+    :label => true, 
+    :fill_color => :blue,
+    :radius => 3,
+    :stroke => :blue,
+    :stroke_width => 0.5,
+    :style => "fill-opacity:0.4;"
+  )
+end
+
+# === new_cDNA_match_track_on page
+def new_cDNA_match_track_on page
+  page.add_track(
+    :glyph => :directed,
+    :name => 'cDNA matches', 
+    :label => true, 
+    :stroke => :red,
+    :height => 15,
+    :fill_color => :red_white_h
+  )
+end
+
+# === new_microarray_probe_track_on page
+def new_microarray_probe_track_on page
+  page.add_track(
+    :glyph => :generic,
+    :height => 15,
+    :name => "Microarray probes", 
+    :label => true, 
+    :fill_color => 'green',
+    :stroke_width => 0,
+    :style => "fill-opacity:1.0;"
+  )
+end
+
+# === new_insertion_track_on page
+def new_insertion_track_on page
+  page.add_track(
+    :glyph => :down_triangle,
+    :name => 'Insertions', 
+    :label => true, 
+    :min_width => 6,
+    :fill_color => :red,
+    :stroke_width => 0,
+    :style => "fill-opacity:0.4;"
+  )
+end
+
+# === new_deletion_track_on page
+def new_deletion_track_on page
+  page.add_track(
+    :glyph => :up_triangle,
+    :name => 'Deletions', 
+    :label => true, 
+    :fill_color => :green,
+    :min_width => 6,
+    :stroke_width => 0,
+    :style => "fill-opacity:0.4;"
+  )
+end
+
+def new_marker_track_on page
+  page.add_track(
+    :glyph => :span,
+    :height => 20,
+    :name => "Markers", 
+    :label => true, 
+    :stroke => :orange,
+    :stroke_width => 15
+  )
+end
+
+# Pass in a .gff file here.
+if ARGV[0]
+  use_this_gff_file = ARGV[0]
+else
+  use_this_gff_file = Bioroebe::HOME_DIRECTORY_OF_USER_X+'DATA/PROGRAMMING_LANGUAGES/RUBY/src/bioroebe/test/test_gene.gff'
+end 
+all_features = Bioroebe::SVG::Page.parse_gff(use_this_gff_file)
+
+%w(
+  gene
+  mRNA
+  cDNA_match
+  microarray_probe
+  insertion
+  deletion
+  substitution
+  transposable_element_insertion_site
+).each do |feature_type|
+  puts "rendering #{feature_type}"
+  case feature_type
+  when 'gene'
+    track = new_gene_track_on(page)
+      all_features.select {|f|
+        f.feature == feature_type
+      }.each do |feature|
+      mf = Bioroebe::SVG::MiniFeature.new(
+                                      :start => feature.start, 
+                                      :end => feature.end,
+                                      :strand => feature.strand,
+                                      :id => feature.attributes.select {|a| a.first == 'Name'}.first.last
+                                      )
+     track.add(mf)
+    end 
+  when 'cDNA_match'
+    track = new_cDNA_match_track_on page
+    all_features.select {|f| f.feature == feature_type }.each do |feature|
+      mf = Bioroebe::SVG::MiniFeature.new(
+                                      :start => feature.start, 
+                                      :strand => feature.strand,
+                                      :end => feature.end    
+      )
+      track.add(mf)
+    end
+  # === mRNA
+  when 'mRNA'
+    track = new_mRNA_track_on page
+    five_utrs  = all_features.select {|x| x.feature_type == 'five_prime_UTR'} 
+    three_utrs = all_features.select {|z| z.feature_type == 'three_prime_UTR'}
+    all_exons  = all_features.select {|z| z.feature_type == 'CDS'}
+    pp all_exons
+    all_features.select {|f| f.feature == feature_type }.each do |feature|
+      feature_id = feature.attributes.select {|y| y.first == "ID"}.first.last
+      five_utr = five_utrs.select {|x|  x.attributes_to_hash["Parent"] == feature_id  }.first
+        three_utr = three_utrs.select {|z| z.attributes_to_hash["Parent"] == feature_id }.first
+        utrs = []
+        if not five_utr.nil? and not three_utr.nil?
+          utrs = [five_utr.start,five_utr.end, three_utr.start,three_utr.end]
+          utrs.sort!
+        end
+        exons = []
+        exons = all_exons.select {|x|  x.attributes_to_hash["Parent"] == feature_id  }
+        exons = exons.collect {|x| [x.start, x.end] }.flatten
+        #if not exons.empty?
+        #  exons = exons.sort
+        #end
+        mf = Bioroebe::SVG::MiniFeature.new(
+                                        :start => feature.start, 
+                                        :end => feature.end,
+                                        :utrs => utrs,
+                                        :exons => exons,
+                                        :strand => feature.strand      
+        )
+        track.add(mf)
+      end
+    # === microarray_probe
+    when 'microarray_probe'
+      track = new_microarray_probe_track_on page
+            all_features.select {|f| f.feature == feature_type }.each do |feature|
+        mf = Bioroebe::SVG::MiniFeature.new(
+                                        :start => feature.start, 
+                                        :strand => feature.strand,
+                                        :end => feature.end    
+        )
+        track.add(mf)
+      end
+    when 'transposable_element_insertion_site'
+      track = new_te_insertion_site_track_on page
+      all_features.select {|f| f.feature == feature_type }.each do |feature|
+        mf = Bioroebe::SVG::MiniFeature.new(
+                                        :start => feature.start, 
+                                        :strand => feature.strand,
+                                        :end => feature.end    
+        )
+        track.add(mf)
+      end
+    # === insertion
+    when 'insertion'
+      track = new_insertion_track_on page
+      all_features.select {|f| f.feature == feature_type }.each do |feature|
+        mf = Bioroebe::SVG::MiniFeature.new(
+                                        :start => feature.start, 
+                                        :end => feature.end    
+        )
+        track.add(mf)
+      end
+     # === deletion
+     when 'deletion'
+      track = new_deletion_track_on page
+      all_features.select {|f| f.feature == feature_type }.each do |feature|
+        mf = Bioroebe::SVG::MiniFeature.new(
+                                        :start => feature.start, 
+                                        :end => feature.end    
+        )
+        track.add(mf)
+      end
+     # === marker
+     when 'marker'
+      track = new_marker_track_on page
+      all_features.select {|f| f.feature == feature_type }.each do |feature|
+        mf = Bioroebe::SVG::MiniFeature.new(
+                                        :start => feature.start, 
+                                        :end => feature.end    
+        )
+        track.add(mf)
+      end
+  end
+end
+
+data_track1 = page.add_track(
+  :glyph => :histogram,  #might also be :density or heatmap  ##page doesn't know how to deal with individual file types, rather page object takes a list of values (e.g bar heights) from pre-processed data source and renders those
+  :stroke_color => 'black',
+  :fill_color => :blue,
+  :track_height => 75,
+  :name => 'Simulated NGS coverage (transformed sine function)', 
+  :label => true, 
+  :stroke_width => 0,
+  :style => 'fill-opacity:0.6;'
+)
+# generate a load of data, each data point becomes a feature...                         
+_data = (19597235..19637234).step(10) { |start|
+#data = (19616011..19618459).step(1) do |start|
+  height = Math::sin(start)
+  height = height * -1 if height < 0
+  height = Math::log(height)
+  height = height * -1 if height < 0
+  data_feature = Bioroebe::SVG::MiniFeature.new(
+    :start => start,
+    :end => start + 30,
+    :segment_height => height * 10
+  )
+  data_track1.add(data_feature)
+}
+
+data_track2 = page.add_track(
+                :glyph => :histogram,  #might also be :density or heatmap  ##page doesn't know how to deal with individual file types, rather page object takes a list of values (e.g bar heights) from pre-processed data source and renders those
+                :stroke_color => 'black',
+                :fill_color => :yellow,
+                :track_height => 75,
+                :name => 'Random bar height', 
+                :label => true, 
+                :stroke_width => 1,
+                :style => 'fill-opacity:0.4;'
+              )
+# Generate a load of data, each data point becomes a feature.                         
+_data = (19597235..19637234).step(200) { |start|
+# data = (19616011..19618459).step(30) do |start|
+  data_feature = Bioroebe::SVG::MiniFeature.new(
+    :start => start,
+    :end => start + 200,
+    :segment_height => rand(30)
+  )
+  data_track2.add(data_feature)
+}
+page.write('/output.svg')

data/test/testing_bioroebe.rb

@@ -0,0 +1,25 @@
+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# Note that this was once thought to test all of the bioroebe project,
+# but I have since then changed my mind, and instead started to
+# create other test*.rb files that test specific subcomponents
+# instead. But perhaps one day we can put this all back together again.
+# =========================================================================== #
+require 'colours/everything/autoinclude'
+require 'bioroebe'
+
+e Bioroebe.rev+'The base directory for the Bioroebe project is at:'
+e
+e '  '+sfancy(Bioroebe.base_directory?)
+e
+
+e 'Did we manage to require the project namespace? '+
+   Object.const_defined?(:Bioroebe).to_s
+
+e 'The version of Bioroebe is: '+sfancy(Bioroebe.version.to_s)
+
+input = 'ATCGNNNNOOO' # Nucleotide Input.
+e 'The input is:               '+sfancy(input)
+e 'This has been changed to:   '+sfancy(Bioroebe.to_dna(input))

data/test/testing_codons.rb

@@ -0,0 +1,45 @@
+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+require 'colours/autoinclude.rb'
+require 'bioroebe/codons/codons.rb'
+
+Bioroebe.initialize_codons
+
+e
+e rev+'Now testing the codons-related aspects of the '+
+  sfancy('Bioroebe')+' project.'
+e
+e Bioroebe.tomato('Showing all stop codons:')
+e
+print '  '; pp Bioroebe.stop_codons?
+e
+e Bioroebe.tomato('Next, showing all start_codons:')
+e
+print '  '; pp Bioroebe.start_codons?
+e
+e Bioroebe.tomato('Returning the most likely codon sequence for the aminoacid sequence ATTAAG')
+e
+print '  '; pp Bioroebe.return_the_most_likely_codon_sequence_for_this_aminoacid_sequence('ATTAAG')
+e
+_ = 'ATGAGCGACACACGACGACGACGCAGTGTCAGCAGACTCGAACTGAGATTGAAAGAGATGATAGTAAATAA'
+e Bioroebe.tomato('How many stop codons are in the following DNA sequence?')
+e
+e "  #{Colours.steelblue(_)}"
+e
+e Bioroebe.n_stop_codons_in_this_sequence?(_)
+e
+e Bioroebe.tomato('Next we will test the very important method ')+
+  Colours.steelblue('Bioroebe.codon_to_aminoacid()')
+e
+e '1) '+Bioroebe.codon_to_aminoacid('ATG') # => "M"
+e '2) '+Bioroebe.codon_to_aminoacid('GUG') # => "V"
+e '3) '+Bioroebe.decode_this_codon('CCG')  # => "P"
+e '4) '+Bioroebe.codon_to_aminoacid('GUGGUG') # => "VV"
+e '5) '+Bioroebe.codon_to_aminoacid('AGGAACGACTTTGGGGACCGGAGCACATGGACT') # => "VV"
+string_result = Bioroebe.codon_to_aminoacid(
+    ['AGG', 'AAC', 'GAC', 'TTT', 'GGG', 'GAC', 'CGG', 'AGC', 'ACA', 'TGG', 'ACT']
+  )
+e '6) '+string_result
+e 'Note: the last two entries are the same because the input is the same.'

data/test/testing_dna_to_rna_conversion.rb

@@ -0,0 +1,15 @@
+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# The code here simply tests whether the DNA→RNA conversion works,
+# through the toplevel API Bioroebe.to_rna().
+# =========================================================================== #
+require 'bioroebe/toplevel_methods/nucleotides.rb'
+
+input = 'GATGGAACTTGACTACGTAAATT'
+
+converted_output = Bioroebe.to_rna(input)
+expected_result  = 'GAUGGAACUUGACUACGUAAAUU'
+
+puts (converted_output == expected_result)

data/test/testing_parse_pdb_file.rb

@@ -0,0 +1,23 @@
+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+require 'colours/autoinclude'
+require 'bioroebe'
+
+target_file = Bioroebe.project_base_dir?+'data/pdb/rcsb_pdb_1VII.fasta'
+target_pdb_file = Bioroebe.project_base_dir?+'data/pdb/1VII.pdb'
+sequence1 = Bioroebe.return_aminoacid_sequence_from_this_pdb_file(target_pdb_file)
+
+# =========================================================================== #
+# The sequence1 should be: 'MLSDEDFKAVFGMTRSAFANLPLWKQQNLKKEKGLF'
+# =========================================================================== #
+if sequence1 == File.readlines(target_file).last.strip
+  e Colours.rev+"All is fine - we compared the two sequences."
+  e Colours.rev+'The sequence is:'
+  e steelblue(sequence1)
+else
+  e swarn('Test comparison failed!')
+  pp sequence1
+  pp File.readlines(target_file).last.strip
+end

data/test/testing_reverse_complement.rb

@@ -0,0 +1,32 @@
+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# This simple test will take a given DNA as input, and output the reverse
+# complement to the given DNA strand at hand.
+#
+# The simple rules are that A pairs with T and C pairs with G.
+#
+# The reverse complement of a DNA string s is the string reverse_s
+# formed by reversing the elements of string s, then taking the
+# complement of each element. For example, the reverse complement
+# of "GTCA" is "TGAC"
+# =========================================================================== #
+require 'bioroebe/sequence/reverse_complement.rb'
+
+alias e puts
+
+if ARGV.empty?
+  sample = 'AAAACCCGGT'
+else
+  sample = ARGV.first
+end
+
+# =========================================================================== #
+# Expected output:
+#   ACCGGGTTTT
+# =========================================================================== #
+# Note that this will output the correct answer as-is.
+# =========================================================================== #
+e 'The sequence '+sample+' is reversed:'
+e '             '+Bioroebe::ReverseComplement[sample]