miga-base 0.4.1.0 → 0.4.2.0

data/actions/tax_index.rb

@@ -1,46 +0,0 @@
-#!/usr/bin/env ruby
-
-# @package MiGA
-# @license Artistic-2.0
-
-require "miga/tax_index"
-
-o = {q:true, format: :json}
-OptionParser.new do |opt|
-  opt_banner(opt)
-  opt_object(opt, o, [:project])
-  opt.on("-i", "--index PATH",
-    "(Mandatory) File to create with the index."){ |v| o[:index]=v }
-  opt.on("-f", "--format STRING",
-    "Format of the index file. By default: #{o[:format]}. Supported: " +
-    "json, tab."){ |v| o[:format]=v.to_sym }
-  opt_filter_datasets(opt, o)
-  opt_common(opt, o)
-end.parse!
-
-##=> Main <=
-opt_require(o, project:"-P", index:"-i")
-
-$stderr.puts "Loading project." unless o[:q]
-p = MiGA::Project.load(o[:project])
-raise "Impossible to load project: #{o[:project]}" if p.nil?
-
-$stderr.puts "Loading datasets." unless o[:q]
-ds = p.datasets
-ds.select!{|d| not d.metadata[:tax].nil? }
-ds = filter_datasets!(ds, o)
-
-$stderr.puts "Indexing taxonomy." unless o[:q]
-tax_index = MiGA::TaxIndex.new
-ds.each { |d| tax_index << d }
-
-$stderr.puts "Saving index." unless o[:q]
-fh = File.open(o[:index], "w")
-if o[:format]==:json
-  fh.print tax_index.to_json
-elsif o[:format]==:tab
-  fh.print tax_index.to_tab
-end
-fh.close
-
-$stderr.puts "Done." unless o[:q]

data/actions/tax_set.rb

@@ -1,63 +0,0 @@
-#!/usr/bin/env ruby
-
-# @package MiGA
-# @license Artistic-2.0
-
-o = {q:true}
-OptionParser.new do |opt|
-  opt_banner(opt)
-  opt_object(opt, o, [:project, :dataset_opt])
-  opt.on("-s", "--tax-string STRING",
-    "String corresponding to the taxonomy of the dataset.",
-    "The MiGA format of string taxonomy is a space-delimited",
-    "set of 'rank:name' pairs."){ |v| o[:taxstring]=v }
-  opt.on("-t", "--tax-file PATH",
-    "(Mandatory unless -D and -s are provided) Tab-delimited file containing",
-    "datasets taxonomy.  Each row corresponds to a datasets and each column",
-    "corresponds to a rank.  The first row must be a header with the rank ",
-    "names, and the first column must contain dataset names."
-    ){ |v| o[:taxfile]=v }
-  opt_common(opt, o)
-end.parse!
-
-##=> Main <=
-opt_require(o, project:"-P")
-raise "-D is mandatory unless -t is provided." if
-  o[:dataset].nil? and o[:taxfile].nil?
-raise "-s is mandatory unless -t is provided." if
-  o[:taxstring].nil? and o[:taxfile].nil?
-
-$stderr.puts "Loading project." unless o[:q]
-p = MiGA::Project.load(o[:project])
-raise "Impossible to load project: #{o[:project]}" if p.nil?
-
-if not o[:taxfile].nil?
-  $stderr.puts "Reading tax-file and registering taxonomy." unless o[:q]
-  tfh = File.open(o[:taxfile], "r")
-  header = nil
-  tfh.each_line do |ln|
-    next if ln =~ /^\s*?$/
-    r = ln.chomp.split(/\t/, -1)
-    dn = r.shift
-    if header.nil?
-      header = r
-      next
-    end
-    d = p.dataset dn
-    if d.nil?
-      warn "Impossible to find dataset at line #{$.}: #{dn}. Ignoring..."
-      next
-    end
-    d.metadata[:tax] = MiGA::Taxonomy.new(r, header)
-    d.save
-    $stderr.puts " #{d.name} registered." unless o[:q]
-  end
-  tfh.close
-else
-  $stderr.puts "Registering taxonomy." unless o[:q]
-  d = p.dataset o[:dataset]
-  d.metadata[:tax] = MiGA::Taxonomy.new(o[:taxstring])
-  d.save
-end
-
-$stderr.puts "Done." unless o[:q]

data/actions/tax_test.rb

@@ -1,80 +0,0 @@
-#!/usr/bin/env ruby
-
-# @package MiGA
-# @license Artistic-2.0
-
-require "miga/tax_dist"
-
-o = {q:true, test:"both", ref_project:false}
-OptionParser.new do |opt|
-  opt_banner(opt)
-  opt_object(opt, o, [:project, :dataset])
-  opt.on("--ref-project",
-    "Use the taxonomy from the reference project, not the current project."
-    ){ |v| o[:ref_project]=v }
-  opt.on("-t", "--test STRING",
-    "Test to perform. Supported values: intax, novel, both."
-    ){ |v| o[:test]=v.downcase }
-  opt_common(opt, o)
-end.parse!
-
-##=> Main <=
-opt_require(o, project:"-P", dataset:"-D")
-
-$stderr.puts "Loading project." unless o[:q]
-p = MiGA::Project.load(o[:project])
-raise "Impossible to load project: #{o[:project]}" if p.nil?
-
-$stderr.puts "Loading dataset." unless o[:q]
-ds = p.dataset(o[:dataset])
-
-$stderr.puts "Finding closest relative." unless o[:q]
-cr = ds.closest_relatives(1, o[:ref_project])
-
-if cr.nil? or cr.empty?
-  raise "This action is not supported for the project or dataset." if cr.nil?
-  raise "No close relatives found."
-else
-  $stderr.puts "Querying probability distributions." unless o[:q]
-  cr = cr[0]
-  puts "Closest relative: #{cr[0]} with AAI: #{cr[1]}."
-  if o[:ref_project]
-    ref = p.metadata[:ref_project]
-    raise "--ref-project requested, but no reference project has been set." if ref.nil?
-    q = MiGA::Project.load(ref)
-    raise "--ref-project requested, but reference project doesn't exist." if q.nil?
-    tax = q.dataset(cr[0]).metadata[:tax]
-  else
-    tax = p.dataset(cr[0]).metadata[:tax]
-  end
-  tax ||= {}
-  
-  if %w[intax both].include? o[:test]
-    # Intax
-    r = MiGA::TaxDist.aai_pvalues(cr[1], :intax).map do |k,v|
-      sig = ""
-      [0.5,0.1,0.05,0.01].each{ |i| sig << "*" if v<i }
-      [MiGA::Taxonomy.LONG_RANKS[k], (tax[k] || "?"), v, sig]
-    end
-    puts ""
-    puts "Taxonomic classification"
-    puts MiGA::MiGA.tabulate(%w[Rank Taxonomy P-value Signif.], r)
-  end
-  
-  if %w[novel both].include? o[:test]
-    # Novel
-    r = MiGA::TaxDist.aai_pvalues(cr[1], :novel).map do |k,v|
-      sig = ""
-      [0.5,0.1,0.05,0.01].each{ |i| sig << "*" if v<i }
-      [MiGA::Taxonomy.LONG_RANKS[k], v, sig]
-    end
-    puts ""
-    puts "Taxonomic novelty"
-    puts MiGA::MiGA.tabulate(%w[Rank P-value Signif.], r)
-  end
-  
-  puts ""
-  puts "Significance at p-value below: *0.5, **0.1, ***0.05, ****0.01."
-end
-
-$stderr.puts "Done." unless o[:q]