miga-base 0.7.7.0 → 0.7.8.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 3682f50e3efe936ce751cd83cc7945edddb8e1c3ea6e654c4d54f8ea79efbfcb
-  data.tar.gz: a5bc821d8f1b6f55baf495eea28e8783c86c61ffaca2d486e4589b818a60038f
+  metadata.gz: 5cce1edf29f5f41ad7a53225978513597f2234abd781c5f179c9f45f9d6f1ec2
+  data.tar.gz: 846a570b68efe9dba8acbc1434c55752373d9864df2cea2ff467330bf7e8b1ac
 SHA512:
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-  data.tar.gz: 3857008111b8a65b1fbf09442eb3a657789ebf964769c7805485be57298141c363296b7d2491ef3379726344f07892211d10d4c72fc74a8095bc0eaf00d4e873
+  metadata.gz: 123117d43c4ef4200ebe4a51cb14d19e48b89d249e66fa27b6e0834cf1c3b738535c3f514856e373259428c42543a25886744b4a8a6775f75b587d0a557e4d48
+  data.tar.gz: fa178d1e899da25212983bf7640cc391f3922e560d5d5ee4ff072781b6301013d928212868c9db1590dfcd1f41449e07b5019765dc866d02295226c9ed8a3e2d

data/lib/miga/cli/action/wf.rb

@@ -89,6 +89,10 @@ module MiGA::Cli::Action::Wf
   end
 
   def opts_for_wf_distances(opt)
+    opt.on('--sensitive', 'Alias to: --aai-p blast+ --ani-p blast+') do
+      cli[:aai_p] = 'blast+'
+      cli[:ani_p] = 'blast+'
+    end
     opt.on('--fast', 'Alias to: --aai-p diamond --ani-p fastani') do
       cli[:aai_p] = 'diamond'
       cli[:ani_p] = 'fastani'

data/lib/miga/result.rb

@@ -45,10 +45,6 @@ class MiGA::Result < MiGA::MiGA
   # Hash with the result metadata
   attr_reader :data
 
-  ##
-  # Array of MiGA::Result objects nested within the result (if any)
-  attr_reader :results
-
   ##
   # Load or create the MiGA::Result described by the JSON file +path+
   def initialize(path)
@@ -78,9 +74,9 @@ class MiGA::Result < MiGA::MiGA
     when :json
       @path
     when :start
-      @path.sub(/\.json$/, ".start")
+      @path.sub(/\.json$/, '.start')
     when :done
-      @path.sub(/\.json$/, ".done")
+      @path.sub(/\.json$/, '.done')
     end
   end
 
@@ -134,7 +130,7 @@ class MiGA::Result < MiGA::MiGA
   ##
   # Initialize and #save empty result
   def create
-    @data = { created: Time.now.to_s, results: [], stats: {}, files: {} }
+    @data = { created: Time.now.to_s, stats: {}, files: {} }
     save
   end
 
@@ -156,20 +152,19 @@ class MiGA::Result < MiGA::MiGA
   def load
     @data = MiGA::Json.parse(path)
     @data[:files] ||= {}
-    @results = (self[:results] || []).map { |rs| MiGA::Result.new rs }
   end
 
   ##
   # Remove result, including all associated files
   def remove!
-    each_file do |file|
-      f = File.expand_path(file, dir)
-      FileUtils.rm_rf(f)
-    end
-    %w(.start .done).each do |ext|
-      f = path.sub(/\.json$/, ext)
-      File.unlink f if File.exist? f
-    end
+    each_file { |file| FileUtils.rm_rf(File.join(dir, file)) }
+    unlink
+  end
+
+  # Unlink result by removing the .done and .start timestamps and the
+  # .json descriptor, but don't remove any other associated files
+  def unlink
+    %i(start done).each { |i| f = path(i) and File.unlink(f) }
     File.unlink path
   end
 
@@ -182,28 +177,19 @@ class MiGA::Result < MiGA::MiGA
   # Note that multiple files may have the same symbol (file_sym), since
   # arrays of files are supported.
   def each_file(&blk)
+    return to_enum(:each_file) unless block_given?
+
     @data[:files] ||= {}
     self[:files].each do |k, files|
       files = [files] unless files.kind_of? Array
       files.each do |file|
         case blk.arity
-        when 1
-          blk.call(file)
-        when 2
-          blk.call(k, file)
-        when 3
-          blk.call(k, file, File.expand_path(file, dir))
-        else
-          raise "Wrong number of arguments: #{blk.arity} for 1..3"
+        when 1; blk.call(file)
+        when 2; blk.call(k, file)
+        when 3; blk.call(k, file, File.expand_path(file, dir))
+        else; raise "Wrong number of arguments: #{blk.arity} for 1..3"
         end
       end
     end
   end
-
-  ##
-  # Add the MiGA::Result +result+ as part of the current result
-  def add_result(result)
-    @data[:results] << result.path
-    save
-  end
 end

data/lib/miga/version.rb

@@ -8,7 +8,7 @@ module MiGA
   # - Float representing the major.minor version.
   # - Integer representing gem releases of the current version.
   # - Integer representing minor changes that require new version number.
-  VERSION = [0.7, 7, 0]
+  VERSION = [0.7, 8, 0]
 
   ##
   # Nickname for the current major.minor version.
@@ -16,7 +16,7 @@ module MiGA
 
   ##
   # Date of the current gem release.
-  VERSION_DATE = Date.new(2020, 6, 4)
+  VERSION_DATE = Date.new(2020, 6, 7)
 
   ##
   # Reference of MiGA.

data/utils/distance/pipeline.rb

@@ -29,6 +29,16 @@ module MiGA::DistanceRunner::Pipeline
     classify(clades, classif, metric, result_fh, val_cls)
   end
 
+  # Run distances against datasets listed in metadata's +:dist_req+
+  def distances_by_request(metric)
+    return unless dataset.metadata[:dist_req]
+
+    $stderr.puts 'Running distances by request'
+    dataset.metadata[:dist_req].each do |target|
+      ds = ref_project.dataset(target) and send(metric, ds)
+    end
+  end
+
   # Builds a tree with all visited medoids from any classification level
   def build_medoids_tree(metric)
     $stderr.puts "Building medoids tree (metric = #{metric})"
@@ -99,7 +109,7 @@ module MiGA::DistanceRunner::Pipeline
 
   # Transfer the taxonomy to the current dataset
   def transfer_taxonomy(tax)
-    $stderr.puts "Transferring taxonomy"
+    $stderr.puts 'Transferring taxonomy'
     return if tax.nil?
 
     pval = (project.metadata[:tax_pvalue] || 0.05).to_f

data/utils/distance/runner.rb

@@ -67,7 +67,7 @@ class MiGA::DistanceRunner
 
   # Launch analysis for reference datasets
   def go_ref!
-    $stderr.puts "Launching analysis for reference dataset"
+    $stderr.puts 'Launching analysis for reference dataset'
     # Initialize databases
     initialize_dbs! true
 
@@ -80,13 +80,13 @@ class MiGA::DistanceRunner
     end
 
     # Finalize
-    [:haai, :aai, :ani].each { |m| checkpoint! m if db_counts[m] > 0 }
+    %i[haai aai ani].each { |m| checkpoint! m if db_counts[m] > 0 }
   end
 
   ##
   # Launch analysis for query datasets
   def go_query!
-    $stderr.puts "Launching analysis for query dataset"
+    $stderr.puts 'Launching analysis for query dataset'
     # Check if project is ready
     tsk = ref_project.is_clade? ? [:subclades, :ani] : [:clade_finding, :aai]
     res = ref_project.result(tsk[0])
@@ -94,6 +94,7 @@ class MiGA::DistanceRunner
 
     # Initialize the databases
     initialize_dbs! false
+    distances_by_request(tsk[1])
     # Calculate the classification-informed AAI/ANI traverse
     results = File.expand_path("#{dataset.name}.#{tsk[1]}-medoids.tsv", home)
     fh = File.open(results, 'w')
@@ -111,7 +112,9 @@ class MiGA::DistanceRunner
           next unless r[1].to_i == val_cls
 
           ani = ani_after_aai(ref_project.dataset(r[0]), 80.0)
-          closest = { ds: r[0], ani: ani } unless ani.nil? or ani < closest[:ani]
+          unless ani.nil? || ani < closest[:ani]
+            closest = { ds: r[0], ani: ani }
+          end
         end
       end
     end
@@ -133,7 +136,7 @@ class MiGA::DistanceRunner
 
   # Launch analysis for taxonomy jobs
   def go_taxonomy!
-    $stderr.puts "Launching taxonomy analysis"
+    $stderr.puts 'Launching taxonomy analysis'
     return unless project.metadata[:ref_project]
 
     go_query! # <- yeah, it's actually the same, just different ref_project

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 0.7.7.0
+  version: 0.7.8.0
 platform: ruby
 authors:
 - Luis M. Rodriguez-R
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2020-06-04 00:00:00.000000000 Z
+date: 2020-06-07 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: daemons