miga-base 1.3.19.0 → 1.3.20.0

checksums.yaml

@@ -1,7 +1,7 @@
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data/lib/miga/cli/action/relatives.rb

@@ -0,0 +1,45 @@
+# @package MiGA
+# @license Artistic-2.0
+
+require 'miga/cli/action'
+
+class MiGA::Cli::Action::Relatives < MiGA::Cli::Action
+  def parse_cli
+    cli.defaults = { metric: :aai, external: false, how_many: 5 }
+    cli.parse do |opt|
+      cli.opt_object(opt, [:project, :dataset_opt])
+      cli.opt_filter_datasets(opt)
+      opt.on(
+        '--metric STRING',
+        'Use this metric of identity, one of ANI or AAI (default)'
+      ) { |v| cli[:metric] = v.downcase.to_sym }
+      opt.on(
+        '--ref-project',
+        'Report distances to the external reference project used for taxonomy',
+        'By default: report distances to other datasets in the project'
+      ) { |v| cli[:external] = v }
+      opt.on(
+        '-n', '--how-many INT', Integer,
+        'Number of top values to report'
+      ) { |v| cli[:how_many] = v }
+      opt.on(
+        '--tab',
+        'Return a tab-delimited table'
+      ) { |v| cli[:tabular] = v }
+      opt.on(
+        '-o', '--output PATH',
+        'Create output file instead of returning to STDOUT'
+      ) { |v| cli[:output] = v }
+    end
+  end
+
+  def perform
+    cr = []
+    cli.load_and_filter_datasets.each do |d|
+      d_cr = d.closest_relatives(cli[:how_many], cli[:external], cli[:metric])
+      cr += d_cr.map { |i| [d.name] + i }
+    end
+    io = cli[:output].nil? ? $stdout : File.open(cli[:output], 'w')
+    cli.table(['dataset_A', 'dataset_B', cli[:metric]], cr, io)
+  end
+end

data/lib/miga/dataset.rb

@@ -177,22 +177,23 @@ class MiGA::Dataset < MiGA::MiGA
   alias is_active? active?
 
   ##
-  # Returns an Array of +how_many+ duples (Arrays) sorted by AAI:
-  # - +0+: A String with the name(s) of the reference dataset.
-  # - +1+: A Float with the AAI.
-  # This function is currently only supported for query datasets when
-  # +ref_project+ is false (default), and only for reference dataset when
-  # +ref_project+ is true. It returns +nil+ if this analysis is not supported.
-  def closest_relatives(how_many = 1, ref_project = false)
-    return nil if (ref? != ref_project) || multi?
+  # Returns an Array of +how_many+ duples (Arrays) sorted by +metric+
+  # (one of +:aai+ or +:ani+):
+  # - +0+: A String with the name(s) of the reference dataset
+  # - +1+: A Float with the AAI/ANI
+  def closest_relatives(how_many = 1, ref_project = false, metric = :aai)
+    return nil if multi?
 
     r = result(ref_project ? :taxonomy : :distances)
     return nil if r.nil?
 
     require 'miga/sqlite'
-    MiGA::SQLite.new(r.file_path(:aai_db)).run(
-      'SELECT seq2, aai FROM aai WHERE seq2 != ? ' \
-      'GROUP BY seq2 ORDER BY aai DESC LIMIT ?', [name, how_many]
+    metric = metric.to_s.downcase.to_sym
+    db_key = :"#{metric}_db"
+    MiGA::SQLite.new(r.file_path(db_key)).run(
+      "SELECT seq2, #{metric} FROM #{metric} WHERE seq2 != ? " \
+      "GROUP BY seq2 ORDER BY #{metric} DESC LIMIT ?",
+      [name, how_many]
     )
   end
 end

data/lib/miga/version.rb

@@ -12,7 +12,7 @@ module MiGA
   # - String indicating release status:
   #   - rc* release candidate, not released as gem
   #   - [0-9]+ stable release, released as gem
-  VERSION = [1.3, 19, 0].freeze
+  VERSION = [1.3, 20, 0].freeze
 
   ##
   # Nickname for the current major.minor version.
@@ -20,7 +20,7 @@ module MiGA
 
   ##
   # Date of the current gem relese.
-  VERSION_DATE = Date.new(2024, 7, 17)
+  VERSION_DATE = Date.new(2024, 7, 23)
 
   ##
   # References of MiGA

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 1.3.19.0
+  version: 1.3.20.0
 platform: ruby
 authors:
 - Luis M. Rodriguez-R
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2024-07-17 00:00:00.000000000 Z
+date: 2024-07-23 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: daemons
@@ -212,6 +212,7 @@ files:
 - lib/miga/cli/action/option.rb
 - lib/miga/cli/action/preproc_wf.rb
 - lib/miga/cli/action/quality_wf.rb
+- lib/miga/cli/action/relatives.rb
 - lib/miga/cli/action/rm.rb
 - lib/miga/cli/action/run.rb
 - lib/miga/cli/action/seqcode_get.rb