miga-base 1.3.21.4 → 1.3.22.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
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-  data.tar.gz: 168cd9a078459088db54aded997cf4a262b6c47c644aad33a4b0b0e418b8b4dd
+  metadata.gz: 18af6df383be9cb5a5ecba8ed914ec5c1878a70c8e8cb3825a590049b44a06b5
+  data.tar.gz: a79ed870803ce5e4c7eb8e3380c79e43157de8090790d7d0ca9ace51fc6b12c7
 SHA512:
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-  data.tar.gz: 67ec41f81a78f163b21c619f6ab600f5d252d0502439f51b3694dfc559b30c4ade40e688de4970fa8608c22df4132a5c355857b40b2544939026822b7fe900ab
+  metadata.gz: bce0394b7a0f750df581b767992d5eb54f842b40aa06bbfa5dbd8b7d0d6e8f8ae813930432756369e6da07a9b0a95d1c6067147d5e6ae2fae7df697f46a0b41d
+  data.tar.gz: 8f5c085855514811ae1b781d4e58ce3af1b82034d0d92e10b3a558fd2130d7312fba7eb548852e67083eff310435bbb44bde074c342971acca140f9be80c88af

data/lib/miga/cli/action/download/gtdb.rb

@@ -23,8 +23,9 @@ module MiGA::Cli::Action::Download::Gtdb
 
   def sanitize_cli
     cli.ensure_par(taxon: '-T')
-    unless cli[:taxon] =~ /^[a-z]__\S+$/
-      raise 'Taxon (-T) must be in GTDB format: s__Macondimonas_diazotrophica'
+    cli[:taxon].gsub!(' ', '%20')
+    unless cli[:taxon] =~ /^[a-z]__[\S ]+$/
+      raise 'Taxon (-T) must be in GTDB format: "s__Macondimonas diazotrophica"'
     end
     cli[:save_every] = 1 if cli[:dry]
   end

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

@@ -124,6 +124,13 @@ module MiGA::Cli::Action::Wf
       cli[:aai_p] = 'diamond'
       cli[:ani_p] = 'fastani'
     end
+    opt.on(
+      '--only-ani', 'Alias to: --haai-p no --aai-p no',
+      'Use only for collections with expected AAI around or above 85%'
+    ) do
+      cli[:haai_p] = 'no'
+      cli[:aai_p] = 'no'
+    end
     opt.on(
       '--haai-p STRING',
       'hAAI search engine. One of: blast+, fastaai, blat, diamond, fastaai, no',
@@ -131,7 +138,7 @@ module MiGA::Cli::Action::Wf
     ) { |v| cli[:haai_p] = v }
     opt.on(
       '--aai-p STRING',
-      'AAI search engine. One of: blast+, blat, diamond (default)'
+      'AAI search engine. One of: blast+, blat, diamond (default), no'
     ) { |v| cli[:aai_p] = v }
     opt.on(
       '--ani-p STRING',

data/lib/miga/daemon.rb

@@ -183,7 +183,7 @@ class MiGA::Daemon < MiGA::MiGA
   end
 
   ##
-  # Traverse datasets, and returns boolean indicating if at any reference
+  # Traverse datasets, and returns boolean indicating if any reference
   # datasets are incomplete
   def check_datasets
     l_say(2, 'Checking datasets')
@@ -196,11 +196,17 @@ class MiGA::Daemon < MiGA::MiGA
       queue_job(:d, ds)
     end
     unless show_log?
+      @_check_datasets_reported_done ||= false
       n = project.dataset_names.count
-      k = jobs_to_run.size + jobs_running.size
-      k -= 1 unless get_job(:maintenance).nil?
-      advance('Datasets:', n - k, n, false)
-      miga_say if k == 0
+      k = (jobs_to_run + jobs_running).select { |i| !i[:ds].nil? }.size
+      if k > 0
+        advance('Datasets:', n - k, n, false)
+        @_check_datasets_reported_done = false
+      elsif !@_check_datasets_reported_done
+        advance('Datasets:', n, n, false)
+        miga_say
+        @_check_datasets_reported_done = true
+      end
     end
     o
   end

data/lib/miga/project/base.rb

@@ -142,7 +142,7 @@ module MiGA::Project::Base
     },
     aai_p: {
       desc: 'Value of aai.rb -p on AAI', default: 'diamond', type: String,
-      in: %w[blast+ blast blat diamond]
+      in: %w[blast+ blast blat diamond no]
     },
     ani_p: {
       desc: 'Value of ani.rb -p on ANI', default: 'fastani', type: String,

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, 21, 4].freeze
+  VERSION = [1.3, 22, 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, 12, 23)
+  VERSION_DATE = Date.new(2025, 2, 17)
 
   ##
   # References of MiGA

data/utils/distance/commands.rb

@@ -60,10 +60,15 @@ module MiGA::DistanceRunner::Commands
   # Note that ANI values may be returned for lower (or failing) AAIs if the
   # value is already stored in the database
   def ani_after_aai(targets, aai_limit = 85.0)
-    # Run AAI and select targets with AAI ≥ aai_limit
-    aai = aai(targets)
-    sbj = aai.each_with_index.map { |i, k| targets[k] if i&.> aai_limit }
-    sbj.compact!
+    sbj =
+      if opts[:aai_p] == 'no'
+        # If we skip AAI, run ANI for all targets
+        targets
+      else
+        # Otherwise, run AAI and select targets with AAI ≥ aai_limit
+        aai = aai(targets)
+        aai.each_with_index.map { |i, k| targets[k] if i&.> aai_limit }.compact
+      end
 
     # Run ANI
     ani(sbj) unless sbj.empty?

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 1.3.21.4
+  version: 1.3.22.0
 platform: ruby
 authors:
 - Luis M. Rodriguez-R
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2024-12-23 00:00:00.000000000 Z
+date: 2025-02-17 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: daemons