miga-base 1.2.13.3 → 1.2.14.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: d01c6cdd3ff689e80079b0bd59a63cc968b1b7e768518ce013d3c4d055032427
-  data.tar.gz: 1701cbb3a0c75dfe96ce6c1543f3aac6b35ba0dd87fb0f3f7ccc5e2780eaf7a3
+  metadata.gz: 6af49f95d3280cf3cbba4bfb12ee9987ce7af7515a329aad9112f3a2ba2357d8
+  data.tar.gz: 024d90b9f7eca754af3dbc13ca2aaa7ad51c5871ad531bffec9bd6c43350b218
 SHA512:
-  metadata.gz: deec1e53d9dae1c995e59406a53b653f503e901821884b1b400da17c5330bbef5d344613fc7896961739cc66253604ad73947d20f178bf92f00f01881f16d0a6
-  data.tar.gz: d991c538708a72b3c9e65eb56a6e121fea4ab25f26838dbd706f27e16cb8d757346eabc9799a3f5b620df3f8e0c5456b65884e3d887f80d1f65f34b762bbfd59
+  metadata.gz: 2f9f66736037ab87ef93a83e08decf55813addc75151f28ac06e6c9d4ee54f21c450cbc2c6b681c90853e6b96974303ffe3ea2aac04d4fb4bbda79386af49b46
+  data.tar.gz: 99fae0ad085c5165bf5232c348b19f89adf3c4b21502ba09636e66e45faadfa2a2a4f4d833bb3878123ac0b11535e739dfbc394668bdb651d834e76b177844ae

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

@@ -25,7 +25,7 @@ module MiGA::Cli::Action::Download::Base
 
   def cli_save_actions(opt)
     cli.opt_flag(
-      opt, '--only-metadata',
+      opt, 'only-metadata',
       'Create datasets without input data but retrieve all metadata',
       :only_md
     )

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

@@ -23,6 +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'
+    end
     cli[:save_every] = 1 if cli[:dry]
   end
 

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

@@ -31,6 +31,10 @@ class MiGA::Cli::Action::GtdbGet < MiGA::Cli::Action
       cli_name_modifiers(opt)
       cli_filters(opt)
       cli_save_actions(opt)
+      opt.on(
+        '--api-key STRING',
+        'NCBI API key'
+      ) { |v| ENV['NCBI_API_KEY'] = v }
     end
   end
 

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

@@ -37,12 +37,16 @@ class MiGA::Cli::Action::Summary < MiGA::Cli::Action
     cli.ensure_par(result: '-r')
     ds = cli.load_and_filter_datasets
     cli.say 'Loading results'
+    k = 0
+    n = ds.size
     stats = ds.map do |d|
+      cli.advance('Datasets:', k += 1, n, false)
       r = d.result(cli[:result])
       r.compute_stats if cli[:compute] && !r.nil? && r[:stats].empty?
       s = r.nil? ? {} : r[:stats]
       s.tap { |i| i[:dataset] = d.name }
     end
+    cli.say ''
     keys = cli[:key_md].nil? ? stats.map(&:keys).flatten.uniq :
       [:dataset, cli[:key_md].downcase.miga_name.to_sym]
     keys.delete :dataset

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

@@ -35,10 +35,18 @@ module MiGA::Cli::Action::Wf
         '-T', '--ncbi-taxon STRING',
         'Download all the genomes in NCBI classified as this taxon'
       ) { |v| cli[:ncbi_taxon] = v }
+      opt.on(
+        '-G', '--gtdb-taxon STRING',
+        'Download all the genomes in GTDB classified as this taxon'
+      ) { |v| cli[:gtdb_taxon] = v }
       opt.on(
         '--no-draft',
-        'Only download complete genomes, not drafts'
+        'Only download complete genomes, not drafts (requires -T)'
       ) { |v| cli[:ncbi_draft] = v }
+      opt.on(
+        '--gtdb-ref',
+        'Only download reference anchor genomes in GTDB (requires -G)'
+      ) { |v| cli[:gtdb_ref] = v }
       opt.on(
         '--max-download INT', Integer,
         'Maximum number of genomes to download (by default: unlimited)'
@@ -136,7 +144,7 @@ module MiGA::Cli::Action::Wf
       p.set_option(i, cli[i])
     end
 
-    # Download datasets
+    # Download datasets from NCBI
     unless cli[:ncbi_taxon].nil?
       what = cli[:ncbi_draft] ? '--all' : '--complete'
       cmd = ['ncbi_get', '-P', cli[:outdir], '-T', cli[:ncbi_taxon], what]
@@ -144,6 +152,14 @@ module MiGA::Cli::Action::Wf
       call_cli(cmd)
     end
 
+    # Download datasets from GTDB
+    unless cli[:gtdb_taxon].nil?
+      cmd = ['gtdb_get', '-P', cli[:outdir], '-T', cli[:gtdb_taxon]]
+      cmd << '--reference' if cli[:gtdb_ref]
+      cmd += ['--max', cli[:ncbi_max]] if cli[:ncbi_max]
+      call_cli(cmd)
+    end
+
     # Add datasets
     call_cli(
       [

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 = [1.2, 13, 3].freeze
+  VERSION = [1.2, 14, 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(2023, 1, 3)
+  VERSION_DATE = Date.new(2023, 1, 16)
 
   ##
   # References of MiGA

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 1.2.13.3
+  version: 1.2.14.0
 platform: ruby
 authors:
 - Luis M. Rodriguez-R
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2023-01-03 00:00:00.000000000 Z
+date: 2023-01-16 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: daemons