miga-base 1.3.9.1 → 1.3.9.2

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: '09d0eb94fc3898aecede549b45d2a0478c944719c3e14b1efcefd83b8ba0f08d'
-  data.tar.gz: 667f5cca17495e22a1f80b396eb1d1d64b2f273c27dbab4628c6d758da51a4a6
+  metadata.gz: 2603688836b87b4be16c9c88bacbb206a93bd6b71b19a5a7febc219638f4e912
+  data.tar.gz: 1df2051e7d1d88facce4e0738828274ca9743807cdf90da959697addde25e424
 SHA512:
-  metadata.gz: c73e6b163aa3be26e728744e29c8a1a6fcba73e3e27c9d2ff40604d0351a263fd6db6b9582bb4eef59a408f937af8ebac99d5360fc3cdc8c2ba1fd1c406c33c0
-  data.tar.gz: ffd3639052114019007db0600a0d84b272e9ef52c4d00f6e8f8ca5a172d36b05f51a365a038521415411f6eddb256132e9e98d1e22624713aed20e5149d0995c
+  metadata.gz: a28d606569bdd37e5d4d33710564573639b103747c9622fae0a3a2d254f6293bf8462decb09bdf67d7656f84bca84fc7094e217c66ff081e75c5f5622bd9711c
+  data.tar.gz: 7e18ecf2487c31b5d99d3fb53b8716ce0dea2f2a8b2bab5015a871be9b703dd63c4384fb050380dad4dd28f5de3d1de5c9bcb1cb8544726870c7314fab626ca9

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

@@ -26,6 +26,9 @@ module MiGA::Cli::Action::Download::Ncbi
       cli[:scaffold] = true
       cli[:contig] = true
     end
+    opt.on('--ncbi-list-json STRING', '::HIDE::') do |v|
+      cli[:ncbi_list_json] = v
+    end
   end
 
   def cli_name_modifiers(opt)
@@ -35,7 +38,9 @@ module MiGA::Cli::Action::Download::Ncbi
       'Only affects --complete and --chromosome'
     ) { |v| cli[:add_version] = v }
     # For backwards compatibility
-    cli.opt_flag(opt, 'legacy-name', '::HIDE::', :legacy_name)
+    opt.on('--legacy-name', '::HIDE::') do
+      warn 'Deprecated flag --legacy-name ignored'
+    end
   end
 
   def sanitize_cli
@@ -49,6 +54,11 @@ module MiGA::Cli::Action::Download::Ncbi
   end
 
   def remote_list
+    if cli[:ncbi_list_json] && File.size?(cli[:ncbi_list_json])
+      cli.say "Reusing remote list: #{cli[:ncbi_list_json]}"
+      return MiGA::Json.parse(cli[:ncbi_list_json])
+    end
+
     list  = {}
     query = remote_list_query
     loop do
@@ -66,6 +76,14 @@ module MiGA::Cli::Action::Download::Ncbi
       break unless page[:next_page_token]
       query[:page_token] = page[:next_page_token]
     end
+
+    if cli[:ncbi_list_json]
+      cli.say "Saving remote list: #{cli[:ncbi_list_json]}"
+      File.open(cli[:ncbi_list_json], 'w') do |fh|
+        fh.puts MiGA::Json.generate_plain(list)
+      end
+    end
+
     list
   end
   
@@ -80,7 +98,8 @@ module MiGA::Cli::Action::Download::Ncbi
       ds[n] = {
         ids: [asm], db: :assembly, universe: :ncbi,
         md: {
-          type: :genome, ncbi_asm: asm, strain: r.dig(:organism, :infraspecific_names, :strain)
+          type: :genome, ncbi_asm: asm,
+          strain: r.dig(:organism, :infraspecific_names, :strain)
         }
       }
       date = r.dig(:assembly_info, :release_date)

data/lib/miga/result/stats.rb

@@ -29,33 +29,15 @@ module MiGA::Result::Stats
     seq_opts = { gc: true, x: true, skew: true }
     if self[:files][:pair1].nil?
       s = MiGA::MiGA.seqs_length(file_path(:single), :fastq, seq_opts)
-      stats = {
-        reads: s[:n],
-        length_average: [s[:avg], 'bp'],
-        length_standard_deviation: [s[:sd], 'bp'],
-        g_c_content: [s[:gc], '%'],
-        x_content: [s[:x], '%'],
-        g_c_skew: [s[:gc_skew], '%'],
-        a_t_skew: [s[:at_skew], '%']
-      }
+      stats = seqs_length_as_stats_hash(s)
     else
-      s1 = MiGA::MiGA.seqs_length(file_path(:pair1), :fastq, seq_opts)
-      s2 = MiGA::MiGA.seqs_length(file_path(:pair2), :fastq, seq_opts)
-      stats = {
-        read_pairs: s1[:n],
-        forward_length_average: [s1[:avg], 'bp'],
-        forward_length_standard_deviation: [s1[:sd], 'bp'],
-        forward_g_c_content: [s1[:gc], '%'],
-        forward_x_content: [s1[:x], '%'],
-        forward_g_c_skew: [s1[:gc_skew], '%'],
-        forward_a_t_skew: [s1[:at_skew], '%'],
-        reverse_length_average: [s2[:avg], 'bp'],
-        reverse_length_standard_deviation: [s2[:sd], 'bp'],
-        reverse_g_c_content: [s2[:gc], '%'],
-        reverse_x_content: [s2[:x], '%'],
-        reverse_g_c_skew: [s2[:gc_skew], '%'],
-        reverse_a_t_skew: [s2[:at_skew], '%']
-      }
+      stats = { read_pairs: nil }
+      { pair1: :forward, pair2: :reverse }.each do |pair, direction|
+        s = MiGA::MiGA.seqs_length(file_path(pair), :fastq, seq_opts)
+        seqs_length_as_stats_hash(s).each do |k, v|
+          stats[k == :reads ? :read_pairs : :"#{direction}_#{k}"] ||= v
+        end
+      end
     end
     stats
   end
@@ -63,15 +45,7 @@ module MiGA::Result::Stats
   def compute_stats_trimmed_fasta
     f = self[:files][:coupled].nil? ? file_path(:single) : file_path(:coupled)
     s = MiGA::MiGA.seqs_length(f, :fasta, gc: true, x: true, skew: true)
-    {
-      reads: s[:n],
-      length_average: [s[:avg], 'bp'],
-      length_standard_deviation: [s[:sd], 'bp'],
-      g_c_content: [s[:gc], '%'],
-      x_content: [s[:x], '%'],
-      g_c_skew: [s[:gc_skew], '%'],
-      a_t_skew: [s[:at_skew], '%']
-    }
+    seqs_length_as_stats_hash(s)
   end
 
   def compute_stats_assembly
@@ -79,16 +53,17 @@ module MiGA::Result::Stats
       file_path(:largecontigs), :fasta,
       n50: true, gc: true, x: true, skew: true
     )
+    h = seqs_length_as_stats_hash(s)
     {
       contigs: s[:n],
       n50: [s[:n50], 'bp'],
       total_length: [s[:tot], 'bp'],
-      longest_sequence: [s[:max], 'bp'],
-      g_c_content: [s[:gc], '%'],
-      x_content: [s[:x], '%'],
-      g_c_skew: [s[:gc_skew], '%'],
-      a_t_skew: [s[:at_skew], '%']
-    }
+      longest_sequence: [s[:max], 'bp']
+    }.tap do |stats|
+      %i[g_c_content x_content g_c_skew a_t_skew].each do |i|
+        stats[i] = h[i]
+      end
+    end
   end
 
   def compute_stats_cds
@@ -253,4 +228,16 @@ module MiGA::Result::Stats
     add_file(:raw_report, "#{source.name}.ess/log")
     add_file(:report, "#{source.name}.ess/log.domain")
   end
+
+  def seqs_length_as_stats_hash(s)
+    {
+      reads: s[:n],
+      length_average: [s[:avg], 'bp'],
+      length_standard_deviation: [s[:sd], 'bp'],
+      g_c_content: [s[:gc], '%'],
+      x_content: [s[:x], '%'],
+      g_c_skew: [s[:gc_skew], '%'],
+      a_t_skew: [s[:at_skew], '%']
+    }
+  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, 9, 1].freeze
+  VERSION = [1.3, 9, 2].freeze
 
   ##
   # Nickname for the current major.minor version.

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 1.3.9.1
+  version: 1.3.9.2
 platform: ruby
 authors:
 - Luis M. Rodriguez-R