miga-base 1.2.13.1 → 1.2.13.3

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 036b7181da39c88a4bf825230359f4efd9852b8aea488943028df6fde68184bf
-  data.tar.gz: 4584f52f0ea297120e23bec511850d2b2eeff7c3b76e1d013978f9a50ea5ea25
+  metadata.gz: d01c6cdd3ff689e80079b0bd59a63cc968b1b7e768518ce013d3c4d055032427
+  data.tar.gz: 1701cbb3a0c75dfe96ce6c1543f3aac6b35ba0dd87fb0f3f7ccc5e2780eaf7a3
 SHA512:
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-  data.tar.gz: 9bc1e223e57db9ce9675994fa4e1a7bb4b1aa5509a296295ad8743a4b02e9ece7efdfaec27287bf397f2cd941ac57a3e87e9ac5597516f292ebda8d5dcd726e8
+  metadata.gz: deec1e53d9dae1c995e59406a53b653f503e901821884b1b400da17c5330bbef5d344613fc7896961739cc66253604ad73947d20f178bf92f00f01881f16d0a6
+  data.tar.gz: d991c538708a72b3c9e65eb56a6e121fea4ab25f26838dbd706f27e16cb8d757346eabc9799a3f5b620df3f8e0c5456b65884e3d887f80d1f65f34b762bbfd59

data/lib/miga/result/stats.rb

@@ -164,18 +164,24 @@ module MiGA::Result::Stats
       lsu: 0, complete_lsu: 0, lsu_fragment: [0.0, '%']
     }
 
+    subunits = {
+      '16S_rRNA' => :ssu, '23S_rRNA' => :lsu,
+      '18S_rRNA' => :ssu, '28S_rRNA' => :lsu
+    }
     Zlib::GzipReader.open(file_path(:gff)) do |fh|
       fh.each_line do |ln|
         next if ln =~ /^#/
 
         rl = ln.chomp.split("\t")
         feat = Hash[rl[8].split(';').map { |i| i.split('=', 2) }]
-        subunit = feat['Name'] == '16S_rRNA' ? :ssu : :lsu
+        subunit = subunits[feat['Name']] or next # Ignore 5S
+
         if subunit == :ssu
           len = (rl[4].to_i - rl[3].to_i).abs + 1
           stats[:max_length] = [stats[:max_length] || 0, len].max
         end
-        stats[:ssu] += 1
+
+        stats[subunit] += 1
         if feat['product'] =~ /\(partial\)/
           if feat['note'] =~ /aligned only (\d+) percent/
             fragment = $1.to_f
@@ -185,7 +191,7 @@ module MiGA::Result::Stats
           end
         else
           stats[:"complete_#{subunit}"] += 1
-          stats[:"#{subunit}_fragment"] = [100.0, '%']
+          stats[:"#{subunit}_fragment"][0] = 100.0
         end
       end
     end
@@ -199,7 +205,7 @@ module MiGA::Result::Stats
         stats[:trna_count] += 1
         row = ln.chomp.split("\t")
         next if row[9] == 'pseudo' || row[4] == 'Undet'
-        aa[row[4].gsub(/^f?([A-Za-z]+)[0-9]?/, '\1')] = true
+        aa[row[4].gsub(/^[a-z]?([A-Za-z]+)[0-9]?/, '\1')] = true
       end
       stats[:trna_aa] = aa.size
     end if file_path(:trna_list)

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, 1].freeze
+  VERSION = [1.2, 13, 3].freeze
 
   ##
   # Nickname for the current major.minor version.
@@ -20,7 +20,7 @@ module MiGA
 
   ##
   # Date of the current gem relese.
-  VERSION_DATE = Date.new(2022, 12, 31)
+  VERSION_DATE = Date.new(2023, 1, 3)
 
   ##
   # References of MiGA

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 1.2.13.1
+  version: 1.2.13.3
 platform: ruby
 authors:
 - Luis M. Rodriguez-R
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2022-12-31 00:00:00.000000000 Z
+date: 2023-01-03 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: daemons