miga-base 1.2.13.0 → 1.2.13.2

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: c997637653ab5c7174be88b049f9ec78c432469a0bf08dc8c3572563480733b8
-  data.tar.gz: 731b7cad9da3266f2d21161dd5669d20214a648cded2a9cb9db3b0f23881a3fb
+  metadata.gz: 4251d1682329f32db78c304d4e35362930f004d07eedce3b176908d6d86f0bf0
+  data.tar.gz: dc3612cbdb962003ec0804b0bc556f30511a69f1a4d945f8b4fb41a7f1c99799
 SHA512:
-  metadata.gz: af2b18c2d3153ee02a8a7aa6f79efda6f451678e63353e9a9e02b9248915d63536ab46aabe5d9e55d942da51d38d66df77c67aa25e15e2df604cf1e6af075dc3
-  data.tar.gz: 3cce4b8c2cce42a87d31e93c14c7c838ad40a90b5daa3c4220070cada7c0b092dfcc7c76e6c3744dcb9d144d9570e552046a6fec82cadfced72857814be27c8a
+  metadata.gz: 969b506228f5757a0ff276bf39df6f3ba2c0eaf0549b60e672c239733cafc92db461c4d622d986e70e5b986c8200625946b3fcbcdebcbfe7a089021865788b60
+  data.tar.gz: 1851f909d65d61f724288830bd4475ce65d9fd16194dd9be1200d7723010cd1fc25f059a9c7c5ebbe6be2e74f2a52a39996aaa13e01d7e32cedf2a23bd228e11

data/lib/miga/result/stats.rb

@@ -160,33 +160,38 @@ module MiGA::Result::Stats
 
   def compute_stats_ssu
     stats = {
-      ssu: 0, complete_ssu: 0, ssu_fragment: 0.0,
-      lsu: 0, complete_lsu: 0, lsu_fragment: 0.0
+      ssu: 0, complete_ssu: 0, ssu_fragment: [0.0, '%'],
+      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
-            stats[:"#{subunit}_fragment"] ||= [fragment, '%']
             if fragment > stats[:"#{subunit}_fragment"][0]
               stats[:"#{subunit}_fragment"][0] = fragment
             end
           end
         else
           stats[:"complete_#{subunit}"] += 1
-          stats[:"#{subunit}_fragment"] = [100.0, '%']
+          stats[:"#{subunit}_fragment"][0] = 100.0
         end
       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 = [1.2, 13, 0].freeze
+  VERSION = [1.2, 13, 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: 1.2.13.0
+  version: 1.2.13.2
 platform: ruby
 authors:
 - Luis M. Rodriguez-R