bacterial-annotator 0.8.8 → 0.8.9

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: b629352a56f96c69564434da84bf58732e519ec6e064551e7cf7a0871a7050a1
-  data.tar.gz: 1659b196791b259db68053ef83ae74acd453f92814ffba807a1b2af87026acb3
+  metadata.gz: 1dc26e2ae283ea0c8163e7c487c95bf0f0b7cffa4095d841b38e709262698a52
+  data.tar.gz: be699876985f29d8269119852b6f027f562c541263abb6afe29b84783375ad3b
 SHA512:
-  metadata.gz: 0cecffe0d0f8ac6cf1c41783927594cdcf952d90b35e5d115efad0a0e87a2d89f6b573397973bcdfd2c390d3f6e08172b3f94c9352e68d0c1d33ecbbfdd19f0f
-  data.tar.gz: bcbddbdf09266cbda5529b60c952afa7e3d92f3b4f14eec1c878ebb2b6a66130f2f0857d54a5f0680fbab3f47dc12bdfc8872387cbe08a085ec793f166c8f6cf
+  metadata.gz: a7615dee5f7d89e8224477dc94798621d72ab8923d1b7027c9b912f46f9fca85beb71bf1b3cd7a058fa27503b07a244ecd97a71330c0816d4b3c41b4f8795e55
+  data.tar.gz: 813dc52e3732accd812e54a9ad998fee65e01cdec8bf79c136c59262512683ed32656e88e860476f405e08441723eef6681648d972f17237ec80d88a64a8a46d

data/bin/bacterial-annotator

@@ -194,6 +194,11 @@ def parseOptions_compare
   options[:software] = "fasttree"
   options[:bootstrap] = 100
 
+  if ARGV.length == 0
+    usage_compare
+    abort
+  end
+
   while x = ARGV.shift
 
     case x.downcase
@@ -254,6 +259,11 @@ def parseOptions_identify
   options[:genome_list] = []
   options[:output] = "tsv"
 
+  if ARGV.length == 0
+    usage_identify
+    abort
+  end
+
   while x = ARGV.shift
 
     case x.downcase

data/lib/bacterial-annotator.rb

@@ -369,6 +369,20 @@ class BacterialAnnotator
           inference: inference
         }
 
+        @annotation_stats[:flagged_cds].each do |flag|
+          if flag.include? "#{k}"
+            if v[:homology][:assert_cutoff].inject(:+) > 2
+              flag.replace("#{flag}\tAnnotated by externaldb (#{v[:homology][:hits][0]}|#{v[:homology][:pId]}|#{cov_query}|#{cov_subject}))")
+            elsif v[:homology][:assert_cutoff] == [1,1,0]
+              flag.replace("#{flag}\tPossible pseudogene (coverage subject = #{cov_subject} with #{v[:homology][:hits][0]}))")
+            elsif v[:homology][:assert_cutoff] == [1,0,1]
+              flag.replace("#{flag}\tPossible pseudogene (coverage query = #{cov_query} with #{v[:homology][:hits][0]}))")
+            elsif v[:homology][:assert_cutoff] == [0,1,1]
+              flag.replace("#{flag}\tLow similarity (percent identity = #{v[:homology][:pId]} with #{v[:homology][:hits][0]}))")
+            end
+          end
+        end
+
       end
 
     end
@@ -463,6 +477,7 @@ class BacterialAnnotator
             flag += "\t#{(@prot_synteny_refgenome.query_sequences[prot][:homology][:cov_query]*100).round(2)}"
             flag += "\t#{(@prot_synteny_refgenome.query_sequences[prot][:homology][:cov_subject]*100).round(2)}"
             @annotation_stats[:flagged_cds] << flag
+            remaining_cds << prot
           end
 
         else
@@ -515,7 +530,7 @@ class BacterialAnnotator
 
     file_flagged_cds = file_dir + "/Prot-flagged.tsv"
     File.open(file_flagged_cds, "w") do |fopen|
-      fopen.write("CDS locus\tAssertion-CutOff\tAA Identity\tCovQuery(%)\tCovSubject(%)\n")
+      fopen.write("CDS locus\tAssertion-CutOff\tAA Identity\tCovQuery(%)\tCovSubject(%)\tNote\n")
       @annotation_stats[:flagged_cds].each do |fcds|
         fopen.write("#{fcds}\n")
       end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bacterial-annotator
 version: !ruby/object:Gem::Version
-  version: 0.8.8
+  version: 0.8.9
 platform: ruby
 authors:
 - Maxime Deraspe
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2018-08-02 00:00:00.000000000 Z
+date: 2018-10-17 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio