bacterial-annotator 0.5.4 → 0.5.5

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 27f8cdf5e843b97030798ac29fc23bf1cc54bb5a
-  data.tar.gz: 77592401985aa2e22cb683c9561f63ef3d23d329
+  metadata.gz: 8ab5e91d3ae7a0f2f62ca3ea90de6e84b0686130
+  data.tar.gz: c0df480e3019afc0d152e25134f3b73a2a57c970
 SHA512:
-  metadata.gz: 15550bd245a460a16507132cf8cec2524b4724cffa909da983f46ce9531c957fbe5e22456973323fe1e2b0af2d0323333642c9c741fa5b614e482a2d0d3afb6a
-  data.tar.gz: 309de7383bbffe46cf68ab5436fc02b095e6069ec769e47b17a5c2e632fa7532e76e4ae399cbcfade0495b633f2fb07da9b77b8590693c9f63f5454e791cfa3a
+  metadata.gz: bea8cc8a8a8ffc3ccda0a2dc222046be507d8fba2e95a17ee84e93330b974584e5562658f8cfd8e512384ba615b40800258628588d0f3b5ed34af3aa587f398d
+  data.tar.gz: 26b0cbeff8c9142c6585bd73ff03fbafeb0cb8be953a846b2ed6ffdad80e355cf78cdeb131ac91624e85bf83e9a6cda049eb5a6983e5ff36c91c5d47ad4209f2

data/lib/bacterial-annotator/sequence-annotation.rb

@@ -196,70 +196,81 @@ class SequenceAnnotation
 
       hit = nil
 
-      next if ! synteny_prot.has_key? prot_id or
-        ! synteny_prot[prot_id].has_key? :homology
+      if ! synteny_prot.has_key? prot_id or
+         ! synteny_prot[prot_id].has_key? :homology or
+         ! annotations.has_key? synteny_prot[prot_id][:homology][:hits][0] or
+         synteny_prot[prot_id][:homology][:assert_cutoff].inject(:+) < 3
+
+        qLocusTag = Bio::Feature::Qualifier.new('locus_tag', "#{prot_id}")
+        qProd = Bio::Feature::Qualifier.new('product', "hypothetical protein")
+
+        ftArray.push(qLocusTag)
+        ftArray.push(qProd)
+
+        if synteny_prot.has_key? prot_id and
+          synteny_prot[prot_id].has_key? :homology and
+          synteny_prot[prot_id][:homology][:assert_cutoff] == [1,1,0]
+          hit = annotations[synteny_prot[prot_id][:homology][:hits][0]]
+          qNote = Bio::Feature::Qualifier.new('note', "possible pseudo gene of #{hit[:locustag]} from #{ref_genome}")
+          ftArray.push(qNote)
+        end
 
-      # puts "#{annotations.keys}"
-      if annotations.has_key? synteny_prot[prot_id][:homology][:hits][0]
-        hit = annotations[synteny_prot[prot_id][:homology][:hits][0]]
-        # puts hit
       else
-        puts "no hit for #{prot_id}"
-        next
-      end
 
-      # hit = annotations[synteny_prot[prot_id][:homology][:hits][0]]
+        hit = annotations[synteny_prot[prot_id][:homology][:hits][0]]
 
-      if synteny_prot.has_key? prot_id
+        if synteny_prot.has_key? prot_id
 
-        locus, gene, product, note, inference = nil
-        locus = hit[:locustag]
-        gene = hit[:gene]
-        product = hit[:product]
-        note = hit[:note]
-        inference = hit[:inference]
-        pId = synteny_prot[prot_id][:homology][:pId]
-        cov_query = (synteny_prot[prot_id][:homology][:cov_query]*100).round(2)
-        cov_subject = (synteny_prot[prot_id][:homology][:cov_subject]*100).round(2)
-        reference_prot_id = synteny_prot[prot_id][:homology][:hits][0]
+          locus, gene, product, note, inference = nil
+          locus = hit[:locustag]
+          gene = hit[:gene]
+          product = hit[:product]
+          note = hit[:note]
+          inference = hit[:inference]
+          pId = synteny_prot[prot_id][:homology][:pId]
+          cov_query = (synteny_prot[prot_id][:homology][:cov_query]*100).round(2)
+          cov_subject = (synteny_prot[prot_id][:homology][:cov_subject]*100).round(2)
+          reference_prot_id = synteny_prot[prot_id][:homology][:hits][0]
 
-        qLocusTag = Bio::Feature::Qualifier.new('locus_tag', "#{prot_id}")
-        ftArray.push(qLocusTag)
+          qLocusTag = Bio::Feature::Qualifier.new('locus_tag', "#{prot_id}")
+          ftArray.push(qLocusTag)
 
-        if gene != nil
-          qGene = Bio::Feature::Qualifier.new('gene', gene)
-          ftArray.push(qGene)
-        end
+          if gene != nil
+            qGene = Bio::Feature::Qualifier.new('gene', gene)
+            ftArray.push(qGene)
+          end
 
-        if product != nil
-          qProd = Bio::Feature::Qualifier.new('product', product)
-          ftArray.push(qProd)
-        end
+          if product != nil
+            qProd = Bio::Feature::Qualifier.new('product', product)
+            ftArray.push(qProd)
+          end
 
-        # check if there is a reference genome.. reference_locus shouldn't be nil in that case
-        if locus != nil
-          qNote = Bio::Feature::Qualifier.new('note', "corresponds to #{locus} locus (AA identity: #{pId}%; coverage(q,s): #{cov_query}%,#{cov_subject}%) from #{ref_genome}")
-          ftArray.push(qNote)
+          # check if there is a reference genome.. reference_locus shouldn't be nil in that case
+          if locus != nil
+            qNote = Bio::Feature::Qualifier.new('note', "corresponds to #{locus} locus (AA identity: #{pId}%; coverage(q,s): #{cov_query}%,#{cov_subject}%) from #{ref_genome}")
+            ftArray.push(qNote)
+
+            db_source = "[DBSource]"
+            if reference_prot_id.include? "_"
+              db_source = "RefSeq"
+            else
+              db_source = "INSD"
+            end
+            qInference = Bio::Feature::Qualifier.new('inference', "similar to AA sequence:#{db_source}:#{reference_prot_id}")
+            ftArray.push(qInference)
 
-          db_source = "[DBSource]"
-          if reference_prot_id.include? "_"
-            db_source = "RefSeq"
-          else
-            db_source = "INSD"
           end
-          qInference = Bio::Feature::Qualifier.new('inference', "similar to AA sequence:#{db_source}:#{reference_prot_id}")
-          ftArray.push(qInference)
 
-        end
+          if note != nil
+            qNote = Bio::Feature::Qualifier.new('note', note)
+            ftArray.push(qNote)
+          end
 
-        if note != nil
-          qNote = Bio::Feature::Qualifier.new('note', note)
-          ftArray.push(qNote)
-        end
+          if inference != nil
+            qInference = Bio::Feature::Qualifier.new('inference', inference)
+            ftArray.push(qInference)
+          end
 
-        if inference != nil
-          qInference = Bio::Feature::Qualifier.new('inference', inference)
-          ftArray.push(qInference)
         end
 
       end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bacterial-annotator
 version: !ruby/object:Gem::Version
-  version: 0.5.4
+  version: 0.5.5
 platform: ruby
 authors:
 - Maxime Deraspe
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2017-06-07 00:00:00.000000000 Z
+date: 2017-06-08 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio