bacterial-annotator 0.1.1 → 0.1.2

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 4279f5b2fc1e4d06ddaeb71c64e7202a344a58b2
-  data.tar.gz: 8a41abd4a1d5dc494636f8a048f193c83330cb1b
+  metadata.gz: e6e8bf0af45b396f1d4744782ef0f929e293c0d6
+  data.tar.gz: 21bcec3c99368690310f7e49752c87b0fa3c3290
 SHA512:
-  metadata.gz: 4ec21441d9c0d9666312972fed6ebd556115b59d0e8fc2b4d7579ac5b35169f6be02c5847a1fe2679fb24df36edf2002c56c926f02707253c3a0583633a7bc1e
-  data.tar.gz: fa310f9eb690b1181c48fd96e7cf3e44065b6e0c7f0cdd00902f1c1c8fc42c612ebeac4b48f585338285bfed8fd66481ec271dbc622af0aa2611462ec0f7b2e4
+  metadata.gz: d67ddd90fb1e96418bbd6bd64cacd7a665f7645b8857b1aee71b9e5ec3c083917f2f8a35a55f14167eb5938274e1c0ab3dd2a4abce0f8bfc802814b2f1f69a39
+  data.tar.gz: 3436ea2e71a099632c2068e7679515a4bc7c85fccbea05fd4f8d79cebccd618b624d6c7e2c70c553fd366abb4142275ee3568de7cbe1d1b7e208290494bcdc48

data/lib/bacterial-annotator/genbank-manip.rb

@@ -102,7 +102,7 @@ class GenbankManip
 
 
   # add annotation to a genbank file produced by prodigal
-  def add_annotation annotations, outdir, mode
+  def add_annotation annotations, outdir, mode, reference_locus
 
     nb_of_added_ft = 0
     i = 0
@@ -134,6 +134,7 @@ class GenbankManip
         gene = hit[:gene]
         product = hit[:product]
         note = hit[:note]
+        pId = hit[:pId]
 
         if gene != nil
           qGene = Bio::Feature::Qualifier.new('gene', gene)
@@ -146,7 +147,7 @@ class GenbankManip
         end
 
         if locus != nil
-          qNote = Bio::Feature::Qualifier.new('note', "correspond to #{locus} locus")
+          qNote = Bio::Feature::Qualifier.new('note', "correspond to #{locus} locus (#{pId}% identity) from #{reference_locus.entry_id}")
           ftArray.push(qNote)
         end
 

data/lib/bacterial-annotator/remote-ncbi.rb

@@ -174,7 +174,7 @@ class RemoteNCBI
                         gsub("RecName: Full=","").
                         split("; AltName")[0].
                         split("; Flags:")[0].
-                        split(" ; Short=")[0]
+                        split(" ; Short=")[0].strip
               gi = hit.hit_id.to_s.split("|")[1]
               organism = ""
               definition_clean = hit.definition.split(">")[0]
@@ -182,7 +182,7 @@ class RemoteNCBI
                 organism = definition_clean[/\[.*\]/].gsub("[","").gsub("]","")
               end
               @aln_hits[prot_id] = {
-                pId: hit.identity.to_f/hit.target_len.to_f*100,
+                pId: (hit.identity.to_f/hit.target_len.to_f*100).round(2),
                 length: hit.target_len.to_i,
                 evalue: hit.evalue,
                 score: hit.bit_score.to_f,

data/lib/bacterial-annotator/synteny-manip.rb

@@ -44,7 +44,7 @@ class SyntenyManip
         if ! @aln_hits.has_key? key
           next if lA[2].to_f < @pidentity
           @aln_hits[key] = {
-            pId: lA[2].to_f,
+            pId: lA[2].to_f.round(2),
             length: lA[3].to_i,
             evalue: lA[10],
             score: lA[11].to_f,
@@ -52,7 +52,7 @@ class SyntenyManip
           }
         elsif lA[11].to_f > @aln_hits[key][:score]
           @aln_hits[key] = {
-            pId: lA[2].to_f,
+            pId: lA[2].to_f.round(2),
             length: lA[3].to_i,
             evalue: lA[10],
             score: lA[11].to_f,
@@ -101,6 +101,7 @@ class SyntenyManip
         h = @aln_hits[p][:hits][hit_index]
         hit = ref_cds[h]
         annotations[p] = hit
+        annotations[p][:pId] = @aln_hits[p][:pId]
         i+=1
 
       else

data/lib/bacterial-annotator.rb

@@ -147,7 +147,7 @@ class BacterialAnnotator
 
         hit_gi = v[:hits][0]
 
-        note = "correspond to gi:#{hit_gi}"
+        note = "Protein homology (#{v[:pId]}% identity) with gi:#{hit_gi}"
 
         # p v
         # p ref_cds[hit_gi]
@@ -200,7 +200,9 @@ class BacterialAnnotator
             if ! @contig_annotations.has_key? contig_of_protein
               @contig_annotations[contig_of_protein] = {}
             end
-            note = "correspond to gi:#{v[:hits][0][:gi]}"
+
+            note = "Protein homology (#{v[:pId]}% identity) with gi:#{v[:hits][0][:gi]}"
+            # note = "correspond to gi:#{v[:hits][0][:gi]}"
             if v[:hits][0][:org] != ""
               note +=  " from #{v[:hits][0][:org]}"
             end
@@ -226,7 +228,7 @@ class BacterialAnnotator
     @contig_annotations.each do |contig, contig_prot_annotations|
       gbk_path = @fasta.prodigal_files[:gbk_path]
       gbk_to_annotate = GenbankManip.new("#{gbk_path}/#{contig}.gbk", "#{gbk_path}")
-      gbk_to_annotate.add_annotation contig_prot_annotations, gbk_path, 0
+      gbk_to_annotate.add_annotation contig_prot_annotations, gbk_path, 0, @refgenome.gbk.locus
     end
 
   end                           # end of method

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bacterial-annotator
 version: !ruby/object:Gem::Version
-  version: 0.1.1
+  version: 0.1.2
 platform: ruby
 authors:
 - Maxime Deraspe
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-04-17 00:00:00.000000000 Z
+date: 2015-04-20 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio