bacterial-annotator 0.5.2 → 0.5.3

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 7ccf904ff27565f88102eb137eadd2103b8e13a5
-  data.tar.gz: 51d6b4c6092e9e7bee7319759de3485c09be8b7c
+  metadata.gz: 48eb79f1ebdf63ad829fe850b9b32db0d89fb3e5
+  data.tar.gz: b0ab93f6623dd6f42fce8dc928b190fda4a1f683
 SHA512:
-  metadata.gz: 12956c4a2c7573735df00228ee645033ebd4a241fca7609342b5cc79f22878c04d4c511d96d05fd9ace582c9f8121090cd85153733b003691156e389ae4c8858
-  data.tar.gz: 417d927324031db3417270df515b2a8d6e346a068c061de2ef346498c785818733921811dff3a8c91e6647f405d19f8e9640cc6c971ed1113d7d66618c756bc8
+  metadata.gz: 17756ba0df70b305ee13deefc9e7f1443858a40deb3f1a9b22f561ca3fb0af5dab82257c809cabd5e255c97b4acf4eace32b61b5536a5651da5efc1a0221aa1a
+  data.tar.gz: d46c6b211ea1674b55dbf7b2a8077e7806b8379951fbe962c2ccc5e8f820eba8742ba04d25e6b840dbf04cd3008ed570a8dd4ad756a20886d9e7c1c5c58aa81e

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

@@ -76,6 +76,7 @@ class SequenceAnnotation
           bioseq_gene: dnaBioSeq,
           bioseq_len: pepBioSeq.length
         }
+
       end
 
     end

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

@@ -164,7 +164,7 @@ class SequenceFasta
       prot_ids[contig] << prot_id
 
       # puts "Prodigal length : " + entry.seq.length.to_s
-      prot_length[prot_id] = entry.seq.length-1 # minus the stop codon
+      prot_length[prot_id] = entry.seq.length
 
     end
 

data/lib/bacterial-annotator.rb

@@ -128,7 +128,7 @@ class BacterialAnnotator
 
         remaining_cds = cumulate_annotation_stats_reference contig
 
-        if ! remaining_cds.empty?
+        if remaining_cds != []
           @contig_foreign_cds[contig] = remaining_cds
         end
 
@@ -503,6 +503,19 @@ class BacterialAnnotator
     synteny_file = File.open("#{@options[:outdir]}/Prot-Synteny.tsv","w")
     synteny_file.write("RefLocusTag\tRefProtID\tRefLength\tRefCoverage\tIdentity\tQueryGene\tQueryLength\tQueryCoverage\n")
     ref_annotated = {}
+
+    @prot_synteny_refgenome.query_sequences.each do |prot, syn_val|
+      next if ! syn_val.has_key? :homology
+      ref_annotated[syn_val[:homology][:hits][0]] = {
+        key: prot,
+        pId: syn_val[:homology][:pId],
+        cov_query: syn_val[:homology][:cov_query],
+        cov_subject: syn_val[:homology][:cov_subject],
+        assert_cutoff: syn_val[:homology][:assert_cutoff],
+        length: syn_val[:homology][:length][0]
+      }
+    end
+
     @contig_annotations.each do |contig, prot_annotations|
       prot_annotations.each do |key,prot|
         ref_annotated[prot[:protId]] = {key: key, length: prot[:length], pId: prot[:pId]} if prot != nil
@@ -518,9 +531,9 @@ class BacterialAnnotator
       pId = ""
       if ref_annotated[ref_v[:protId]] != nil
         gene = ref_annotated[ref_v[:protId]][:key]
-        coverage_ref = (ref_annotated[ref_v[:protId]][:length].to_f/ref_v[:bioseq].seq.length.to_f).round(2)
+        coverage_ref = ref_annotated[ref_v[:protId]][:cov_subject]
         query_length = @query_fasta.annotation_files[:prot_ids_length][gene]
-        coverage_query = (ref_annotated[ref_v[:protId]][:length].to_f/query_length.to_f).round(2)
+        coverage_query = ref_annotated[ref_v[:protId]][:cov_query]
         pId = ref_annotated[ref_v[:protId]][:pId]
       end
 
@@ -535,6 +548,7 @@ class BacterialAnnotator
       synteny_file.write("\n")
 
     end
+
     synteny_file.close
 
   end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bacterial-annotator
 version: !ruby/object:Gem::Version
-  version: 0.5.2
+  version: 0.5.3
 platform: ruby
 authors:
 - Maxime Deraspe
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2017-05-31 00:00:00.000000000 Z
+date: 2017-06-06 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio