bacterial-annotator 0.3.9 → 0.4.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: b46c0c48f45550ea7deb1580acb72927435df345
-  data.tar.gz: b5511795149b832c27fc8867dc3904c9c96d9561
+  metadata.gz: cd091580560639a95025ce9d6d188068ebd5518c
+  data.tar.gz: 3c470334e7aff680a48fe4132236d2bb646dedc5
 SHA512:
-  metadata.gz: ac790dd5249a74cf559912dc88ebaad614d3f934a43c297848e1bda2db146c682b11862489170ddc21683fed070509f505cdc6759530ab0e1d2f8c80d8951ac7
-  data.tar.gz: 0de96df50d2e3a1ad4274134969007b8efef2f1a63b24e7063c45f102c9020ba3e6c337de2214bc1a2f26ae1d33057d9ec7c6ef0ea182e23c77633b3cd8d5e0a
+  metadata.gz: 3ed95c575eb03b791c5f848a1417f4690f0141720992f2832ede949c1e81a7d8d74d3528d0951105affc3abcb2f4418ab89948c3cd4512cad1afeb7f3570d8d3
+  data.tar.gz: 90a71c6d106aef5fd570d7a3b497e5426bde5f72aad1eba533dde1b55530bb0c9e6282ceb54f174c80a68291b45161a5661d56ffd1dc0105456c57909f504095

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

@@ -176,9 +176,10 @@ class RemoteNCBI
                         split("; Flags:")[0].
                         split(" ; Short=")[0].strip
               gi = hit.hit_id.to_s.split("|")[1]
+              accession = hit.hit_accession.to_s
               organism = ""
               definition_clean = hit.definition.split(">")[0]
-              if ! definition_clean[/\[.*\]/].nil?                
+              if ! definition_clean[/\[.*\]/].nil?
                 organism = definition_clean[/\[.*\]/].gsub("[","").gsub("]","")
               end
               @aln_hits[prot_id] = {
@@ -186,7 +187,7 @@ class RemoteNCBI
                 length: hit.target_len.to_i,
                 evalue: hit.evalue,
                 score: hit.bit_score.to_f,
-                hits: [{gi: gi, product: product, org: organism}]
+                hits: [{gi: gi, accession: accession, product: product, org: organism}]
               }
             end
           end

data/lib/bacterial-annotator.rb

@@ -118,9 +118,7 @@ class BacterialAnnotator
       @rna_synteny.extract_hits_dna :rna
       @contig_annotations_rna = {}
       @fasta.prodigal_files[:contigs].each_with_index do |contig, contig_index|
-        puts "adding rna_annotation for contig #{contig}"
         @contig_annotations_rna[contig] = @rna_synteny.get_annotation_for_contig contig
-        p @contig_annotations_rna[contig]
       end
 
     else                        # no reference genome
@@ -250,7 +248,7 @@ class BacterialAnnotator
       gbk_to_annotate.add_annotations contig_prot_annotations, "inplace", reference_locus
 
       if @contig_annotations_rna.has_key? contig
-        puts "Trying RNA annotation"
+        # puts "RNA annotation"
         gbk_to_annotate.add_annotations @contig_annotations_rna[contig], "new"
       end
 

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bacterial-annotator
 version: !ruby/object:Gem::Version
-  version: 0.3.9
+  version: 0.4.0
 platform: ruby
 authors:
 - Maxime Deraspe
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2017-02-13 00:00:00.000000000 Z
+date: 2017-02-14 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio