bacterial-annotator 0.5.0 → 0.5.1

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: befd57ce78f0c186da1553c7372c3aa6faeb9d90
-  data.tar.gz: 5e37d6a7e579a1e9e428deb9864e4a9d5ea9f057
+  metadata.gz: 6b2b8f795b50e094ffd301c5394515668f6b9952
+  data.tar.gz: c156912ed593c75aebd43d0ff96e3830e642210b
 SHA512:
-  metadata.gz: a9a9766113cef56ae7ed35749cd5fbc10d746aa82e403596dccd0c5e7946786b136a69e19c74a4cece73549b0f1a8de077a8c106fc0e2310f7b000dc6cbad962
-  data.tar.gz: 00a0c5cf815252fa45ffae194318f730cf69e27dd53643659fb06d2dac131a3de881cbad2595b43df6ba5014be75cef8b337e6710afb46e42b420fdd1cf9b178
+  metadata.gz: 8bece4ed7722eafc0be05f4e57f449cfa68d44397c1621a84b1dfe0224599f6f575bd5e1d77c1fe486e582adcbac452270e6ef0720bb084720fa1e7a35f2f2c1
+  data.tar.gz: 04f636eca3997c507720a8deb65a7234fc82dc8a3fa990206a03a67c36bf843690087699d18aabc789cccf584fe3192a27182ee27528c3fc55b8091000bfb86d

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

@@ -277,8 +277,6 @@ class SequenceAnnotation
     # nb_of_added_ft = 0
     i = 0
 
-    fdebug = File.open("debug-add-annotation.txt","w")
-
     contig = @gbk.definition
 
     if mode == "inplace"
@@ -304,9 +302,6 @@ class SequenceAnnotation
 
         if hit != nil
 
-          fdebug.write(hit)
-          fdebug.write("\n")
-
           locus, gene, product, note = nil
           locus = hit[:locustag]
           gene = hit[:gene]
@@ -380,8 +375,6 @@ class SequenceAnnotation
 
     end
 
-    fdebug.close
-
   end
 
 

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

@@ -294,10 +294,6 @@ class SequenceSynteny
           annotations[p][:length] = @aln_hits[p][:length][hit_index]
           i+=1
 
-          File.open("debug-annotation-by-contig.txt","a") do |fout|
-            fout.write("#{p} #{@aln_hits[p][:pId]} #{@aln_hits[p][:cov_query]} #{@aln_hits[p][:cov_subject]} #{ref_cds[h][:product]}\n")
-          end
-
         else
 
           annotations[p] = nil

data/lib/bacterial-annotator.rb

@@ -95,18 +95,12 @@ class BacterialAnnotator
 
     ref_synteny_prot.extract_hits :refgenome
 
-    fdebug = File.open("debug-synteny.tsv", "w")
-
     ref_synteny_prot.query_sequences.each do |k,v|
       if v.has_key? :homology
         @contig_annotations_cds[v[:contig]] = [] if ! @contig_annotations_cds.has_key? v[:contig]
         @contig_annotations_cds[v[:contig]] << k
-        fdebug.write("#{v[:contig]}\t#{k}\t#{v[:homology][:pId]}\t#{v[:homology][:cov_query]}\t#{v[:homology][:cov_subject]}\t#{v[:homology][:hits].join(',')}\t#{@ref_genome.coding_seq[v[:homology][:hits][0]][:locustag]}\t#{@ref_genome.coding_seq[v[:homology][:hits][0]][:product]}\t#{v[:homology][:assert_cutoff].join(',')}\n")
-      else
-        fdebug.write("#{v[:contig]} #{k} NONE...\n")
       end
     end
-    fdebug.close
 
     ref_synteny_prot
 
@@ -249,7 +243,7 @@ class BacterialAnnotator
         gbk_to_annotate.add_annotation_ref_synteny_prot(
           (@prot_synteny_refgenome.query_sequences.merge(@externaldb_synteny.query_sequences)),
           @contig_annotations_externaldb[contig].merge(@ref_genome.coding_seq),
-          @options[:refgenome].gsub(/.gb.*/,"")
+          (File.basename @options[:refgenome]).gsub(/.gb.*/,"")
         )
       else
         gbk_to_annotate.add_annotation_ref_synteny_prot(

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bacterial-annotator
 version: !ruby/object:Gem::Version
-  version: 0.5.0
+  version: 0.5.1
 platform: ruby
 authors:
 - Maxime Deraspe
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2017-05-30 00:00:00.000000000 Z
+date: 2017-05-31 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio
@@ -71,7 +71,7 @@ dependencies:
       - !ruby/object:Gem::Version
         version: 1.9.0
 description: GEM to annotate bacterial genome sequence based on a reference genome
-  and complete the annotation with an external database or a remote database.
+  and complete the annotation with an external database.
 email: maximilien1er@gmail.com
 executables:
 - bacterial-annotator