bacterial-annotator 0.3.5 → 0.3.6

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 62858524bd177b9b7db9ba7f0172a8acf00e0bc8
-  data.tar.gz: a0338a29fff5690cfcaea22f74449b05a59fcc19
+  metadata.gz: 57201d0ab8b7b095e6c33f8e446f907360bdb99f
+  data.tar.gz: cb08fd283c1d3c61b68d715c44217ad479dfba92
 SHA512:
-  metadata.gz: 5fa60b6872156f35ad82812c706e80e0500c1391cdd972d7a84a946a8f10b293b7c660017391c1346cbb5fd80be975eabe76da5dd44cc2a910e34949a7b91469
-  data.tar.gz: 84eeab61552c417fef7ff7e457fdf88064475ed1a0a36be26e21a69176fe47b3c749deefed57de82eb555feb1c111893c96bd189e9e2c67da8959afaf594359b
+  metadata.gz: 74860f69f0c777a40c9417f840ffc388d4ce81ccd0bf10d92eab63a38d6a5d0e231a80d4e2021d4a0a079742e54042996abf12e957987912d29b5d9bd20b22ab
+  data.tar.gz: 186cca9709f39f20e2cf5c6b4b57bea5df5cecfafd19bc9f3a635a3d22a709a09e4e3d75fa4bc42ade631d36d37e929418041bafe917abb88cf073475e9ab77a

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

@@ -18,7 +18,7 @@ class RemoteNCBI
   def initialize db, seq_file, outfile, pidentity
 
     if ! ["swissprot", "refseq_protein", "nr"].include? db
-      @db = "bad database"
+      @db = "nr"                # bad database
     else
       @db = db
     end

data/lib/bacterial-comparator.rb

@@ -64,6 +64,7 @@ class BacterialComparator
     flatfile.each_entry do |entry|
       ref_prot << entry.definition.split(" ")[0]
     end
+    flatfile.close
     ref_prot
   end
 
@@ -93,9 +94,11 @@ class BacterialComparator
       pep_file = Dir["#{@genomes_list[0]}/*.pep"]
       flatfile = Bio::FlatFile.auto("#{pep_file[0]}")
       pep_out.write(get_sequence_from_flatfile flatfile, ref_prot)
+      flatfile.close
       @genomes_list.each_with_index do |g,i|
         flatfile = Bio::FlatFile.auto("#{g}/Proteins.fa")
         pep_out.write(get_sequence_from_flatfile flatfile, synteny[i][:query_prot])
+        flatfile.close
       end
       pep_out.close
     end
@@ -107,9 +110,11 @@ class BacterialComparator
       dna_file = Dir["#{@genomes_list[0]}/*.dna"]
       flatfile = Bio::FlatFile.auto("#{dna_file[0]}")
       dna_out.write(get_sequence_from_flatfile flatfile, ref_prot)
+      flatfile.close
       @genomes_list.each_with_index do |g,i|
         flatfile = Bio::FlatFile.auto("#{g}/Genes.fa")
         dna_out.write(get_sequence_from_flatfile flatfile, synteny[i][:query_prot])
+        flatfile.close
       end
       dna_out.close
     end
@@ -276,6 +281,7 @@ class BacterialComparator
     Dir["*.aln"].each do |f|
       flat = Bio::FlatFile.auto(f)
       ref_seq = flat.entries[0]
+      flat.close
       seq += ref_seq.seq
     end
 
@@ -299,6 +305,7 @@ class BacterialComparator
             break
           end
         end
+        flat.close
       end
       bioseq = Bio::Sequence.auto(seq)
       out = bioseq.output_fasta("#{@genomes_list[i-1]}",60)

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bacterial-annotator
 version: !ruby/object:Gem::Version
-  version: 0.3.5
+  version: 0.3.6
 platform: ruby
 authors:
 - Maxime Deraspe
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2017-01-11 00:00:00.000000000 Z
+date: 2017-01-19 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio