bacterial-annotator 0.1.5 → 0.1.6

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 5515eba9f5210f5ab1ec8d32ec6c88f3ef1579b9
-  data.tar.gz: eb6abf3a4b876c8078c5dfb3c1e19ed9a17dc76e
+  metadata.gz: 394e3bf854b173d4998e9d26aad260ba63ecc4fd
+  data.tar.gz: 34de847a44130804fd4886e64cc6b51d3e568991
 SHA512:
-  metadata.gz: 4c55bca9cea54aaf3104a0b1bf7d34e3390b3971b234391f39ad95b043d1320ee2abbb0092a3a387d87b7ed258cd2be4bbc65ed37bf24811f434ca878f99ea60
-  data.tar.gz: b33840baec3794e1a9509026c1da43f3ac27438cd7c53be1cd4373548c22f9c760efab4f48a54e77c9e6341143d2c47834a26223afcb7fe38fe1cfcccd02d9af
+  metadata.gz: baea5e38ce01916a1e9f0444b238ee62c9f6915139e2d8109ec1590948a52081accdfbca1897cc5af826bfc7a59a51b9eeb3c9f5e6c5d5689766a6d6be517283
+  data.tar.gz: 2c834356aec685bdc2bd910cf7150ee5212e075d0f4ef253da18577a96243aed51015b9a56ef20c9f3992d9bc3d5ff435af473045c9a728d2e97a25845d3dd39

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

@@ -86,13 +86,13 @@ class FastaManip
           day = "%02d" % date.day
           year = date.year
           locus = "LOCUS       #{file_name}#{spacer}#{seq_length.to_s} bp    DNA     linear   BCT #{day}-#{month}-#{year}\n"
+          locus += "DEFINITION  #{file_name}\n"
           fopen = File.open("#{outdir}/single-genbank/#{file_name}.gbk", "w")
           fopen.write(locus)
-          fopen.write(l)
         elsif l[0..1] == "//"
           fopen.write(outseq)
           fopen.close
-        else
+        elsif ! l.include? "                     /note="
           fopen.write(l)
         end
       end

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

@@ -106,11 +106,8 @@ class GenbankManip
 
     nb_of_added_ft = 0
     i = 0
-    contig = @gbk.definition.split(";")[2].
-             gsub("seqhdr","").
-             delete("\"").
-             delete("=").
-             split(" ")[0]
+
+    contig = @gbk.definition
 
     # iterate through 
     @gbk.features.each_with_index do |cds, ft_index|
@@ -119,6 +116,7 @@ class GenbankManip
 
       if mode == 0
         ftArray = []
+        cds.qualifiers = []
       else
         ftArray = cds.qualifiers
       end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bacterial-annotator
 version: !ruby/object:Gem::Version
-  version: 0.1.5
+  version: 0.1.6
 platform: ruby
 authors:
 - Maxime Deraspe
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-06-03 00:00:00.000000000 Z
+date: 2015-06-04 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio