bacterial-annotator 0.3.6 → 0.3.7

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 57201d0ab8b7b095e6c33f8e446f907360bdb99f
-  data.tar.gz: cb08fd283c1d3c61b68d715c44217ad479dfba92
+  metadata.gz: 0f8c89d68e4afea5b49e88e68159f573b8fe44c1
+  data.tar.gz: a0742812f0e42a3346b63c79f590df774fb5e16c
 SHA512:
-  metadata.gz: 74860f69f0c777a40c9417f840ffc388d4ce81ccd0bf10d92eab63a38d6a5d0e231a80d4e2021d4a0a079742e54042996abf12e957987912d29b5d9bd20b22ab
-  data.tar.gz: 186cca9709f39f20e2cf5c6b4b57bea5df5cecfafd19bc9f3a635a3d22a709a09e4e3d75fa4bc42ade631d36d37e929418041bafe917abb88cf073475e9ab77a
+  metadata.gz: 0f8d59637356bc752bea3271d9f9d733eee83699928312becf7fbbf319ffc482e976c5dc7927f5ba300aa1b263b8909c63b8d17afb2e0c3d4a0b9497c5c49f80
+  data.tar.gz: 55857b474d7e88373d295f3bf8ea7d9d99d431b8192e8f24d63dec012a511725bad7f1e43edc6e7b1259688c9c84cc868d08c3add2b2e082efca085cf2636489

data/lib/bacterial-comparator.rb

@@ -41,9 +41,11 @@ class BacterialComparator
   end
 
   def read_prot_synteny
+    puts "# Reading genomes synteny files (from genome annotations) .."
     synteny = {}
     @genomes_list.each do |g|
-      puts "#{g}/Prot-Synteny.tsv"
+      puts "   #{g}/Prot-Synteny.tsv"
+      genome_synteny = []
       file = File.open("#{g}/Prot-Synteny.tsv", "r")
       l = file.gets             # skip header
       while l = file.gets
@@ -51,6 +53,12 @@ class BacterialComparator
         lA = l.chomp.split("\t")
         synteny[lA[0]] =  [] if ! synteny.has_key? lA[0]
         synteny[lA[0]] << {ref_cov: lA[3].to_f, pId: lA[4].to_f, query_prot: lA[5], query_cov: lA[7].to_f}
+        genome_synteny << lA[0]
+      end
+      @ref_prot.each do |ref_prot|
+        if ! genome_synteny.include? ref_prot
+          synteny[lA[0]] << {ref_cov: "-", pId: "-", query_prot: "-", query_cov: "-"}
+        end
       end
       file.close
     end
@@ -124,7 +132,7 @@ class BacterialComparator
 
   def extract_syntenic_fasta min_cov, min_pid
 
-    "# Extracting Proteins and Genes multifasta.."
+    puts "# Extracting Proteins and Genes multifasta.."
     nb_of_syntenic = 0
     stats = {}
     stats[:syntenic] = []
@@ -136,7 +144,7 @@ class BacterialComparator
     @synteny.each do |k,v|
       is_syntenic = 1
       v.each do |v_|
-        if v_[:query_cov].nil?
+        if v_[:query_cov] == "-"
           is_syntenic = 0
           break
         elsif v_[:query_cov] > min_cov and
@@ -149,16 +157,25 @@ class BacterialComparator
         end
       end
 
+      fout.write("#{k}")
       if is_syntenic == 1
         nb_of_syntenic += 1
         # build_multifasta k, v
         to_build_multifasta << [k,v]
-        fout.write("#{k}")
         v.each do |x|
-          fout.write("\t#{x[:query_prot]}|#{x[:query_cov]}|#{x[:ref_cov]}")
+          fout.write("\t#{x[:query_prot]}|#{x[:pId]}|#{x[:query_cov]}|#{x[:ref_cov]}")
           stats[:syntenic] << k
         end
         fout.write("\n")
+      else
+        v.each do |x|
+          if x[:pId] == 0.0
+            fout.write("\t-")
+          else
+            fout.write("\t#{x[:query_prot]}|#{x[:pId]}|#{x[:query_cov]}|#{x[:ref_cov]}")
+          end
+        end
+        fout.write("\n")
       end
 
     end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bacterial-annotator
 version: !ruby/object:Gem::Version
-  version: 0.3.6
+  version: 0.3.7
 platform: ruby
 authors:
 - Maxime Deraspe
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2017-01-19 00:00:00.000000000 Z
+date: 2017-01-25 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio