bacterial-annotator 0.9.1 → 0.9.3

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: c3f04aa6e41b8214a3f3d46b77afc21f8c4471326721cf29aae3c810d798b553
-  data.tar.gz: 959c216c280eb6c62f4b27bc01b03f59f00efef9e393d036cc04519ab7f6c54a
+  metadata.gz: e6b26cd37618fedd557b8d9f7fe2c27a3b95dee5404d7751a8fb10ddcb63edc8
+  data.tar.gz: 2129f8372c3a48654cf3bdf6b75eccce3148b45f0e15191f3a555ff0769f9bd4
 SHA512:
-  metadata.gz: ef78d609d9c3bb1a0af64d4f662206038683c67cb3a55386e5dcde0e3200cbc4ecdf6d5844bb361fb5841e247b1d2e19fc4e1d68c7db963fa8cdcf6e564c9453
-  data.tar.gz: b58553928bf63cbbf845a84ddb30765ebb04ec83e73494bf8caaf2784b3c29a5bf17f9c587c99feb7bf80f24eb041f331618705d61d04bf4191628dd8d48af73
+  metadata.gz: 2400660df26bab507b5f9a3310105514d415a4950a06fdb7a3cbc9a4de2b4268d77c3725a13507e19c92fcdcc688f2bda4184aeadb88afd4a444addce1117fb9
+  data.tar.gz: 9caef8af954e6de43ed3eb2cd5a729065bafd2451aa5c73e00e60b400cb849666a53fb1e39d549f4b33925edbfea33f209a966da7f64d91ac1aa3d8b75e5f4d2

data/bin/ba_diamond

@@ -2,28 +2,27 @@
 # -*- coding: utf-8 -*-
 # author:  	maxime déraspe
 # email:	maximilien1er@gmail.com
-# review:  	
+# review:
 # date:    	17-08-24
 # version: 	0.01
-# licence:  	
+# licence:
 
 require 'open-uri'
 
 ROOT_path = File.dirname(__FILE__)
-# diamond URL = "https://github.com/bbuchfink/diamond/releases/download/v0.9.10/diamond-linux64.tar.gz"
+# diamond URL = "https://github.com/bbuchfink/diamond/releases/download/v2.0.15/diamond-linux64.tar.gz"
 
 # Install diamond on the user system
 def installDiamond
 
   begin
-    resp = open("https://github.com/bbuchfink/diamond/releases/download/v0.9.10/diamond-linux64.tar.gz")
+    resp = open("https://github.com/bbuchfink/diamond/releases/download/v2.0.15/diamond-linux64.tar.gz")
     open("#{ROOT_path}/diamond-linux64.tar.gz", "wb") do |file|
       file.write(resp.read)
     end
     Dir.chdir("#{ROOT_path}/")
     `tar xvf diamond-linux64.tar.gz; rm diamond-linux64.tar.gz`
     `mv diamond ./diamond.linux`
-    `rm diamond_manual.pdf`
     File.chmod(0755, "#{ROOT_path}/diamond.linux")
   rescue
     abort "Problem installing Diamond, aborting"
@@ -43,4 +42,3 @@ if ! File.exists? "#{ROOT_path}/diamond.linux"
   puts ""
 
 end
-

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

@@ -3,7 +3,7 @@
 # email:	maximilien1er@gmail.com
 # date:    	15-02-24
 # version: 	0.0.1
-# licence:  	
+# licence:
 
 require 'json'
 require 'zlib'
@@ -104,7 +104,16 @@ class SequenceAnnotation
     if flat_gbk.dbclass != Bio::GenBank
       abort "Aborting : The input #{gbk_file} is not a valid genbank file !"
     else
-      @gbk = flat_gbk.next_entry
+
+      @gbk_all = []
+      @bioseq_all = []
+      flat_gbk.each_entry do |e|
+        @gbk_all << e
+        @bioseq_all << e.to_biosequence
+      end
+
+      @gbk = @gbk_all[0]
+
     end
 
     @bioseq = @gbk.to_biosequence
@@ -221,41 +230,45 @@ class SequenceAnnotation
 
     if @coding_seq.empty?
 
-      # Iterate over each CDS
-      @gbk.each_cds do |ft|
-        ftH = ft.to_hash
-        loc = ft.locations
-        gene = []
-        product = []
-        protId = ""
-        if ftH.has_key? "pseudo"
-          next
-        end
-        gene = ftH["gene"] if !ftH["gene"].nil?
-        product = ftH["product"] if !ftH["product"].nil?
-        protId = ftH["protein_id"][0] if !ftH["protein_id"].nil?
-        locustag = ftH["locus_tag"][0] if !ftH["locus_tag"].nil?
-
-        dna = get_DNA(ft,@bioseq)
-        pep = dna.translate
-        pepBioSeq = Bio::Sequence.auto(pep)
-        dnaBioSeq = Bio::Sequence.auto(dna)
-
-        if protId.strip == ""
-          protId = locustag
-        end
+      @gbk_all.each_with_index do |gb, gb_i|
+
+        # Iterate over each CDS
+        gb.each_cds do |ft|
+          ftH = ft.to_hash
+          loc = ft.locations
+          gene = []
+          product = []
+          protId = ""
+          if ftH.has_key? "pseudo"
+            next
+          end
 
-        @coding_seq[protId] = {
-          protId: protId,
-          location: loc,
-          locustag: locustag,
-          gene: gene[0],
-          product: product[0],
-          bioseq: pepBioSeq,
-          bioseq_gene: dnaBioSeq,
-          length: pepBioSeq.length
-        }
+          gene = ftH["gene"] if !ftH["gene"].nil?
+          product = ftH["product"] if !ftH["product"].nil?
+          protId = ftH["protein_id"][0] if !ftH["protein_id"].nil?
+          locustag = ftH["locus_tag"][0] if !ftH["locus_tag"].nil?
+
+          dna = get_DNA(ft,@bioseq_all[gb_i])
+          pep = dna.translate
+          pepBioSeq = Bio::Sequence.auto(pep)
+          dnaBioSeq = Bio::Sequence.auto(dna)
+
+          if protId.strip == ""
+            protId = locustag
+          end
 
+          @coding_seq[protId] = {
+            protId: protId,
+            location: loc,
+            locustag: locustag,
+            gene: gene[0],
+            product: product[0],
+            bioseq: pepBioSeq,
+            bioseq_gene: dnaBioSeq,
+            length: pepBioSeq.length
+          }
+
+        end
       end
 
     end
@@ -270,43 +283,45 @@ class SequenceAnnotation
     if @rna_seq.empty?
 
       @rna_seq = {}
-      @gbk.features do |ft|
 
-        next if ! ft.feature.to_s.include? "RNA"
+      @gbk_all.each_with_index do |gb, gb_i|
+        gb.features do |ft|
 
-        ftH = ft.to_hash
-        loc = ft.locations
-        # seqBeg = loc[0].from.to_s
-        # seqEnd = loc[0].to.to_s
-        # strand = loc[0].strand.to_s
-        if ftH.has_key? "pseudo"
-          next
-        end
-        # gene = ftH["gene"] if !ftH["gene"].nil?
-        # protId = ftH["protein_id"][0] if !ftH["protein_id"].nil?
-        product = ""
+          next if ! ft.feature.to_s.include? "RNA"
 
-        if !ftH["product"].nil?
-          product = ftH["product"][0]
-          # puts ftH["product"].join(",") + "---" + ftH["product"][0]
-        end
+          ftH = ft.to_hash
+          loc = ft.locations
+          # seqBeg = loc[0].from.to_s
+          # seqEnd = loc[0].to.to_s
+          # strand = loc[0].strand.to_s
+          if ftH.has_key? "pseudo"
+            next
+          end
+          # gene = ftH["gene"] if !ftH["gene"].nil?
+          # protId = ftH["protein_id"][0] if !ftH["protein_id"].nil?
+          product = ""
 
-        locustag = ftH["locus_tag"][0] if !ftH["locus_tag"].nil?
+          if !ftH["product"].nil?
+            product = ftH["product"][0]
+            # puts ftH["product"].join(",") + "---" + ftH["product"][0]
+          end
 
-        # puts "#{@accession}\t#{seqBeg}\t#{seqEnd}\t#{strand}\t#{protId}\t#{locustag}\t#{gene[0]}\t#{product[0]}"
-        dna = get_DNA(ft,@bioseq)
-        dnaBioSeq = Bio::Sequence.auto(dna)
+          locustag = ftH["locus_tag"][0] if !ftH["locus_tag"].nil?
 
-        @rna_seq[locustag] = {
-          type: ft.feature.to_s,
-          location: loc,
-          locustag: locustag,
-          product: product,
-          bioseq_gene: dnaBioSeq
-        }
+          # puts "#{@accession}\t#{seqBeg}\t#{seqEnd}\t#{strand}\t#{protId}\t#{locustag}\t#{gene[0]}\t#{product[0]}"
+          dna = get_DNA(ft,@bioseq_all[gb_i])
+          dnaBioSeq = Bio::Sequence.auto(dna)
 
-      end
+          @rna_seq[locustag] = {
+            type: ft.feature.to_s,
+            location: loc,
+            locustag: locustag,
+            product: product,
+            bioseq_gene: dnaBioSeq
+          }
 
+        end
+      end
     end
 
     @rna_seq
@@ -622,4 +637,3 @@ class SequenceAnnotation
 
 
 end                             # end of Class
-

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bacterial-annotator
 version: !ruby/object:Gem::Version
-  version: 0.9.1
+  version: 0.9.3
 platform: ruby
 authors:
 - Maxime Deraspe
 autorequire:
 bindir: bin
 cert_chain: []
-date: 2022-09-05 00:00:00.000000000 Z
+date: 2022-12-19 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio