bacterial-annotator 0.9.3 → 1.0.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: e6b26cd37618fedd557b8d9f7fe2c27a3b95dee5404d7751a8fb10ddcb63edc8
-  data.tar.gz: 2129f8372c3a48654cf3bdf6b75eccce3148b45f0e15191f3a555ff0769f9bd4
+  metadata.gz: 1dad9c41b499dc463758390648f19af38b55a660e0ac408303fca0383bbf9463
+  data.tar.gz: 3d58da07ceced3fabba23a685d8f7b25e0bddc511cd690a5e6b4e24666ad3c89
 SHA512:
-  metadata.gz: 2400660df26bab507b5f9a3310105514d415a4950a06fdb7a3cbc9a4de2b4268d77c3725a13507e19c92fcdcc688f2bda4184aeadb88afd4a444addce1117fb9
-  data.tar.gz: 9caef8af954e6de43ed3eb2cd5a729065bafd2451aa5c73e00e60b400cb849666a53fb1e39d549f4b33925edbfea33f209a966da7f64d91ac1aa3d8b75e5f4d2
+  metadata.gz: d860ebf490024dad6ec9a28c8b68a21cc8447b347236cff9938ebc372244fdcc3f414bb9f2280fa58bded32e221a5614d6b5d1e9e681837d8f8948c4a20dc3c2
+  data.tar.gz: 7ad1c1444c156679632129799120b303055e90316baceb2c17f3441afa58298aeaf7840f1bdc5989bb2931452cd76a26e723ed54a602d41f73efc781b23f5215

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

@@ -1,10 +1,10 @@
 # -*- coding: utf-8 -*-
 # author:  	maxime déraspe
 # email:	maximilien1er@gmail.com
-# review:  	
+# review:
 # date:    	15-02-24
 # version: 	0.0.1
-# licence:  	
+# licence:
 
 require 'json'
 require 'zlib'
@@ -111,7 +111,7 @@ class SequenceSynteny
         system("#{@root}/diamond.linux makedb --db #{subject_file} --in #{subject_file} > /dev/null 2>&1")
         db_file = subject_file
       end
-      system("#{@root}/diamond.linux blastp --db #{db_file} -q #{query_file} -o #{@outdir}/#{@name}.diamond.tsv -f 6 > /dev/null 2>&1")
+      system("#{@root}/diamond.linux blastp --masking none --db #{db_file} -q #{query_file} -o #{@outdir}/#{@name}.diamond.tsv -f 6 > /dev/null 2>&1")
     else
       # system("#{@root}/glsearch36.linux -b 3 -E 1e-25 -m 8 #{@subject_file} #{@query_file} > #{@outdir}/#{@name}.fasta36.tsv")
     end

data/lib/bacterial-comparator.rb

@@ -45,6 +45,9 @@ class BacterialComparator
       min_pid = min_pid/100
     end
 
+    @min_cov = min_cov
+    @min_pid = min_pid
+
     @aln_opt = options[:align].downcase
     @run_phylo = 0
     if options[:phylogeny] == 1
@@ -592,8 +595,8 @@ class BacterialComparator
                                            query_prot_file,
                                            ref_prot_file,
                                            "Prot-Ref",
-                                           0.80,
-                                           0.80,
+                                           @min_cov,
+                                           @min_cov,
                                            "prot")
 
     print "# Running alignment with Reference Genome CDS (diamond).."
@@ -612,7 +615,10 @@ class BacterialComparator
     ref_synteny_prot.query_sequences.each do |prot, syn_val|
       next if ! syn_val.has_key? :homology
       next if syn_val[:homology][:assert_cutoff].inject(:+) < 3
-      next if ref_annotated.has_key? syn_val[:homology][:hits][0] and ref_annotated[syn_val[:homology][:hits][0]][:partial] == 0
+      next if ref_annotated.has_key? syn_val[:homology][:hits][0] and
+        ref_annotated[syn_val[:homology][:hits][0]][:partial] == 0 and
+        ref_annotated[syn_val[:homology][:hits][0]][:score] > syn_val[:homology][:score]
+
       ref_annotated[syn_val[:homology][:hits][0]] = {
         key: prot,
         pId: syn_val[:homology][:pId],
@@ -622,6 +628,7 @@ class BacterialComparator
         length: syn_val[:homology][:length][0],
         partial: (syn_val[:partial] ? 1 : 0)
       }
+
       # ref_annotated[syn_val[:homology][:hits][0]] = {
       #   key: prot,
       #   pId: syn_val[:homology][:pId],
@@ -631,6 +638,7 @@ class BacterialComparator
       #   length: syn_val[:homology][:length][0],
       #   partial: (syn_val[:partial] ? 1 : 0)
       # }
+
     end
 
     # print ref_annotated
@@ -642,13 +650,21 @@ class BacterialComparator
       coverage_query = ""
       query_length = ""
       pId = ""
+
       if ref_annotated[ref_v[:protId]] != nil
-        gene = ref_annotated[ref_v[:protId]][:key]
-        coverage_ref = ref_annotated[ref_v[:protId]][:cov_subject]
-        query_length = query_lengths[ref_annotated[ref_v[:protId]][:key]]
-        coverage_query = ref_annotated[ref_v[:protId]][:cov_query]
-        pId = ref_annotated[ref_v[:protId]][:pId]
-        partial = ref_annotated[ref_v[:protId]][:partial]
+
+        if ref_annotated[ref_v[:protId]][:pId] >= @min_pid and
+          ref_annotated[ref_v[:protId]][:cov_query] >= @min_cov and
+          ref_annotated[ref_v[:protId]][:cov_subject] >= @min_cov
+
+          gene = ref_annotated[ref_v[:protId]][:key]
+          coverage_ref = ref_annotated[ref_v[:protId]][:cov_subject]
+          query_length = query_lengths[ref_annotated[ref_v[:protId]][:key]]
+          coverage_query = ref_annotated[ref_v[:protId]][:cov_query]
+          pId = ref_annotated[ref_v[:protId]][:pId]
+          partial = ref_annotated[ref_v[:protId]][:partial]
+        end
+
       end
 
       _locus_tag = ref_v[:locustag] || ""

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bacterial-annotator
 version: !ruby/object:Gem::Version
-  version: 0.9.3
+  version: 1.0.0
 platform: ruby
 authors:
 - Maxime Deraspe
 autorequire:
 bindir: bin
 cert_chain: []
-date: 2022-12-19 00:00:00.000000000 Z
+date: 2024-01-13 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio