bacterial-annotator 0.9.4 → 1.0.1

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 6873b45085524788e9ea2c82b29c5e3cfb6998c6cd7ff1f16d56dc64378c910e
-  data.tar.gz: 7b02f34f8ffef086ade18526db05b5fffdeabee339a4808ec09181a7cb108b53
+  metadata.gz: 7355a51394c598b6f53b033eb6889918961a6a6f85004f64887852adc76e2a6a
+  data.tar.gz: cfbaa022c31eedbd16d2f66127d3c7c652fc8fe512f63e416c132aaadf3bb029
 SHA512:
-  metadata.gz: 4b01f90fe7bc53e79a4245fbd64830a8fa967447e4a609715feef1ec21a68583531b9d1120631234204215bfa3bf6cfdd0b311704f030cf4cdf08d670fcabcf8
-  data.tar.gz: 15f9a395c37249bf937052d1917c89a42122a720bb1beddd1c4b2bddef3883111cb7e2e883da7757ccd9170eb3675499bbb70ac8dcfc62d4e722b9434549c92c
+  metadata.gz: 65a929fffcdabfaba9771fbc50a02205773e6f59bea6acfb98f12bdf6b4ff0e26e4be0ec1a5521cb51f68e21276d6555de4ce900872823e3c90987c00c17afd1
+  data.tar.gz: ad1f6f48a49a9319184ae02c612f294cd735b7fc28f0721b7f4b30aabf57de31a184b87527927593b7ae4bbe814024dbbeccbfa91135b69f5052021039fe0882

data/bin/ba_cdhit

@@ -16,7 +16,7 @@ ROOT_path = File.dirname(__FILE__)
 def installcdhit
 
   begin
-    resp = open("https://github.com/weizhongli/cdhit/releases/download/V4.6.8/cd-hit-v4.6.8-2017-0621-source.tar.gz")
+    resp = URI.open("https://github.com/weizhongli/cdhit/releases/download/V4.6.8/cd-hit-v4.6.8-2017-0621-source.tar.gz")
     open("#{ROOT_path}/cdhit-4.6.8.tar.gz", "wb") do |file|
       file.write(resp.read)
     end

data/bin/ba_diamond

@@ -14,9 +14,8 @@ ROOT_path = File.dirname(__FILE__)
 
 # Install diamond on the user system
 def installDiamond
-
   begin
-    resp = open("https://github.com/bbuchfink/diamond/releases/download/v2.0.15/diamond-linux64.tar.gz")
+    resp = URI.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

data/bin/ba_fasta36

@@ -16,7 +16,7 @@ ROOT_path = File.dirname(__FILE__)
 def installFasta36
 
   begin
-    resp = open("https://github.com/wrpearson/fasta36/releases/download/fasta-v36.3.8g/fasta-36.3.8g-linux64.tar.gz")
+    resp = URI.open("https://github.com/wrpearson/fasta36/releases/download/fasta-v36.3.8g/fasta-36.3.8g-linux64.tar.gz")
     open("#{ROOT_path}/fasta-36.3.8g-linux64.tar.gz", "wb") do |file|
       file.write(resp.read)
     end

data/bin/ba_fasttree

@@ -16,7 +16,7 @@ ROOT_path = File.dirname(__FILE__)
 def installFastTree
 
   begin
-    resp = open("http://www.microbesonline.org/fasttree/FastTreeMP")
+    resp = URI.open("http://www.microbesonline.org/fasttree/FastTreeMP")
     open("#{ROOT_path}/fasttree.linux", "wb") do |file|
       file.write(resp.read)
     end

data/bin/ba_mafft

@@ -15,7 +15,7 @@ ROOT_path = File.dirname(__FILE__)
 def installMafft
 
   begin
-    resp = open("https://mafft.cbrc.jp/alignment/software/mafft-7.222-without-extensions-src.tgz")
+    resp = URI.open("https://mafft.cbrc.jp/alignment/software/mafft-7.222-without-extensions-src.tgz")
     open("#{ROOT_path}/mafft-7.222-without-extensions-src.tgz", "wb") do |file|
       file.write(resp.read)
     end

data/bin/ba_mash

@@ -16,7 +16,7 @@ ROOT_path = File.dirname(__FILE__)
 def installMash
 
   begin
-    resp = open("https://github.com/marbl/Mash/releases/download/v2.0/mash-Linux64-v2.0.tar")
+    resp = URI.open("https://github.com/marbl/Mash/releases/download/v2.0/mash-Linux64-v2.0.tar")
     open("#{ROOT_path}/mash.tar", "wb") do |file|
       file.write(resp.read)
     end

data/bin/ba_prodigal

@@ -16,7 +16,7 @@ ROOT_path = File.dirname(__FILE__)
 def installProdigal
 
   begin
-    resp = open("https://github.com/hyattpd/Prodigal/archive/v2.6.2.tar.gz")
+    resp = URI.open("https://github.com/hyattpd/Prodigal/archive/v2.6.2.tar.gz")
     open("#{ROOT_path}/v2.6.2.tar.gz", "wb") do |file|
       file.write(resp.read)
     end

data/bin/ba_raxml

@@ -15,7 +15,7 @@ ROOT_path = File.dirname(__FILE__)
 def installRaxml
 
   begin
-    resp = open("https://github.com/stamatak/standard-RAxML/archive/v8.2.11.zip")
+    resp = URI.open("https://github.com/stamatak/standard-RAxML/archive/v8.2.11.zip")
     open("#{ROOT_path}/master.zip", "wb") do |file|
       file.write(resp.read)
     end

data/bin/ba_trnascan

@@ -18,7 +18,7 @@ def installTrnascan
   begin
 
     # infernal as dependencies
-    resp = open("http://eddylab.org/infernal/infernal-1.1.2.tar.gz")
+    resp = URI.open("http://eddylab.org/infernal/infernal-1.1.2.tar.gz")
     open("#{ROOT_path}/infernal-1.1.2.tar.gz", "wb") do |file|
       file.write(resp.read)
     end
@@ -27,7 +27,7 @@ def installTrnascan
     `cd infernal-1.1.2 && ./configure --prefix=#{ROOT_path}/infernal-1.1.2/build && make && make install`
 
     # trnascan-se
-    resp = open("http://trna.ucsc.edu/software/trnascan-se-2.0.0.tar.gz")
+    resp = URI.open("http://trna.ucsc.edu/software/trnascan-se-2.0.0.tar.gz")
     open("#{ROOT_path}/trnascan-se-2.0.0.tar.gz", "wb") do |file|
       file.write(resp.read)
     end

data/lib/bacterial-comparator.rb

@@ -615,7 +615,9 @@ 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,

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bacterial-annotator
 version: !ruby/object:Gem::Version
-  version: 0.9.4
+  version: 1.0.1
 platform: ruby
 authors:
 - Maxime Deraspe
 autorequire:
 bindir: bin
 cert_chain: []
-date: 2023-07-17 00:00:00.000000000 Z
+date: 2025-01-06 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio
@@ -125,7 +125,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.1.6
+rubygems_version: 3.3.3
 signing_key:
 specification_version: 4
 summary: Bacterial Annotator