miga-base 1.4.2.4 → 1.4.2.5

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 5e0cb44349d861128c762b5285e8013f3086283c9a86e9e34197d3b37a6ed3e6
-  data.tar.gz: 9f890c7b7288067ce20f61e0ec83edf50c79407abbfcf7dd470d852f73f7aa44
+  metadata.gz: 725b5f62ffeba49a813504c3cfaf5a222ba5259f82eb2cb0430150483e83cc83
+  data.tar.gz: 5c3d9e21668edeb12d022a193a045ec43749c2704484976fa08bcb248cdf8fed
 SHA512:
-  metadata.gz: c0b2768551937f51919e74e7df35790d957418facc0498db6752662d8192d6c5c6fdd59b9ab5eec91e4d345675ed47e5154077a03722d84a79ea32d5501f1afb
-  data.tar.gz: 5e4cb5dc6ad5c82cde159e3ff854111659d8b7c0d5b665a86a54757dc43cd95284dd97f870d921f37bd3711391669ae990282c9bbee8f8df832718afdd5292d6
+  metadata.gz: c9746ea4048074e5478c087f81293bd0ee64da5a9e4c51b86d4a62d1c76f0de43a92a8a539349df8b8e0adb5fe8ad58f6594d523ce7858bcc861f265dc62c7d6
+  data.tar.gz: 276f2aabeb61253b8d2a6d219517c9334f9ac63317b0daa4482af474ed9106adc667458214619f1245cdc9c1b88627dd6440b5369c1752bfbc5e63cba6e474b8

data/Gemfile

@@ -7,3 +7,5 @@ group :test do
 end
 
 gem 'rake', '~> 13.0'
+
+gem "csv", "~> 3.3"

data/lib/miga/common/format.rb

@@ -24,10 +24,11 @@ module MiGA::Common::Format
 
   ##
   # Cleans a FastA file in place, removing all sequences shorter than
-  # +min_len+
+  # +min_len+ and renaming duplicate sequence identifiers
   def clean_fasta_file(file, min_len = 1)
     tmp_fh = nil
     tmp_path = nil
+    names = Set.new
     begin
       if file =~ /\.gz/
         tmp_path = Tempfile.new('MiGA.gz').tap(&:close).path
@@ -45,11 +46,14 @@ module MiGA::Common::Format
         ln.chomp!
         if ln =~ /^>\s*(\S+)(.*)/
           id, df = $1, $2
+          id = id.gsub(/[^A-Za-z0-9_\|\.]/, '_')
+          id = id + '_dup' while names.include?(id)
+          names << id
           if next_seq[1].length >= min_len
             tmp_fh.puts next_seq[0]
             tmp_fh.print next_seq[1].wrap_width(80)
           end
-          next_seq = [">#{id.gsub(/[^A-Za-z0-9_\|\.]/, '_')}#{df}", '']
+          next_seq = [">#{id}#{df}", '']
         else
           next_seq[1] += ln.gsub(/[^A-Za-z]/, '')
         end

data/lib/miga/common/net.rb

@@ -118,7 +118,7 @@ module MiGA::Common::Net
   def http_request(method, url, *opts)
     doc = nil
     remote_connection(url).start do |http|
-      res = http.send(method, remote_connection_uri.to_s, *opts)
+      res = http.send(method, remote_connection_uri, *opts)
       if %w[301 302].include?(res.code)
         DEBUG "REDIRECTION #{res.code}: #{res['location']}"
         return http_request(method, res['location'], *opts)

data/lib/miga/version.rb

@@ -12,7 +12,7 @@ module MiGA
   # - String indicating release status:
   #   - rc* release candidate, not released as gem
   #   - [0-9]+ stable release, released as gem
-  VERSION = [1.4, 2, 4].freeze
+  VERSION = [1.4, 2, 5].freeze
 
   ##
   # Nickname for the current major.minor version.
@@ -20,7 +20,7 @@ module MiGA
 
   ##
   # Date of the current gem relese.
-  VERSION_DATE = Date.new(2026, 4, 28)
+  VERSION_DATE = Date.new(2026, 5, 20)
 
   ##
   # References of MiGA

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 1.4.2.4
+  version: 1.4.2.5
 platform: ruby
 authors:
 - Luis M. Rodriguez-R
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2026-04-28 00:00:00.000000000 Z
+date: 2026-05-20 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: daemons