miga-base 1.1.3.0 → 1.1.3.1

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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+  metadata.gz: 8d9d8a12b9eaa48b63df43b871f3cc7da598997f3d208cde9fcf31f2d605d66c
+  data.tar.gz: 72d58adbbbea43886e1e60a608f3f7e0da542c26b3b29ecf202a3b34b9f8ac35
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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 = [1.1, 3, 0].freeze
+  VERSION = [1.1, 3, 1].freeze
 
   ##
   # Nickname for the current major.minor version.
@@ -20,7 +20,7 @@ module MiGA
 
   ##
   # Date of the current gem relese.
-  VERSION_DATE = Date.new(2021, 11, 21)
+  VERSION_DATE = Date.new(2021, 11, 24)
 
   ##
   # References of MiGA

data/utils/FastAAI/FastAAI

@@ -2702,6 +2702,8 @@ def merge_db_opts():
 			
 	parser.add_argument('-d', '--donors',      dest = 'donors',    default = None,   help =  'Comma-separated string of paths to one or more donor databases. The genomes FROM the donors will be added TO the recipient and the donors will be unaltered')
 
+	parser.add_argument('--donor_file',        dest = 'donor_file',    default = None,   help =  'Alternative way to supply donors. A file containing paths to the donor databases, 1 per line')
+
 	parser.add_argument('-r', '--recipient',   dest = 'recipient', default = None, help =  'Path to the recipient database. Any genomes FROM the donor database not already in the recipient will be added to this database.')	
 		
 	parser.add_argument('--verbose',           dest = 'verbose',   action='store_true', help = 'Print minor updates to console. Major updates are printed regardless.')
@@ -2720,16 +2722,23 @@ def merge_db_thread_starter(rev_index, per_db_accs):
 	
 	
 	
-def merge_db(recipient, donors, verbose, threads):
+def merge_db(recipient, donors, donor_file, verbose, threads):
 	#Prettier on the CLI
-
+	
+	if donor_file is not None:
+		fh = agnostic_reader(donor_file)
+		donors = [line.strip() for line in fh]
+		fh.close()
+	
 	if donors is None or recipient is None:
 		print("Either donor or target not given. FastAAI is exiting.")
 		return None
 	
 	print("")
 	
-	donors = donors.split(",")
+	if donor_file is None:
+		donors = donors.split(",")
+	
 	valid_donors = []
 	for d in donors:
 		if os.path.exists(d):
@@ -3454,10 +3463,11 @@ def main():
 			
 		recipient = opts.recipient
 		donors = opts.donors
+		donor_file = opts.donor_file
 		verbose = opts.verbose
 		threads = opts.threads
 		
-		merge_db(recipient, donors, verbose, threads)
+		merge_db(recipient, donors, donor_file, verbose, threads)
 		
 #################### Query files vs DB ########################	
 		

data/utils/distance/commands.rb

@@ -151,8 +151,11 @@ module MiGA::DistanceRunner::Commands
       donors << tgt_idx if tgt_idx
     end
     return nil if donors.empty?
+
+    # Build target database
+    File.open(f0 = tmp_file, 'w') { |fh| donors.each { |i| fh.puts i } }
     run_cmd <<~CMD
-              FastAAI merge_db --donors "#{donors.join(',')}" \
+              FastAAI merge_db --donor_file "#{f0}" \
                 --recipient "#{f1 = tmp_file}" --threads #{opts[:thr]}
             CMD
 
@@ -166,7 +169,7 @@ module MiGA::DistanceRunner::Commands
     # Save values in the databases
     haai_data = {}
     aai_data = {}
-    # Ugly workaround to the insistence of FastAAI to not provide the files
+    # Ugly workaround to the insistence of FastAAI not to provide the files
     # I ask for ;-)
     qry_results = File.basename(qry_idx, '.faix') + '_results.txt'
     out_file = File.join(f2, 'results', qry_results)

data/utils/distance/database.rb

@@ -127,6 +127,7 @@ module MiGA::DistanceRunner::Database
     db = tmp_dbs[metric]
     table = metric == :haai ? :aai : metric
     SQLite3::Database.new(db) do |conn|
+      conn.execute('BEGIN TRANSACTION')
       data.each do |k, v|
         sql = <<~SQL
                 insert into #{table} (
@@ -135,6 +136,7 @@ module MiGA::DistanceRunner::Database
               SQL
         conn.execute(sql, [dataset.name, k] + v)
       end
+      conn.execute('COMMIT')
     end
     checkpoint(metric)
   end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 1.1.3.0
+  version: 1.1.3.1
 platform: ruby
 authors:
 - Luis M. Rodriguez-R
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2021-11-21 00:00:00.000000000 Z
+date: 2021-11-24 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: daemons