miga-base 1.3.20.2 → 1.3.20.4

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 0ed682917cf2e5645f7ae31789932c2d14eaf06faa29aca1b13142862f653d49
-  data.tar.gz: fce8e42084a3896c49a01ce603d0c99ac766b1bade878b43ac55fd5be11ba523
+  metadata.gz: c11dfa7c37bbfd12ff0b9d71c3760489a685f048e1692c9c608b38726d91af36
+  data.tar.gz: 7d6db500aa13fd518a0b702b205d592c9af218ecb9c26d6c78cb25ef41d88e9a
 SHA512:
-  metadata.gz: 1eacee695bac46bbed8c1bb13694c2ff614020eef89d8547939a6d976f21659464185d648ff2244f25e5ddba2ae429a1d87758034eefa48ce84e8636f072c686
-  data.tar.gz: 04fb36c2c58b9fde72e48f9a9983a3505f6368ac231e412c7844380fa4a497dcd71d3209c09b97d961f393b6b3c9965092e72620b88d226fa4275a3a8993db0d
+  metadata.gz: 808778c7f3e3264ccbd5b45251cebd81a12e7dd91328e0bfed8e1d3aa27376e6d610f3f0ae6f3e80b11549d85ec2499fdb9d69a1e4776435ad3b1fafb3985d0d
+  data.tar.gz: e68bb859e5dd6f6568b712e23cdd125486dd911ed0ce63b2046cdad921f1f1fe39e23f3b4980f3b9c1352404ca68d6989b8fa8a7613bdf01f21b8224a9d969a0

data/lib/miga/cli/action/doctor/distances.rb

@@ -77,8 +77,15 @@ module MiGA::Cli::Action::Doctor::Distances
   def partial_bidir_tmp(project, ref_ds)
     n = ref_ds.size
 
-    # Read data first (threaded)
+    # Check first if a previous run is complete (and recover it)
     tmp = File.join(project.path, 'doctor-bidirectional.tmp')
+    tmp_done = File.join(tmp, 'done.txt')
+    if File.size?(tmp_done) &&
+          File.readlines(tmp_done)[0].chomp.to_i == cli[:threads]
+      return tmp
+    end
+
+    # Read data first (threaded)
     FileUtils.mkdir_p(tmp)
     MiGA::Parallel.process(cli[:threads]) do |thr|
       file = File.join(tmp, "#{thr}.json")
@@ -102,6 +109,8 @@ module MiGA::Cli::Action::Doctor::Distances
       end
     end
 
+    # Save information to indicate that the run is complete and return
+    File.open(tmp_done, 'w') { |fh| fh.puts cli[:threads] }
     return tmp
   end
 
@@ -113,7 +122,14 @@ module MiGA::Cli::Action::Doctor::Distances
     dist = { aai: {}, ani: {} }
     cli[:threads].times do |i|
       cli.advance('Merging:', i + 1, cli[:threads], false)
+
+      next if File.size?(File.join(tmp, "#{i+1}.json.marshal"))
       file = File.join(tmp, "#{i}.json")
+      if File.size?("#{file}.marshal")
+        dist = Marshal.load(File.read("#{file}.marshal"))
+        next
+      end
+
       File.open(file, 'r') do |fh|
         metric = nil
         fh.each do |ln|
@@ -135,6 +151,7 @@ module MiGA::Cli::Action::Doctor::Distances
         end
         raise "Incomplete thread dump: #{file}" unless metric == :end
       end
+      File.open("#{file}.marshal", 'w') { |fh| Marshal.dump(dist, fh) }
     end
     cli.say
 

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 = [1.3, 20, 2].freeze
+  VERSION = [1.3, 20, 4].freeze
 
   ##
   # Nickname for the current major.minor version.
@@ -20,7 +20,7 @@ module MiGA
 
   ##
   # Date of the current gem relese.
-  VERSION_DATE = Date.new(2024, 8, 29)
+  VERSION_DATE = Date.new(2024, 9, 1)
 
   ##
   # References of MiGA

data/scripts/cds.bash

@@ -16,6 +16,14 @@ if [[ -e "../05.assembly/$DATASET.LargeContigs.fna.gz" \
   miga add_result -P "$PROJECT" -D "$DATASET" -r assembly -f
 fi
 
+# Check if the input assembly is empty
+ASM_LEN=$(grep -v '^>' "../05.assembly/${DATASET}.LargeContigs.fna" \
+            | wc -lc | awk '{ print $2-$1 }')
+if [[ "$ASM_LEN" -lt 1 ]] ; then
+  miga edit -P "$PROJECT" -D "$DATASET" --inactivate "Empty assembly"
+  exit 0
+fi
+
 # Run Prodigal
 TYPE=$(miga ls -P "$PROJECT" -D "$DATASET" -m type | cut -f 2)
 case "$TYPE" in
@@ -27,8 +35,6 @@ case "$TYPE" in
     P_LEN=0
     BEST_CT=0
     PROCEDURE=single
-    ASM_LEN=$(grep -v '^>' "../05.assembly/${DATASET}.LargeContigs.fna" \
-      | wc -lc | awk '{ print $2-$1 }')
     [[ "$ASM_LEN" -lt 2000 ]] && PROCEDURE=meta
     echo "# Codon table selection:" > "${DATASET}.ct.t"
     for ct in 11 4 ; do

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 1.3.20.2
+  version: 1.3.20.4
 platform: ruby
 authors:
 - Luis M. Rodriguez-R
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2024-08-29 00:00:00.000000000 Z
+date: 2024-09-01 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: daemons