miga-base 1.1.3.1 → 1.1.3.2

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
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-  data.tar.gz: 72d58adbbbea43886e1e60a608f3f7e0da542c26b3b29ecf202a3b34b9f8ac35
+  metadata.gz: 869314efef2d92764d569f6ba5bc7cf03182a8a4dddb27405349923ca1518100
+  data.tar.gz: 9bd3e4a7fb5d34c0d34b850a0f300b4f6ddbc4607d63fc92a5240c7674ce53b6
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+  metadata.gz: b2deb4fd773f70d362d2d22224917bc4c72ed39e61951a403d6b9a8584cc99580425d140db4c6048dbf3680d696e26d6683802f88797a08f851b92d70389b79a
+  data.tar.gz: 1448247c7b883b5a52f92000a7085301b27645f8dc8ef069620815d8dd29f3a0c2ad2d9e3ace1821530bccaa91623793bd8b1f33f158ecf0d731b87c0cd6bc25

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

@@ -59,13 +59,14 @@ module MiGA::Cli::Action::Doctor::Base
         next if (lineno += 1) == 1
 
         r = ln.split("\t")
-        next unless [1, 2].map { |i| p.dataset(r[i]).nil? }.any?
+        names = [r[0], r[1]]
+        next unless names.any? { |i| p.dataset(i).nil? }
 
-        [1, 2].each do |i|
-          if p.dataset(r[i]).nil? || !p.dataset(r[i]).active?
-            notok[r[i]] = true
+        names.each do |i|
+          if p.dataset(i).nil? || !p.dataset(i).active?
+            notok[i] = true
           else
-            fix[r[i]] = true
+            fix[i] = true
           end
         end
       end

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, 1].freeze
+  VERSION = [1.1, 3, 2].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, 24)
+  VERSION_DATE = Date.new(2021, 11, 26)
 
   ##
   # References of MiGA

data/utils/distance/commands.rb

@@ -153,18 +153,27 @@ module MiGA::DistanceRunner::Commands
     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 --donor_file "#{f0}" \
-                --recipient "#{f1 = tmp_file}" --threads #{opts[:thr]}
-            CMD
+    f1 = donors.first
+    if donors.size > 1
+      File.open(f0 = tmp_file, 'w') { |fh| donors.each { |i| fh.puts i } }
+      run_cmd(
+        <<~CMD
+          FastAAI merge_db --threads #{opts[:thr]} \
+            --donor_file "#{f0}" --recipient "#{f1 = tmp_file}"
+        CMD
+      )
+      raise "Cannot merge databases into: #{f1}" unless File.size?(f1)
+    end
 
     # Run FastAAI
-    run_cmd <<~CMD
-              FastAAI db_query --query "#{qry_idx}" --target "#{f1}" \
-                --output "#{f2 = tmp_file}" --threads #{opts[:thr]} \
-                --do_stdev
-            CMD
+    run_cmd(
+      <<~CMD
+        FastAAI db_query --query "#{qry_idx}" --target "#{f1}" \
+          --output "#{f2 = tmp_file}" --threads #{opts[:thr]} \
+          --do_stdev
+      CMD
+    )
+    raise "Cannot find FastAAI output directory: #{f2}" unless Dir.exist?(f2)
 
     # Save values in the databases
     haai_data = {}
@@ -217,6 +226,6 @@ module MiGA::DistanceRunner::Commands
 
   def run_cmd(cmd)
     puts "CMD: #{cmd}"
-    `#{cmd}`
+    puts `#{cmd} 2>&1`
   end
 end

data/utils/subclade/pipeline.rb

@@ -7,9 +7,12 @@ module MiGA::SubcladeRunner::Pipeline
       aai90: [:aai_distances, opts[:gsp_aai], :aai]
     }
     tasks.each do |k, par|
+      # Run only the requested metric
+      next unless par[2].to_s == opts[:gsp_metric]
+
       # Final output
       ogs_file = "miga-project.#{k}-clades"
-      next if File.size? ogs_file
+      next if File.size?(ogs_file)
 
       # Build ABC files
       abc_path = tmp_file("#{k}.abc")
@@ -20,7 +23,7 @@ module MiGA::SubcladeRunner::Pipeline
           next if ln =~ /^a\tb\tvalue\t/
 
           r = ln.chomp.split("\t")
-          ofh.puts "G>#{r[0]}\tG>#{r[1]}\t#{r[2]}" if r[2].to_f >= par[1]
+          ofh.puts("G>#{r[0]}\tG>#{r[1]}\t#{r[2]}") if r[2].to_f >= par[1]
         end
       end
       ofh.close
@@ -29,16 +32,14 @@ module MiGA::SubcladeRunner::Pipeline
         `ogs.mcl.rb -o '#{ogs_file}.tmp' --abc '#{abc_path}' -t '#{opts[:thr]}'`
         File.open(ogs_file, 'w') do |fh|
           File.foreach("#{ogs_file}.tmp").with_index do |ln, lno|
-            fh.puts ln if lno > 0
+            fh.puts(ln) if lno > 0
           end
         end
         File.unlink "#{ogs_file}.tmp"
       else
-        FileUtils.touch ogs_file
-      end
-      if par[2].to_s == opts[:gsp_metric]
-        FileUtils.cp(ogs_file, "miga-project.gsp-clades")
+        FileUtils.touch(ogs_file)
       end
+      FileUtils.cp(ogs_file, 'miga-project.gsp-clades')
     end
 
     # Find genomospecies medoids
@@ -67,7 +68,7 @@ module MiGA::SubcladeRunner::Pipeline
     metric_res = project.result(step) or raise "Incomplete step #{step}"
     matrix = metric_res.file_path(:matrix)
     `Rscript '#{src}' '#{matrix}' miga-project '#{opts[:thr]}' \
-      miga-project.ani95-medoids '#{opts[:run_clades] ? 'cluster' : 'empty'}'`
+      miga-project.gsp-medoids '#{opts[:run_clades] ? 'cluster' : 'empty'}'`
     if File.exist? 'miga-project.nwk'
       File.rename('miga-project.nwk', "miga-project.#{metric}.nwk")
     end

data/utils/subclades.R

@@ -26,14 +26,18 @@ subclades <- function(ani_file, out_base, thr = 1, ani.d = dist(0), sel = NA) {
   # Normalize input matrix
   dist_rds <- paste(out_base, "dist.rds", sep = ".")
   if (!missing(ani_file)) {
-    if(length(ani.d) == 0 && !file.exists(dist_rds)){
-      # Read from ani_file
-      ani.d <- ani_distance(ani_file, sel)
-      if (is.null(ani.d)) {
-        generate_empty_files(out_base)
-        return(NULL)
+    if (length(ani.d) == 0) {
+      if (file.exists(dist_rds)) {
+        ani.d <- readRDS(dist_rds)
       } else {
-        saveRDS(ani.d, dist_rds)
+        # Read from ani_file
+        ani.d <- ani_distance(ani_file, sel)
+        if (is.null(ani.d)) {
+          generate_empty_files(out_base)
+          return(NULL)
+        } else {
+          saveRDS(ani.d, dist_rds)
+        }
       }
     }
   }
@@ -104,17 +108,6 @@ subclade_clustering <- function (out_base, thr, ani.d, dist_rds) {
   }
   if (length(labels(ani.d)) <= 8L) return(list())
   
-  # Build tree
-  say("Tree")
-  ani.ph <- bionj(ani.d)
-  say("- Write")
-  express.ori <- options("expressions")$expressions
-  if(express.ori < ani.ph$Nnode * 4){
-    options(expressions=min(c(5e7, ani.ph$Nnode * 4)))
-  }
-  write.tree(ani.ph, paste(out_base, ".nwk", sep = ""))
-  options(expressions=express.ori)
-
   # Silhouette
   say("Silhouette")
   nn <- length(labels(ani.d))
@@ -146,6 +139,17 @@ subclade_clustering <- function (out_base, thr, ani.d, dist_rds) {
   ani.types <- ani.cl$clustering
   ani.medoids <- ani.cl$medoids
 
+  # Build tree
+  say("Tree")
+  ani.ph <- bionj(ani.d)
+  say("- Write")
+  express.ori <- options("expressions")$expressions
+  if(express.ori < ani.ph$Nnode * 4){
+    options(expressions=min(c(5e7, ani.ph$Nnode * 4)))
+  }
+  write.tree(ani.ph, paste(out_base, ".nwk", sep = ""))
+  options(expressions=express.ori)
+
   # Generate graphic report
   say("Graphic report")
   pdf(paste(out_base, ".pdf", sep = ""), 7, 12)

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 1.1.3.1
+  version: 1.1.3.2
 platform: ruby
 authors:
 - Luis M. Rodriguez-R
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2021-11-24 00:00:00.000000000 Z
+date: 2021-11-26 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: daemons