miga-base 0.3.6.1 → 0.3.6.2

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: c629b49cedd42f76fd8c466ecbc561e915dcaeef9dbbc2140f66300ac21c4e86
-  data.tar.gz: 2174cd7e010340ea865b7ec251a9d8b2823a059bbcec782924052a5da0c0a247
+  metadata.gz: 18d4ed2342a1b2d1e1b35b1bbb060a79bd573af5cdc9c286fe9dc9d7b7b9c6aa
+  data.tar.gz: 723c593505c7a54c26316862d0a5eef7072dbd2de174154517f7cb14a8bd3bae
 SHA512:
-  metadata.gz: f20e4c7312402beec67de7a458356f76bd932edbeadffdee83061d040c8eaaddf31ada6304873638237ca299b806054e7de9656ecfebaeaa7e8e5ddb83710a93
-  data.tar.gz: 5dcae9006b7b84d75ce05019f9ac3f6defe4305c52f574a7c3426a3f8ee098ee4cd0ecf0968d5669066886fbc77185cd477ea265df5509eaf66733e2d4dfb421
+  metadata.gz: d955e1011f1f02730adb0fdf689740cb494b15552fccc07ce86c4427170f42f599a87fc527512809af99d0d7365fb7a5af55c101e87e7b16df013e3e648781e7
+  data.tar.gz: 63fa2a296df01ba78e281be1bf4fed252bdad7959d355d5b112228b25f71a79e1a6af1094a623967eaaf69431fb440529b481a9b5b9a06ff90c6660a22d2c73f

data/actions/init.rb

@@ -87,7 +87,7 @@ if File.exist? o[:config]
   o[:config] = File.expand_path o[:config]
   $stderr.puts "Found bash configuration script: #{o[:config]}."
   rc_fh.puts "MIGA_STARTUP='#{o[:config]}'"
-  rc_fh.puts "source \"$MIGA_STARTUP\""
+  rc_fh.puts ". \"$MIGA_STARTUP\""
 end
 $stderr.puts ""
 
@@ -108,7 +108,7 @@ File.open(File.expand_path("utils/requirements.txt", miga), "r") do |fh|
     path = nil
     loop do
       if File.exist? o[:config]
-        d_path = File.dirname(`source "#{o[:config]}" && which "#{r[1]}"`)
+        d_path = File.dirname(`. "#{o[:config]}" && which "#{r[1]}"`)
       else
         d_path = File.dirname(`which "#{r[1]}"`)
       end

data/lib/miga/daemon.rb

@@ -86,10 +86,26 @@ class MiGA::Daemon < MiGA::MiGA
   def report_status
     f = File.open(File.expand_path('daemon/status.json', project.path), 'w')
     f.print JSON.pretty_generate(
-      jobs_running:@jobs_running, jobs_to_run:@jobs_to_run)
+      jobs_running: @jobs_running, jobs_to_run: @jobs_to_run)
     f.close
   end
 
+  ##
+  # Load the status of a previous instance.
+  def load_status
+    f_path = File.expand_path('daemon/status.json', project.path)
+    return unless File.size? f_path
+    status = JSON.parse(File.read(f_path), symbolize_names: true)
+    status.keys.each do |i|
+      status[i].map! do |j|
+        j.tap { |k| k[:ds] = project.dataset(k[:ds_name]) unless k[:ds].nil? }
+      end
+    end
+    @jobs_to_run = status[:jobs_to_run]
+    @jobs_running = status[:jobs_running]
+    purge!
+  end
+
   ##
   # Traverse datasets
   def check_datasets
@@ -192,15 +208,16 @@ class MiGA::Daemon < MiGA::MiGA
   ##
   # Run one loop step. Returns a Boolean indicating if the loop should continue.
   def in_loop
+    declare_alive
+    project.load
     if loop_i == -1
       say '-----------------------------------'
       say 'MiGA:%s launched.' % project.name
       say '-----------------------------------'
+      load_status
       @loop_i = 0
     end
     @loop_i += 1
-    declare_alive
-    project.load
     check_datasets
     check_project
     flush!

data/lib/miga/version.rb

@@ -10,7 +10,7 @@ module MiGA
   # - Float representing the major.minor version.
   # - Integer representing gem releases of the current version.
   # - Integer representing minor changes that require new version number.
-  VERSION = [0.3, 6, 1]
+  VERSION = [0.3, 6, 2]
   
   ##
   # Nickname for the current major.minor version.

data/utils/distance/commands.rb

@@ -14,17 +14,17 @@ module MiGA::DistanceRunner::Commands
     end
     # Full AAI
     aai_cmd(
-          tmp_file("proteins.fa"), target.result(:cds).file_path(:proteins),
+          tmp_file('proteins.fa'), target.result(:cds).file_path(:proteins),
           dataset.name, target.name, tmp_dbs[:aai]).tap{ checkpoint :aai }
   end
 
   ##
   # Estimates AAI against +target+ using hAAI
   def haai(target)
-    haai = aai_cmd(tmp_file("ess_genes.fa"),
+    haai = aai_cmd(tmp_file('ess_genes.fa'),
           target.result(:essential_genes).file_path(:ess_genes),
           dataset.name, target.name, tmp_dbs[:haai],
-          aai_save_rbm: "no-save-rbm", aai_p: opts[:haai_p])
+          aai_save_rbm: 'no-save-rbm', aai_p: opts[:haai_p])
     checkpoint :haai
     return nil if haai.nil? or haai.zero? or haai > 90.0
     aai = 100.0 - Math.exp(2.435076 + 0.4275193*Math.log(100.0-haai))
@@ -32,6 +32,7 @@ module MiGA::DistanceRunner::Commands
       conn.execute "insert into aai values(?, ?, ?, 0, 0, 0)",
             [dataset.name, target.name, aai]
     end
+    checkpoint :aai
     aai
   end
 
@@ -39,7 +40,7 @@ module MiGA::DistanceRunner::Commands
   # Calculates ANI against +target+
   def ani(target)
     # Check if the request makes sense
-    t = tmp_file("largecontigs.fa")
+    t = tmp_file('largecontigs.fa')
     r = target.result(:assembly)
     return nil if r.nil? or !File.size?(t)
     # Check if it's been calculated

data/utils/distance/pipeline.rb

@@ -64,9 +64,9 @@ module MiGA::DistanceRunner::Pipeline
     # Get taxonomy of closest relative
     from_ref_project = (project != ref_project)
     res_dir = from_ref_project ?
-          File.expand_path("data/09.distances/05.taxonomy", project.path) : home
+      File.expand_path('data/09.distances/05.taxonomy', project.path) : home
     Dir.mkdir res_dir unless Dir.exist? res_dir
-    File.open(File.expand_path("#{dataset.name}.done", res_dir), "w") do |fh|
+    File.open(File.expand_path("#{dataset.name}.done", res_dir), 'w') do |fh|
       fh.puts Time.now.to_s
     end
     dataset.add_result(from_ref_project ? :taxonomy : :distances, true)
@@ -75,25 +75,28 @@ module MiGA::DistanceRunner::Pipeline
     tax = ref_project.dataset(cr[0][0]).metadata[:tax] || {}
     # Run the test for each rank
     r = MiGA::TaxDist.aai_pvalues(cr[0][1], :intax).map do |k,v|
-      sig = ""
-      [0.5,0.1,0.05,0.01].each{ |i| sig << "*" if v<i }
-      [MiGA::Taxonomy.LONG_RANKS[k], (tax[k] || "?"), v, sig]
+      sig = ''
+      [0.5,0.1,0.05,0.01].each{ |i| sig << '*' if v<i }
+      [MiGA::Taxonomy.LONG_RANKS[k], (tax[k] || '?'), v, sig]
     end
     # Save test
     File.open(File.expand_path("#{dataset.name}.intax.txt", home), "w") do |fh|
       fh.puts "Closest relative: #{cr[0][0]} with AAI: #{cr[0][1]}."
-      fh.puts ""
+      fh.puts ''
       fh.puts MiGA::MiGA.tabulate(%w[Rank Taxonomy P-value Signif.], r)
-      fh.puts ""
-      fh.puts "Significance at p-value below: *0.5, **0.1, ***0.05, ****0.01."
+      fh.puts ''
+      fh.puts 'Significance at p-value below: *0.5, **0.1, ***0.05, ****0.01.'
     end
     return r
   end
 
   # Transfer the taxonomy to the current dataset
   def transfer_taxonomy(tax)
+    return if tax.nil?
     pval = (project.metadata[:tax_pvalue] || 0.05).to_f
-    tax_a = tax.select{ |i| i[1]!="?" && i[2]<=pval }.map { |i| i[0,2].join(":") }
+    tax_a = tax.
+      select { |i| i[1] != '?' && i[2] <= pval }.
+      map { |i| i[0,2].join(':') }
     dataset.metadata[:tax] = MiGA::Taxonomy.new(tax_a)
     dataset.save
   end

data/utils/find-medoid.R

@@ -7,8 +7,12 @@
 #= Load stuff
 argv <- commandArgs(trailingOnly=T)
 suppressPackageStartupMessages(library(ape))
+suppressPackageStartupMessages(library(enveomics.R))
 
-find_medoids <- function(dist, out, clades) {
+find_medoids <- function(ani.df, out, clades) {
+  if(nrow(ani.df)==0) return(NULL)
+  ani.df$d <- 1 - (ani.df$value/100)
+  dist <- enve.df2dist(ani.df, 'a', 'b', 'd', default.d = max(ani.df$d)*1.2)
   dist <- as.matrix(dist)
   cl <- read.table(clades, header = FALSE, sep = '\t', as.is = TRUE)[,1]
   medoids <- c()
@@ -27,5 +31,5 @@ find_medoids <- function(dist, out, clades) {
 
 #= Main
 load(argv[1])
-find_medoids(dist = ani.d, out = argv[2], clades = argv[3])
+find_medoids(ani.df = ani, out = argv[2], clades = argv[3])
 

data/utils/subclade/pipeline.rb

@@ -33,11 +33,9 @@ module MiGA::SubcladeRunner::Pipeline
     end
 
     # Find species medoids
-    if File.size? 'miga-project.dist.rdata'
-      src = File.expand_path('utils/find-medoid.R', MiGA::MiGA.root_path)
-      `Rscript '#{src}' miga-project.dist.rdata \
-        miga-project.ani95-medoids miga-project.ani95-clades`
-    end
+    src = File.expand_path('utils/find-medoid.R', MiGA::MiGA.root_path)
+    `Rscript '#{src}' ../../09.distances/03.ani/miga-project.Rdata \
+      miga-project.ani95-medoids miga-project.ani95-clades`
 
     # Propose clades
     ofh = File.open('miga-project.proposed-clades', 'w')

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 0.3.6.1
+  version: 0.3.6.2
 platform: ruby
 authors:
 - Luis M. Rodriguez-R
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2018-11-28 00:00:00.000000000 Z
+date: 2018-12-06 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: daemons