miga-base 0.7.4.0 → 0.7.5.0

data/utils/subclade/temporal.rb

@@ -1,8 +1,6 @@
-
 require 'tmpdir'
 
 module MiGA::SubcladeRunner::Temporal
-
   # Create the empty temporal structure
   def create_temporals
   end

data/utils/subclades-compile.rb

@@ -1,49 +1,51 @@
 #!/usr/bin/env ruby
 
-$:.push File.expand_path(File.dirname(__FILE__) + "/lib")
 dir = ARGV.shift
 out = ARGV.shift or abort "Usage: #{$0} <classif.dir> <out.base>"
 
-def read_classif(dir, classif={})
-   classif_file = File.expand_path("miga-project.classif", dir)
-   return classif unless File.exist? classif_file
-   ready = File.expand_path('miga-project.ready', dir)
-   File.size?(ready) or raise "Incomplete recursion found at #{dir}"
-   File.unlink ready
-   fh = File.open(classif_file, "r")
-   klass = []
-   while ln = fh.gets
-      r = ln.chomp.split("\t")
-      classif[r[0]] ||= []
-      classif[r[0]] << r[1]
-      klass[r[1].to_i] = r[1]
-   end
-   fh.close
-   klass.each do |i|
-      d = File.expand_path("miga-project.sc-#{i}", dir)
-      classif = read_classif(d, classif) if Dir.exist? d
-   end
-   classif
+def read_classif(dir, classif = {})
+  classif_file = File.expand_path('miga-project.classif', dir)
+  return classif unless File.exist? classif_file
+
+  ready = File.expand_path('miga-project.ready', dir)
+  File.size?(ready) or raise "Incomplete recursion found at #{dir}"
+  File.unlink ready
+  fh = File.open(classif_file, 'r')
+  klass = []
+  while ln = fh.gets
+    r = ln.chomp.split("\t")
+    classif[r[0]] ||= []
+    classif[r[0]] << r[1]
+    klass[r[1].to_i] = r[1]
+  end
+  fh.close
+  klass.each do |i|
+    d = File.expand_path("miga-project.sc-#{i}", dir)
+    classif = read_classif(d, classif) if Dir.exist? d
+  end
+  classif
 end
 
-def print_tree(classif, col=0)
-   klass = classif.values.map{ |i| i[col] }.compact.uniq
-   if klass.size<=1
-      o = classif.keys
-   else
-      o = klass.map do |c|
-	 oo = print_tree(classif.select{ |k,v| v[col]==c }, col+1)
-	 "#{oo}[#{c}]" unless oo.nil?
-      end.compact
-   end
-   o.size==0 ? nil :
-      o.size==1 ? o[0] :
-      "(#{o.join(",")})"
+def print_tree(classif, col = 0)
+  klass = classif.values.map { |i| i[col] }.compact.uniq
+  if klass.size <= 1
+    o = classif.keys
+  else
+    o = klass.map do |c|
+      oo = print_tree(classif.select { |k, v| v[col] == c }, col + 1)
+      "#{oo}[#{c}]" unless oo.nil?
+    end.compact
+  end
+  case o.size
+  when 0; nil
+  when 1; o[0]
+  else; "(#{o.join(',')})"
+  end
 end
 
 c = read_classif(dir)
-max_depth = c.values.map{|i| i.count}.max
+max_depth = c.values.map { |i| i.count }.max
 File.open("#{out}.tsv", 'w') do |fh|
-  c.each { |k,v| fh.puts ([k] + v + ["0"]*(max_depth-v.count)).join("\t") }
+  c.each { |k, v| fh.puts ([k] + v + ['0'] * (max_depth - v.count)).join("\t") }
 end
-File.open("#{out}.nwk", 'w') { |fh| fh.puts print_tree(c).to_s + ";" }
+File.open("#{out}.nwk", 'w') { |fh| fh.puts print_tree(c).to_s + ';' }

data/utils/subclades.rb

@@ -4,6 +4,6 @@ require_relative 'subclade/runner.rb'
 
 project = ARGV.shift
 step = ARGV.shift
-opts = Hash[ ARGV.map{ |i| i.split("=",2).tap{ |j| j[0] = j[0].to_sym } } ]
+opts = Hash[ARGV.map { |i| i.split("=", 2).tap { |j| j[0] = j[0].to_sym } }]
 runner = MiGA::SubcladeRunner.new(project, step, opts)
 runner.go!

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 0.7.4.0
+  version: 0.7.5.0
 platform: ruby
 authors:
 - Luis M. Rodriguez-R
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2020-04-28 00:00:00.000000000 Z
+date: 2020-05-13 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: daemons
@@ -214,6 +214,7 @@ files:
 - scripts/trimmed_fasta.bash
 - scripts/trimmed_reads.bash
 - test/common_test.rb
+- test/daemon_helper.rb
 - test/daemon_test.rb
 - test/dataset_test.rb
 - test/format_test.rb