miga-base 0.5.5.0 → 0.5.5.1

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 59649a6c1b7aaa4e3c0db090a828469e9595eba42d311eff114417741a2816bd
-  data.tar.gz: a765a214e5b64d3f1758ae50942dc7f0649f438e8c2b12312648012d9cceeacc
+  metadata.gz: 405d3cf6f84fa7f78f8026d1392be3fd8c32b3caea3d9e2c4c29a511ffeccb6c
+  data.tar.gz: 29108306ca8358a1155f791a4a586fce73eb9dccbbf2841869ed450064508774
 SHA512:
-  metadata.gz: f76b1691a30d7ce94314a4bd8d22601d86d3101c2db33f262b53548bba817d17bc783f2c93ec0502844adda1f5a17bd0c530e82c82c7fb590f07abf8ffc6788c
-  data.tar.gz: c27cd47089f65633cefaca74cd217967b583df43d60682dce9f755a6610fdc6e728638d8d7b884f4de627de79b48080c8325f7b4d60794253f69511c15f997a4
+  metadata.gz: 84e3264d6d55ff810b6ba0ae415abac248b65ec411fde5780107c1974923c2ef7da2cd1ae86c74f36aad94af03534b1f326327f797eaf6aec1c2a20c444dfa8d
+  data.tar.gz: cff5d84655677d1eabe298478d099074c1769cb4c74a753b10e3cbd62fb9fb0ed3b4df2ccc8924799c04d8a2e6be6ac7b3720f8ccbf7d83885cf17c5537fcd97

data/lib/miga/cli/action/tax_dist.rb

@@ -16,7 +16,12 @@ class MiGA::Cli::Action::TaxDist < MiGA::Cli::Action
         '-i', '--index FILE',
         'Pre-calculated tax-index (in tabular format) to be used',
         'If passed, dataset filtering arguments are ignored'
-        ){ |v| cli[:index] = v }
+      ) { |v| cli[:index] = v }
+      opt.on(
+        '-m', '--metric STR',
+        'Distance metric used to evaluate the distribution',
+        'By default: AAI for genomes projects, ANI for clade projects'
+      ) { |v| cli[:metric] = v.downcase }
     end
   end
 
@@ -43,9 +48,9 @@ class MiGA::Cli::Action::TaxDist < MiGA::Cli::Action
 
   def read_distances
     p = cli.load_project
-    metric = p.is_clade? ? 'ani' : 'aai'
-    res_n  = "#{metric}_distances"
-    cli.say "Reading distances: 1-#{metric.upcase}"
+    cli[:metric] ||= p.is_clade? ? 'ani' : 'aai'
+    res_n  = "#{cli[:metric]}_distances"
+    cli.say "Reading distances: 1-#{cli[:metric].upcase}"
     res = p.result(res_n)
     raise "#{res_n} not yet calculated" if res.nil?
     matrix = res.file_path(:matrix)
@@ -57,9 +62,9 @@ class MiGA::Cli::Action::TaxDist < MiGA::Cli::Action
       next if mfh.lineno == 1
       row = ln.chomp.split("\t")
       dist[cannid(row[1], row[2])] = [row[3], row[5], row[6], 0, ['root:biota']]
-      cli.advance("Ln: #{mfh.lineno}") if (mfh.lineno % 1_000) == 0
+      cli.advance('Lines:', mfh.lineno, nil, false) if (mfh.lineno % 1_000) == 0
     end
-    cli.say "  Lines: #{mfh.lineno}"
+    cli.say ''
     mfh.close
     dist
   end
@@ -84,7 +89,7 @@ class MiGA::Cli::Action::TaxDist < MiGA::Cli::Action
     cli.say 'Traversing taxonomy'
     rank_i = 0
     Taxonomy.KNOWN_RANKS.each do |rank|
-      cli.say "o #{rank}: "
+      next if rank == :ns
       rank_n = 0
       rank_i += 1
       in_rank = nil
@@ -110,7 +115,7 @@ class MiGA::Cli::Action::TaxDist < MiGA::Cli::Action
           end
         end
       end
-      cli.say "#{rank_n} pairs of datasets"
+      cli.say "o #{rank}: #{rank_n} pairs of datasets"
     end
     dist
   end

data/lib/miga/cli/action/tax_index.rb

@@ -26,11 +26,14 @@ class MiGA::Cli::Action::TaxIndex < MiGA::Cli::Action
   def perform
     cli.ensure_par(index: '-i')
     ds = cli.load_and_filter_datasets
-    ds.keep_if {|d| !d.metadata[:tax].nil? }
 
     cli.say 'Indexing taxonomy'
     tax_index = MiGA::TaxIndex.new
-    ds.each { |d| tax_index << d }
+    ds.each_with_index do |d, i|
+      cli.advance('Datasets:', i, ds.size, false)
+      tax_index << d unless d.metadata[:tax].nil?
+    end
+    cli.say ''
 
     cli.say 'Saving index'
     File.open(cli[:index], 'w') do |fh|

data/lib/miga/cli/objects_helper.rb

@@ -40,14 +40,20 @@ module MiGA::Cli::ObjectsHelper
     say 'Listing datasets'
     ds = self[:dataset].nil? ?
       load_project.datasets : [load_dataset(silent)].compact
-    ds.select! { |d| d.is_ref? == self[:ref] } unless self[:ref].nil?
-    ds.select! { |d| d.is_active? == self[:active] } unless self[:active].nil?
+    k = 0
+    n = ds.size
     ds.select! do |d|
-      self[:multi] ? d.is_multi? : d.is_nonmulti?
-    end unless self[:multi].nil?
-    ds.select! do |d|
-      (not d.metadata[:tax].nil?) && d.metadata[:tax].in?(self[:taxonomy])
-    end unless self[:taxonomy].nil?
+      advance('Datasets:', k += 1, n, false)
+      o = true
+      o &&= (d.is_ref? == self[:ref]) unless self[:ref].nil?
+      o &&= (d.is_active? == self[:active]) unless self[:active].nil?
+      o &&= (self[:multi] ? d.is_multi? :
+            d.is_nonmulti?) unless self[:multi].nil?
+      o &&= (not d.metadata[:tax].nil?) &&
+            d.metadata[:tax].in?(self[:taxonomy]) unless self[:taxonomy].nil?
+      o
+    end
+    say ''
     ds = ds.values_at(self[:dataset_k]-1) unless self[:dataset_k].nil?
     @objects[:filtered_datasets] = ds
   end

data/lib/miga/cli.rb

@@ -118,7 +118,7 @@ class MiGA::Cli < MiGA::MiGA
   # The report goes to $stderr iff --verborse
   def advance(step, n = 0, total = nil, bin = true)
     return unless self[:verbose]
-    adv = total.nil? ? '' :
+    adv = total.nil? ? (n == 0 ? '' : num_suffix(n, bin)) :
       ('%.1f%% (%s/%s)' % [100 * n / total,
         num_suffix(n, bin), num_suffix(total, bin)])
     $stderr.print("[%s] %s %s    \r" % [Time.now, step, adv])

data/lib/miga/dataset.rb

@@ -38,16 +38,12 @@ class MiGA::Dataset < MiGA::MiGA
   # Datasets are uniquely identified by +name+ in a project.
   attr_reader :name
   
-  ##
-  # MiGA::Metadata with information about the dataset.
-  attr_reader :metadata
-  
   ##
   # Create a MiGA::Dataset object in a +project+ MiGA::Project with a
   # uniquely identifying +name+. +is_ref+ indicates if the dataset is to
   # be treated as reference (true, default) or query (false). Pass any
   # additional +metadata+ as a Hash.
-  def initialize(project, name, is_ref=true, metadata={})
+  def initialize(project, name, is_ref = true, metadata = {})
     unless name.miga_name?
       raise 'Invalid name, please use only alphanumerics and underscores: ' +
         name.to_s
@@ -55,8 +51,16 @@ class MiGA::Dataset < MiGA::MiGA
     @project = project
     @name = name
     metadata[:ref] = is_ref
-    @metadata = MiGA::Metadata.new(
-      File.expand_path("metadata/#{name}.json", project.path), metadata )
+    @metadata_future = [
+      File.expand_path("metadata/#{name}.json", project.path),
+      metadata
+    ]
+  end
+
+  ##
+  # MiGA::Metadata with information about the dataset.
+  def metadata
+    @metadata ||= MiGA::Metadata.new(*@metadata_future)
   end
   
   ##

data/lib/miga/project.rb

@@ -49,11 +49,11 @@ class MiGA::Project < MiGA::MiGA
     dirs = [path] + @@FOLDERS.map{|d| "#{path}/#{d}" } +
       @@DATA_FOLDERS.map{ |d| "#{path}/data/#{d}"}
     dirs.each{ |d| Dir.mkdir(d) unless Dir.exist? d }
-    @metadata = MiGA::Metadata.new(self.path + "/miga.project.json",
+    @metadata = MiGA::Metadata.new(
+      File.expand_path('miga.project.json', path),
       {datasets: [], name: File.basename(path)})
-    FileUtils.cp("#{ENV["MIGA_HOME"]}/.miga_daemon.json",
-      "#{path}/daemon/daemon.json") unless
-        File.exist? "#{path}/daemon/daemon.json"
+    d_path = File.expand_path('daemon/daemon.json', path)
+    File.open(d_path, 'w') { |fh| fh.puts '{}' } unless File.exist? d_path
     self.load
   end
 

data/lib/miga/tax_index.rb

@@ -1,7 +1,7 @@
 # @package MiGA
 # @license Artistic-2.0
 
-require "miga/taxonomy"
+require 'miga/taxonomy'
 
 ##
 # Indexing methods based on taxonomy.
@@ -18,7 +18,7 @@ class MiGA::TaxIndex < MiGA::MiGA
   ##
   # Initialize an empty MiGA::TaxIndex
   def initialize
-    @root = MiGA::TaxIndexTaxon.new :root, "biota"
+    @root = MiGA::TaxIndexTaxon.new :root, 'biota'
     @datasets = []
   end
 
@@ -64,7 +64,9 @@ class MiGA::TaxIndex < MiGA::MiGA
 
   ##
   # Generate tabular String for the index.
-  def to_tab(unknown=false) ; root.to_tab(unknown) ; end
+  def to_tab(unknown = false)
+    root.to_tab(unknown)
+  end
 end
 
 ##
@@ -94,7 +96,7 @@ class MiGA::TaxIndexTaxon < MiGA::MiGA
 
   ##
   # String representation of the taxon.
-  def tax_str ; "#{rank}:#{name.nil? ? "?" : name}" ; end
+  def tax_str ; "#{rank}:#{name.nil? ? '?' : name}" ; end
 
   ##
   # Add child at +rank+ with +name+.
@@ -142,11 +144,12 @@ class MiGA::TaxIndexTaxon < MiGA::MiGA
   ##
   # Tabular String of the taxon.
   def to_tab(unknown, indent=0)
-    o = ""
-    o = "#{" " * indent}#{tax_str}: #{datasets_count}\n" if
-      unknown or not datasets.empty? or not name.nil?
+    o = ''
+    if unknown or not datasets.empty? or not name.nil?
+      o = "#{' ' * indent}#{tax_str}: #{datasets_count}\n"
+    end
     indent += 2
-    datasets.each{ |ds| o << "#{" " * indent}# #{ds.name}\n" }
+    datasets.each{ |ds| o << "#{' ' * indent}# #{ds.name}\n" }
     children.each{ |it| o << it.to_tab(unknown, indent) }
     o
   end

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 = [0.5, 5, 0]
+  VERSION = [0.5, 5, 1]
 
   ##
   # Nickname for the current major.minor version.

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 0.5.5.0
+  version: 0.5.5.1
 platform: ruby
 authors:
 - Luis M. Rodriguez-R