miga-base 0.7.25.0 → 0.7.26.1

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: fefd5ed0ec84f2b49d25243ecaec7e567000c04598605ba8a78d0a866c35e5b1
-  data.tar.gz: b0f473401ccf64d31fcfc0ed19b54a2b84d29c138e3f983a69083659fcfe547e
+  metadata.gz: 74e57f731ce86c12ef281aedd1e30448d432f793d3e1c1be85b91dc360f3e50b
+  data.tar.gz: 50ee4a65a402a35be72b21f4258b6b74b1cc2fb90bb4a675f77ad7ecf6090cc2
 SHA512:
-  metadata.gz: 2520f7169e91e38aed0027e679d0cbc126271a6948ce27916bef9a34299eb50df249568d06bbdb09c5ff13754ec7628d48d7154a18c5bf363628b69d241757c2
-  data.tar.gz: 0e684e321ec13e022f95d0499c2c83fea6230bbcadbaacce226e20423cda9ea7466fac929b579e29b6a50745b243da53b9d1697a5e08876b2d423d577205e269
+  metadata.gz: 8148b3c9693200bd02168118967122c0d77ba32bcf512b73e3c3951593f921f81d18f579f64c791859d4de3aba3d742ed06cbbd9926baa00dff832be7062a193
+  data.tar.gz: aa4d25c09558448455ee08a25b584802de1354298d5b3cc9881dd87b116bf2c98c834d6ae54efa097a7e3b802996db24714abbc76bc68d069533133b155c9d5d

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

@@ -14,6 +14,8 @@ class MiGA::Cli::Action::Init < MiGA::Cli::Action
     cli.defaults = {
       mytaxa: nil,
       rdp: nil,
+      reads: nil,
+      optional: nil,
       config: File.join(ENV['MIGA_HOME'], '.miga_modules'),
       ask: false,
       auto: false,
@@ -35,6 +37,16 @@ class MiGA::Cli::Action::Init < MiGA::Cli::Action
         'Should I try setting up the RDP classifier?',
         'By default: interactive (true if --auto)'
       ) { |v| cli[:rdp] = v }
+      opt.on(
+        '--[no-]read-processing',
+        'Should I try setting up read processing software?',
+        'By default: interactive (true if --auto)'
+      ) { |v| cli[:reads] = v }
+      opt.on(
+        '--[no-]optional',
+        'Should I try setting up the optional software?',
+        'Automatically sets answers for mytaxa, rdp, and reads'
+      ) { |v| cli[:optional] = v }
       opt.on(
         '--daemon-type STRING',
         'Type of daemon launcher, one of: bash, ssh, qsub, msub, slurm',
@@ -104,6 +116,8 @@ class MiGA::Cli::Action::Init < MiGA::Cli::Action
     rc_fh.puts "export MIGA_MYTAXA='#{cli[:mytaxa] ? 'yes' : 'no'}'"
     ask_for_optional(:rdp, 'RDP classifier')
     rc_fh.puts "export MIGA_RDP='#{cli[:rdp] ? 'yes' : 'no'}'"
+    ask_for_optional(:reads, 'read processing')
+    rc_fh.puts "export MIGA_READS='#{cli[:reads] ? 'yes' : 'no'}'"
     paths = {}
     rc_fh.puts 'MIGA_PATH=""'
     req_path = File.expand_path('utils/requirements.txt', MiGA.root_path)
@@ -123,20 +137,20 @@ class MiGA::Cli::Action::Init < MiGA::Cli::Action
   def define_software(ln)
     r = ln.chomp.split(/\t+/)
     return if %w[Software --------].include?(r[0])
-    return if r[0] =~ /\(mytaxa\)$/ && !cli[:mytaxa]
-    return if r[0] =~ /\(rdp\)$/ && !cli[:rdp]
+    %i[mytaxa rdp reads].each { |i| return if r[0] =~ /\(#{i}\)$/ && !cli[i] }
 
     r
   end
 
   def ask_for_optional(symbol, name)
-    if cli[symbol].nil?
-      cli[symbol] =
-        cli.ask_user(
-          "Should I include #{name} modules?",
-          'yes', %w(yes no)
-        ) == 'yes'
-    end
+    cli[symbol] = cli[:optional] if !cli[:optional].nil? && cli[symbol].nil?
+    return cli[symbol] unless cli[symbol].nil?
+
+    cli[symbol] =
+      cli.ask_user(
+        "Should I include #{name} modules?",
+        'yes', %w(yes no)
+      ) == 'yes'
   end
 
   def find_software(exec)
@@ -220,7 +234,7 @@ class MiGA::Cli::Action::Init < MiGA::Cli::Action
       run_cmd(cli, x)
     when :python
       x = "#{paths['python3'].shellescape} \
-            -m pip install #{pkg.shellescape} 2>&1"
+            -m pip install --user #{pkg.shellescape} 2>&1"
       run_cmd(cli, x)
     else
       raise "Unrecognized language: #{language}"

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

@@ -17,6 +17,14 @@ class MiGA::Cli::Action::Option < MiGA::Cli::Action
         'Value of the option to set (by default, option value is not changed)',
         'Recognized tokens: nil, true, false'
       ) { |v| cli[:value] = v }
+      opt.on(
+        '--about',
+        'Print additional information about the values supported by this option'
+      ) { |v| cli[:about] = v }
+      opt.on(
+        '--tab',
+        'Return a tab-delimited table'
+      ) { |v| cli[:tabular] = v }
       opt.on(
         '-o', '--output PATH',
         'Create output file instead of returning to STDOUT'
@@ -28,13 +36,24 @@ class MiGA::Cli::Action::Option < MiGA::Cli::Action
     unless cli[:value].nil?
       cli.ensure_par(
         { key: '-k' },
-        '%<name>s is mandatory when --value is set: please provide %<flag>s'
+        '%<name>s is mandatory when --value is set: provide %<flag>s'
       )
     end
     obj = cli.load_project_or_dataset
     io = cli[:output].nil? ? $stdout : File.open(cli[:output], 'w')
     if cli[:key].nil?
-      cli.table(%w[Key Value], obj.all_options.to_a, io)
+      opts = obj.all_options
+                .map { |k, v| [k, v, obj.assert_has_option(k)[:desc]] }
+      cli.table(%w[Key Value Definition], opts, io)
+    elsif cli[:about]
+      opt = obj.assert_has_option(cli[:key])
+      title = "#{cli[:key]}: #{opt[:desc]}"
+      io.puts title
+      io.puts '-' * title.length
+      opt.each do |k, v|
+        v = v[obj] if v.is_a? Proc
+        io.puts "#{k.to_s.capitalize}: #{v}" unless k == :desc
+      end
     else
       obj.set_option(cli[:key], cli[:value], true) unless cli[:value].nil?
       io.puts obj.option(cli[:key])

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

@@ -87,7 +87,7 @@ module MiGA::Cli::Action::Wf
     end
     opt.on(
       '--haai-p STRING',
-      'hAAI search engine. One of: blast+ (default), blat, diamond, no'
+      'hAAI search engine. One of: blast+ (default), fastaai, blat, diamond, no'
     ) { |v| cli[:haai_p] = v }
     opt.on(
       '--aai-p STRING',

data/lib/miga/result.rb

@@ -1,5 +1,4 @@
-# @package MiGA
-# @license Artistic-2.0
+# frozen_string_literal: true
 
 require 'miga/result/dates'
 require 'miga/result/source'
@@ -29,13 +28,17 @@ class MiGA::Result < MiGA::MiGA
       MiGA::Result.new(path)
     end
 
-    def create(path, force = false, &blk)
+    ##
+    # Check if +path+ describes a result and otherwise create
+    # it using the passed block. If +force+, ignore existing
+    # JSON in +path+ if any.
+    def create(path, force = false)
       FileUtils.rm(path) if force && File.exist?(path)
-      r_pre = self.load(path)
+      r_pre = load(path)
       return r_pre unless r_pre.nil?
 
       yield
-      self.load(path)
+      load(path)
     end
   end
 
@@ -49,7 +52,7 @@ class MiGA::Result < MiGA::MiGA
   # Load or create the MiGA::Result described by the JSON file +path+
   def initialize(path)
     @path = File.absolute_path(path)
-    MiGA::Result.exist?(@path) ? self.load : create
+    MiGA::Result.exist?(@path) ? load : create
   end
 
   ##
@@ -162,7 +165,7 @@ class MiGA::Result < MiGA::MiGA
       File.unlink s
     end
     MiGA::Json.generate(data, path)
-    self.load
+    load
   end
 
   ##
@@ -182,10 +185,9 @@ class MiGA::Result < MiGA::MiGA
   # Unlink result by removing the .done and .start timestamps and the
   # .json descriptor, but don't remove any other associated files
   def unlink
-    %i(start done).each do |i|
-      f = path(i) and File.exists?(f) and File.unlink(f)
+    %i[start done json].each do |i|
+      f = path(i) and File.exist?(f) and File.unlink(f)
     end
-    File.unlink path
   end
 
   ##
@@ -201,13 +203,14 @@ class MiGA::Result < MiGA::MiGA
 
     @data[:files] ||= {}
     self[:files].each do |k, files|
-      files = [files] unless files.kind_of? Array
+      files = [files] unless files.is_a? Array
       files.each do |file|
         case blk.arity
-        when 1; blk.call(file)
-        when 2; blk.call(k, file)
-        when 3; blk.call(k, file, File.expand_path(file, dir))
-        else; raise "Wrong number of arguments: #{blk.arity} for 1..3"
+        when 1 then blk.call(file)
+        when 2 then blk.call(k, file)
+        when 3 then blk.call(k, file, File.expand_path(file, dir))
+        else
+          raise "Wrong number of arguments: #{blk.arity} for 1..3"
         end
       end
     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 = [0.7, 25, 0].freeze
+  VERSION = [0.7, 26, 1].freeze
 
   ##
   # Nickname for the current major.minor version.
@@ -18,7 +18,7 @@ module MiGA
 
   ##
   # Date of the current gem release.
-  VERSION_DATE = Date.new(2021, 2, 22)
+  VERSION_DATE = Date.new(2021, 3, 1)
 
   ##
   # Reference of MiGA.

data/test/result_test.rb

@@ -38,6 +38,28 @@ class ResultTest < Test::Unit::TestCase
     assert_instance_of(MiGA::Result, r)
   end
 
+  def test_unlink
+    r = project.add_result(:clade_finding)
+    path = r.path
+    done = r.path(:done)
+    data = r.file_path(:empty)
+    assert(File.exist?(path))
+    assert(File.exist?(done))
+    assert(File.exist?(data))
+    r.unlink
+    assert(!File.exist?(path))
+    assert(!File.exist?(done))
+    assert(File.exist?(data))
+  end
+
+  def test_remove
+    r = project.add_result(:clade_finding)
+    data = r.file_path(:empty)
+    assert(File.exist?(data))
+    r.remove!
+    assert(!File.exist?(data))
+  end
+
   def test_result_source
     r = dataset.add_result(:trimmed_reads)
     assert_equal(dataset.name, r.source.name)

data/utils/distance/pipeline.rb

@@ -15,7 +15,7 @@ module MiGA::DistanceRunner::Pipeline
     values = send(metric, sbj_datasets)
     max_idx = values.map(&:to_f).each_with_index.max[1]
     max_val = values[max_idx]
-    val_med = sbj_dataset[max_idx].name
+    val_med = sbj_datasets[max_idx].name
     val_cls = max_idx + 1
     puts "[#{classif}] New max: #{val_med} (#{val_cls}): #{max_val}"
 

data/utils/distance/runner.rb

@@ -102,7 +102,8 @@ class MiGA::DistanceRunner
     cl_path = res.file_path :clades_ani95
     if !cl_path.nil? && File.size?(cl_path) && tsk[0] == :clade_finding
       clades = File.foreach(cl_path).map { |i| i.chomp.split(',') }
-      sbj_datasets = clades.find { |i| i.include?(closest[:ds]) }
+      sbj_dataset_names = clades.find { |i| i.include?(closest[:ds]) }
+      sbj_datasets = sbj_dataset_names&.map { |i| ref_project.dataset(i) }
       ani_after_aai(sbj_datasets, 80.0) if sbj_datasets
     end
 

data/utils/requirements.txt

@@ -10,12 +10,12 @@ FastANI		fastANI		https://github.com/ParBLiSS/FastANI				Required version: 1.1+
 HMMer 3.0+	hmmsearch	http://hmmer.janelia.org/software
 Bedtools	bedtools	http://bedtools.readthedocs.org/en/latest/
 Prodigal	prodigal	http://prodigal.ornl.gov
-IDBA		idba_ud		http://i.cs.hku.hk/~alse/hkubrg/projects/idba
 MCL		mcl		http://micans.org/mcl/
 Barrnap		barrnap		http://www.vicbioinformatics.com/software.barrnap.shtml
-Scythe		scythe		https://github.com/vsbuffalo/scythe				Required version: 0.991+
-FastQC		fastqc		http://www.bioinformatics.babraham.ac.uk/projects/fastqc
-SolexaQA++	SolexaQA++	http://solexaqa.sourceforge.net					Required version: v3.1.3+
+IDBA (reads)	idba_ud		http://i.cs.hku.hk/~alse/hkubrg/projects/idba
+Scythe (reads)	scythe		https://github.com/vsbuffalo/scythe				Required version: 0.991+
+FastQC (reads)	fastqc		http://www.bioinformatics.babraham.ac.uk/projects/fastqc
+SolexaQA++ (reads)	SolexaQA++	http://solexaqa.sourceforge.net				Required version: v3.1.3+
 OpenJDK (rdp)	java		https://adoptopenjdk.net/					Any Java VM would work
 MyTaxa (mytaxa)	MyTaxa		http://enve-omics.ce.gatech.edu/mytaxa
 Krona (mytaxa)	ktImportText	https://github.com/marbl/Krona/wiki

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 0.7.25.0
+  version: 0.7.26.1
 platform: ruby
 authors:
 - Luis M. Rodriguez-R
 autorequire:
 bindir: bin
 cert_chain: []
-date: 2021-02-22 00:00:00.000000000 Z
+date: 2021-03-01 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: daemons