miga-base 0.7.23.0 → 0.7.25.3

data/utils/distance/database.rb

@@ -22,12 +22,16 @@ module MiGA::DistanceRunner::Database
         end
       end
       # Initialize if it doesn't exist
-      SQLite3::Database.new(dbs[m]) do |conn|
-        conn.execute "create table if not exists #{t}(" +
-                     "seq1 varchar(256), seq2 varchar(256), " +
-                     "#{t} float, sd float, n int, omega int" +
-                     ")"
-      end unless File.size? dbs[m]
+      unless File.size? dbs[m]
+        SQLite3::Database.new(dbs[m]) do |conn|
+          conn.execute <<~SQL
+            create table if not exists #{t}(
+              seq1 varchar(256), seq2 varchar(256),
+              #{t} float, sd float, n int, omega int
+            )
+          SQL
+        end
+      end
       # Copy over to (local) temporals
       @tmp_dbs[m] = tmp_file("#{m}.db")
       FileUtils.cp(dbs[m], tmp_dbs[m])
@@ -66,7 +70,7 @@ module MiGA::DistanceRunner::Database
     return y unless y.nil? || y.zero?
 
     # Check if self.dataset <- target is done (another thread)
-    if dataset.is_ref? && project.path == ref_project.path
+    if dataset.ref? && project.path == ref_project.path
       y = data_from_db(
         target.name, dataset.name, ref_db(metric, target.name), metric
       )
@@ -92,27 +96,72 @@ module MiGA::DistanceRunner::Database
   # possible number of matches
   def data_from_db(n1, n2, db, metric)
     y = nil
+    table = metric == :haai ? :aai : metric
     SQLite3::Database.new(db) do |conn|
       y = conn.execute(
-        "select #{metric}, sd, n, omega from #{metric} where seq1=? and seq2=?",
+        "select #{table}, sd, n, omega from #{table} where seq1=? and seq2=?",
         [n1, n2]
       ).first
-    end if File.size? db
+    end if File.size?(db)
     y
   end
 
   ##
   # Save +data+ of +metric+ between +n1+ and +n2+ in the +db+ database.
   def data_to_db(n1, n2, db, metric, data)
+    table = metric == :haai ? :aai : metric
     SQLite3::Database.new(db) do |conn|
       conn.execute(
-        "insert into #{metric} (seq1, seq2, #{metric}, sd, n, omega) " +
+        "insert into #{table} (seq1, seq2, #{table}, sd, n, omega) " +
         "values (?, ?, ?, ?, ?, ?)", [n1, n2] + data
       )
     end
     checkpoint metric
   end
 
+  ##
+  # Saves +data+ of +metric+ in batch to the temporary database,
+  # and assumes query is +#dataset+. +data+ must be a hash with target names
+  # as key and arrays as values with: [val, sd, n, omega]
+  def batch_data_to_db(metric, data)
+    db = tmp_dbs[metric]
+    table = metric == :haai ? :aai : metric
+    `cp #{db} ~/here.db`
+    SQLite3::Database.new(db) do |conn|
+      data.each do |k, v|
+        sql = <<~SQL
+                insert into #{table} (
+                  seq1, seq2, #{table}, sd, n, omega
+                ) values (?, ?, ?, ?, ?, ?)
+              SQL
+        conn.execute(sql, [dataset.name, k] + v)
+      end
+    end
+    checkpoint(metric)
+  end
+
+  ##
+  # Retrieves data of +metric+ in batch from the temporary database,
+  # and assumes query is +#dataset+. The output data is a hash with the same
+  # structure described for +#batch_data_to_db+
+  def batch_data_from_db(metric)
+    db = tmp_dbs[metric]
+    table = metric == :haai ? :aai : metric
+    data = {}
+    SQLite3::Database.new(db) do |conn|
+      sql = "select seq2, #{table}, sd, n, omega from #{table}"
+      conn.execute(sql).each { |row| data[row.shift] = row }
+    end
+    data
+  end
+
+  ##
+  # Retrieve only +metric+ values against +names+
+  def batch_values_from_db(metric, names)
+    data = batch_data_from_db(metric)
+    names.map { |i| data[i]&.first }
+  end
+
   ##
   # Iterates for each entry in +db+
   def foreach_in_db(db, metric, &blk)
@@ -120,4 +169,14 @@ module MiGA::DistanceRunner::Database
       conn.execute("select * from #{metric}").each { |r| blk[r] }
     end
   end
+
+  ##
+  # Select only those targets that are not yet stored in either direction
+  def pending_targets(targets, metric)
+    saved = batch_data_from_db(metric).keys
+    targets
+      .compact
+      .select { |i| !saved.include?(i.name) }
+      .select { |i| !stored_value(i, metric)&.> 0.0 }
+  end
 end

data/utils/distance/pipeline.rb

@@ -11,19 +11,14 @@ module MiGA::DistanceRunner::Pipeline
     val_med = ''
     val_cls = nil
     i_n = 0
-    File.open(med, 'r') do |med_fh|
-      med_fh.each_line do |med_ln|
-        i_n += 1
-        med_ln.chomp!
-        val = send(metric, ref_project.dataset(med_ln))
-        if !val.nil? and val >= max_val
-          max_val = val
-          val_med = med_ln
-          val_cls = i_n
-          puts "[#{classif}] New max: #{val_med} (#{val_cls}): #{max_val}"
-        end
-      end
-    end
+    sbj_datasets = File.foreach(med).map { |i| ref_project.dataset(i.chomp) }
+    values = send(metric, sbj_datasets)
+    max_idx = values.map(&:to_f).each_with_index.max[1]
+    max_val = values[max_idx]
+    val_med = sbj_datasets[max_idx].name
+    val_cls = max_idx + 1
+    puts "[#{classif}] New max: #{val_med} (#{val_cls}): #{max_val}"
+
     classif = "#{classif}/miga-project.sc-#{val_cls}"
     result_fh.puts [val_cls, val_med, max_val, classif].join("\t")
     classify(clades, classif, metric, result_fh, val_cls)
@@ -31,12 +26,9 @@ module MiGA::DistanceRunner::Pipeline
 
   # Run distances against datasets listed in metadata's +:dist_req+
   def distances_by_request(metric)
-    return unless dataset.metadata[:dist_req]
-
     $stderr.puts 'Running distances by request'
-    dataset.metadata[:dist_req].each do |target|
-      ds = ref_project.dataset(target) and send(metric, ds)
-    end
+    sbj_datasets = dataset.option(:dist_req).map { |i| ref_project.dataset(i) }
+    send(metric, sbj_datasets)
   end
 
   # Builds a tree with all visited medoids from any classification level
@@ -76,8 +68,10 @@ module MiGA::DistanceRunner::Pipeline
     $stderr.puts "Testing taxonomy | opts = #{opts}"
     # 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
+    res_dir =
+      from_ref_project ?
+        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|
       fh.puts Time.now.to_s
@@ -112,7 +106,7 @@ module MiGA::DistanceRunner::Pipeline
     $stderr.puts 'Transferring taxonomy'
     return if tax.nil?
 
-    pval = (project.metadata[:tax_pvalue] || 0.05).to_f
+    pval = project.option(:tax_pvalue)
     tax_a = tax
             .select { |i| i[1] != '?' && i[2] <= pval }
             .map { |i| i[0, 2].join(':') }

data/utils/distance/runner.rb

@@ -1,67 +1,48 @@
 require_relative 'base.rb'
-require_relative 'temporal.rb'
-require_relative 'database.rb'
-require_relative 'commands.rb'
-require_relative 'pipeline.rb'
 
 class MiGA::DistanceRunner
-  include MiGA::DistanceRunner::Temporal
-  include MiGA::DistanceRunner::Database
-  include MiGA::DistanceRunner::Commands
-  include MiGA::DistanceRunner::Pipeline
-
   attr_reader :project, :ref_project, :dataset, :opts, :home
   attr_reader :tmp, :tmp_dbs, :dbs, :db_counts
 
   def initialize(project_path, dataset_name, opts_hash = {})
     @opts = opts_hash
-    @project = MiGA::Project.load(project_path) or
-      raise "No project at #{project_path}"
+    @project = MiGA::Project.load(project_path)
+    @project or raise "No project at #{project_path}"
     @dataset = project.dataset(dataset_name)
     @home = File.expand_path('data/09.distances', project.path)
 
     # Default opts
-    if project.metadata[:aai_save_rbm] == false
-      @opts[:aai_save_rbm] ||= 'no-save-rbm'
-    end
-    @opts[:aai_save_rbm] ||= ENV.fetch('MIGA_AAI_SAVE_RBM') do
-      project.is_clade? ? 'save-rbm' : 'no-save-rbm'
-    end
-    @opts[:thr] ||= ENV.fetch('CORES') { 2 }.to_i
-    if opts[:run_taxonomy] and project.metadata[:ref_project]
-      ref_path = project.metadata[:ref_project]
+    if opts[:run_taxonomy] && project.option(:ref_project)
+      ref_path = project.option(:ref_project)
       @home = File.expand_path('05.taxonomy', @home)
       @ref_project = MiGA::Project.load(ref_path)
       raise "Cannot load reference project: #{ref_path}" if @ref_project.nil?
-    elsif !opts[:run_taxonomy] and dataset.metadata[:db_project]
-      ref_path = dataset.metadata[:db_project]
-      if project.metadata[:db_proj_dir]
-        ref_path = File.expand_path(ref_path, project.metadata[:db_proj_dir])
+    elsif !opts[:run_taxonomy] && dataset.option(:db_project)
+      ref_path = dataset.option(:db_project)
+      if project.option(:db_proj_dir)
+        ref_path = File.expand_path(ref_path, project.option(:db_proj_dir))
       end
       @ref_project = MiGA::Project.load(ref_path)
       raise "Cannot load reference project: #{ref_path}" if @ref_project.nil?
     else
       @ref_project = project
     end
-    [:haai_p, :aai_p, :ani_p, :distances_checkpoint].each do |m|
-      @opts[m] ||= ref_project.metadata[m]
+    @opts[:thr] ||= ENV.fetch('CORES') { 1 }.to_i
+    %i[haai_p aai_p ani_p distances_checkpoint aai_save_rbm].each do |m|
+      @opts[m] ||= ref_project.option(m)
     end
-    @opts[:aai_p] ||= 'blast+'
-    @opts[:ani_p] ||= 'blast+'
-    @opts[:distances_checkpoint] ||= 10
-    @opts[:distances_checkpoint] = @opts[:distances_checkpoint].to_i
     $stderr.puts "Options: #{opts}"
   end
 
   # Launch the appropriate analysis
   def go!
     $stderr.puts "Launching analysis"
-    return if dataset.is_multi?
+    return if dataset.multi?
 
     Dir.mktmpdir do |tmp_dir|
       @tmp = tmp_dir
       create_temporals
-      opts[:run_taxonomy] ? go_taxonomy! : dataset.is_ref? ? go_ref! : go_query!
+      opts[:run_taxonomy] ? go_taxonomy! : dataset.ref? ? go_ref! : go_query!
     end
   end
 
@@ -72,12 +53,11 @@ class MiGA::DistanceRunner
     initialize_dbs! true
 
     # first-come-first-serve traverse
+    sbj = []
     ref_project.each_dataset do |ds|
-      next if !ds.is_ref? or ds.is_multi? or ds.result(:essential_genes).nil?
-
-      puts "[ #{Time.now} ] #{ds.name}"
-      ani_after_aai(ds)
+      sbj << ds if ds.ref? && !ds.multi? && ds.result(:essential_genes)
     end
+    ani_after_aai(sbj)
 
     # Finalize
     %i[haai aai ani].each { |m| checkpoint! m if db_counts[m] > 0 }
@@ -88,7 +68,7 @@ class MiGA::DistanceRunner
   def go_query!
     $stderr.puts 'Launching analysis for query dataset'
     # Check if project is ready
-    tsk = ref_project.is_clade? ? [:subclades, :ani] : [:clade_finding, :aai]
+    tsk = ref_project.clade? ? [:subclades, :ani] : [:clade_finding, :aai]
     res = ref_project.result(tsk[0])
     return if res.nil?
 
@@ -105,27 +85,26 @@ class MiGA::DistanceRunner
     par_dir = File.dirname(File.expand_path(classif, res.dir))
     par = File.expand_path('miga-project.classif', par_dir)
     closest = { dataset: nil, ani: 0.0 }
+    sbj_datasets = []
     if File.size? par
       File.open(par, 'r') do |fh|
         fh.each_line do |ln|
           r = ln.chomp.split("\t")
-          next unless r[1].to_i == val_cls
-
-          ani = ani_after_aai(ref_project.dataset(r[0]), 80.0)
-          unless ani.nil? || ani < closest[:ani]
-            closest = { ds: r[0], ani: ani }
-          end
+          sbj_datasets << ref_project.dataset(r[0]) if r[1].to_i == val_cls
         end
       end
+      ani = ani_after_aai(sbj_datasets, 80.0)
+      ani_max = ani.map(&:to_f).each_with_index.max
+      closest = { ds: sbj_datasets[ani_max[1]].name, ani: ani_max[0] }
     end
 
     # Calculate all the AAIs/ANIs against the closest ANI95-clade (if AAI > 80%)
     cl_path = res.file_path :clades_ani95
-    if !cl_path.nil? and File.size? cl_path and tsk[0] == :clade_finding
-      File.foreach(cl_path)
-          .map { |i| i.chomp.split(',') }
-          .find(lambda { [] }) { |i| i.include? closest[:ds] }
-          .each { |i| ani_after_aai(ref_project.dataset(i), 80.0) }
+    if !cl_path.nil? && File.size?(cl_path) && tsk[0] == :clade_finding
+      clades = File.foreach(cl_path).map { |i| i.chomp.split(',') }
+      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
 
     # Finalize
@@ -137,7 +116,7 @@ class MiGA::DistanceRunner
   # Launch analysis for taxonomy jobs
   def go_taxonomy!
     $stderr.puts 'Launching taxonomy analysis'
-    return unless project.metadata[:ref_project]
+    return unless project.option(:ref_project)
 
     go_query! # <- yeah, it's actually the same, just different ref_project
   end

data/utils/distance/temporal.rb

@@ -24,8 +24,10 @@ module MiGA::DistanceRunner::Temporal
     end
   end
 
-  # Temporal file with extension +ext+
-  def tmp_file(ext)
+  # Temporal file with extension +ext+, or a unique ID if +ext+ is +nil+
+  def tmp_file(ext = nil)
+    @_tmp_count ||= 0
+    ext ||= "#{@_tmp_count += 1}.tmp"
     File.expand_path("#{dataset.name}.#{ext}", tmp)
   end
 

data/utils/distances.rb

@@ -2,8 +2,8 @@
 
 require_relative 'distance/runner.rb'
 
-dataset = ARGV.shift
 project = ARGV.shift
+dataset = ARGV.shift
 opts = Hash[ARGV.map { |i| i.split("=", 2).tap { |j| j[0] = j[0].to_sym } }]
-runner = MiGA::DistanceRunner.new(dataset, project, opts)
+runner = MiGA::DistanceRunner.new(project, dataset, opts)
 runner.go!

data/utils/index_metadata.rb

@@ -17,8 +17,7 @@ def searchable(db, d, k, v)
 end
 
 p.each_dataset do |d|
-  next unless d.is_ref?
-  next unless d.is_active?
+  next unless d.ref? && d.active?
 
   searchable(db, d, :name, d.name)
   d.metadata.each do |k, v|

data/utils/requirements.txt

@@ -1,7 +1,7 @@
 Software	Test exec	Website								Notes
 --------	---------	-------								-----
 Ruby		ruby		https://www.ruby-lang.org/					Required version: 2.3+
-Python		python		https://www.python.org/						Required version: 3+
+Python		python3		https://www.python.org/						Required version: 3+
 R		R		http://www.r-project.org/
 SQLite3		sqlite3		https://www.sqlite.org/
 NCBI BLAST+	blastp		ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST

data/utils/subclade/runner.rb

@@ -18,19 +18,18 @@ class MiGA::SubcladeRunner
       @step == :clade_finding ? '01.find.running' : '02.ani.running'
     )
     @opts[:thr] ||= ENV.fetch('CORES') { 2 }.to_i
-    @opts[:run_clades] = !!@project.metadata.data.fetch(:run_clades) { true }
-    @opts[:gsp_ani] = @project.metadata.data.fetch(:gsp_ani) { 95.0 }.to_f
-    @opts[:gsp_aai] = @project.metadata.data.fetch(:gsp_aai) { 90.0 }.to_f
-    @opts[:gsp_metric] =
-      @project.metadata.data.fetch(:gsp_metric) { 'ani' }.to_s
+    @opts[:run_clades] = @project.option(:run_clades)
+    @opts[:gsp_ani] = @project.option(:gsp_ani)
+    @opts[:gsp_aai] = @project.option(:gsp_aai)
+    @opts[:gsp_metric] = @project.option(:gsp_metric)
   end
 
   # Launch the appropriate analysis
   def go!
     return if project.type == :metagenomes
 
-    unless @project.dataset_names.any? { |i| @project.dataset(i).is_ref? }
-      FileUtils.touch(File.expand_path('miga-project.empty', @home))
+    unless @project.dataset_names.any? { |i| @project.dataset(i).ref? }
+      FileUtils.touch(File.join(@home, 'miga-project.empty'))
       return
     end
     Dir.chdir home
@@ -44,15 +43,15 @@ class MiGA::SubcladeRunner
   # Launch analysis for clade_finding
   def go_clade_finding!
     cluster_species
-    unless project.is_clade?
-      subclades :aai
+    unless project.clade?
+      subclades(:aai)
       compile
     end
   end
 
   # Launch analysis for subclades
   def go_subclades!
-    subclades :ani
+    subclades(:ani)
     compile
   end
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 0.7.23.0
+  version: 0.7.25.3
 platform: ruby
 authors:
 - Luis M. Rodriguez-R
-autorequire:
+autorequire: 
 bindir: bin
 cert_chain: []
-date: 2021-02-09 00:00:00.000000000 Z
+date: 2021-02-26 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: daemons
@@ -152,6 +152,7 @@ files:
 - lib/miga/cli/action/ncbi_get.rb
 - lib/miga/cli/action/new.rb
 - lib/miga/cli/action/next_step.rb
+- lib/miga/cli/action/option.rb
 - lib/miga/cli/action/preproc_wf.rb
 - lib/miga/cli/action/quality_wf.rb
 - lib/miga/cli/action/rm.rb
@@ -174,6 +175,7 @@ files:
 - lib/miga/common/path.rb
 - lib/miga/common/with_daemon.rb
 - lib/miga/common/with_daemon_class.rb
+- lib/miga/common/with_option.rb
 - lib/miga/common/with_result.rb
 - lib/miga/daemon.rb
 - lib/miga/daemon/base.rb
@@ -247,6 +249,7 @@ files:
 - test/taxonomy_test.rb
 - test/test_helper.rb
 - test/with_daemon_test.rb
+- test/with_option_test.rb
 - utils/adapters.fa
 - utils/cleanup-databases.rb
 - utils/core-pan-plot.R
@@ -258,273 +261,6 @@ files:
 - utils/distance/temporal.rb
 - utils/distances.rb
 - utils/domain-ess-genes.rb
-- utils/enveomics/Docs/recplot2.md
-- utils/enveomics/Examples/aai-matrix.bash
-- utils/enveomics/Examples/ani-matrix.bash
-- utils/enveomics/Examples/essential-phylogeny.bash
-- utils/enveomics/Examples/unus-genome-phylogeny.bash
-- utils/enveomics/LICENSE.txt
-- utils/enveomics/Makefile
-- utils/enveomics/Manifest/Tasks/aasubs.json
-- utils/enveomics/Manifest/Tasks/blasttab.json
-- utils/enveomics/Manifest/Tasks/distances.json
-- utils/enveomics/Manifest/Tasks/fasta.json
-- utils/enveomics/Manifest/Tasks/fastq.json
-- utils/enveomics/Manifest/Tasks/graphics.json
-- utils/enveomics/Manifest/Tasks/mapping.json
-- utils/enveomics/Manifest/Tasks/ogs.json
-- utils/enveomics/Manifest/Tasks/other.json
-- utils/enveomics/Manifest/Tasks/remote.json
-- utils/enveomics/Manifest/Tasks/sequence-identity.json
-- utils/enveomics/Manifest/Tasks/tables.json
-- utils/enveomics/Manifest/Tasks/trees.json
-- utils/enveomics/Manifest/Tasks/variants.json
-- utils/enveomics/Manifest/categories.json
-- utils/enveomics/Manifest/examples.json
-- utils/enveomics/Manifest/tasks.json
-- utils/enveomics/Pipelines/assembly.pbs/CONFIG.mock.bash
-- utils/enveomics/Pipelines/assembly.pbs/FastA.N50.pl
-- utils/enveomics/Pipelines/assembly.pbs/FastA.filterN.pl
-- utils/enveomics/Pipelines/assembly.pbs/FastA.length.pl
-- utils/enveomics/Pipelines/assembly.pbs/README.md
-- utils/enveomics/Pipelines/assembly.pbs/RUNME-2.bash
-- utils/enveomics/Pipelines/assembly.pbs/RUNME-3.bash
-- utils/enveomics/Pipelines/assembly.pbs/RUNME-4.bash
-- utils/enveomics/Pipelines/assembly.pbs/RUNME.bash
-- utils/enveomics/Pipelines/assembly.pbs/kSelector.R
-- utils/enveomics/Pipelines/assembly.pbs/newbler.pbs
-- utils/enveomics/Pipelines/assembly.pbs/newbler_preparator.pl
-- utils/enveomics/Pipelines/assembly.pbs/soap.pbs
-- utils/enveomics/Pipelines/assembly.pbs/stats.pbs
-- utils/enveomics/Pipelines/assembly.pbs/velvet.pbs
-- utils/enveomics/Pipelines/blast.pbs/01.pbs.bash
-- utils/enveomics/Pipelines/blast.pbs/02.pbs.bash
-- utils/enveomics/Pipelines/blast.pbs/03.pbs.bash
-- utils/enveomics/Pipelines/blast.pbs/BlastTab.recover_job.pl
-- utils/enveomics/Pipelines/blast.pbs/CONFIG.mock.bash
-- utils/enveomics/Pipelines/blast.pbs/FastA.split.pl
-- utils/enveomics/Pipelines/blast.pbs/README.md
-- utils/enveomics/Pipelines/blast.pbs/RUNME.bash
-- utils/enveomics/Pipelines/blast.pbs/TASK.check.bash
-- utils/enveomics/Pipelines/blast.pbs/TASK.dry.bash
-- utils/enveomics/Pipelines/blast.pbs/TASK.eo.bash
-- utils/enveomics/Pipelines/blast.pbs/TASK.pause.bash
-- utils/enveomics/Pipelines/blast.pbs/TASK.run.bash
-- utils/enveomics/Pipelines/blast.pbs/sentinel.pbs.bash
-- utils/enveomics/Pipelines/idba.pbs/README.md
-- utils/enveomics/Pipelines/idba.pbs/RUNME.bash
-- utils/enveomics/Pipelines/idba.pbs/run.pbs
-- utils/enveomics/Pipelines/trim.pbs/README.md
-- utils/enveomics/Pipelines/trim.pbs/RUNME.bash
-- utils/enveomics/Pipelines/trim.pbs/run.pbs
-- utils/enveomics/README.md
-- utils/enveomics/Scripts/AAsubs.log2ratio.rb
-- utils/enveomics/Scripts/Aln.cat.rb
-- utils/enveomics/Scripts/Aln.convert.pl
-- utils/enveomics/Scripts/AlphaDiversity.pl
-- utils/enveomics/Scripts/BedGraph.tad.rb
-- utils/enveomics/Scripts/BedGraph.window.rb
-- utils/enveomics/Scripts/BlastPairwise.AAsubs.pl
-- utils/enveomics/Scripts/BlastTab.addlen.rb
-- utils/enveomics/Scripts/BlastTab.advance.bash
-- utils/enveomics/Scripts/BlastTab.best_hit_sorted.pl
-- utils/enveomics/Scripts/BlastTab.catsbj.pl
-- utils/enveomics/Scripts/BlastTab.cogCat.rb
-- utils/enveomics/Scripts/BlastTab.filter.pl
-- utils/enveomics/Scripts/BlastTab.kegg_pep2path_rest.pl
-- utils/enveomics/Scripts/BlastTab.metaxaPrep.pl
-- utils/enveomics/Scripts/BlastTab.pairedHits.rb
-- utils/enveomics/Scripts/BlastTab.recplot2.R
-- utils/enveomics/Scripts/BlastTab.seqdepth.pl
-- utils/enveomics/Scripts/BlastTab.seqdepth_ZIP.pl
-- utils/enveomics/Scripts/BlastTab.seqdepth_nomedian.pl
-- utils/enveomics/Scripts/BlastTab.subsample.pl
-- utils/enveomics/Scripts/BlastTab.sumPerHit.pl
-- utils/enveomics/Scripts/BlastTab.taxid2taxrank.pl
-- utils/enveomics/Scripts/BlastTab.topHits_sorted.rb
-- utils/enveomics/Scripts/Chao1.pl
-- utils/enveomics/Scripts/CharTable.classify.rb
-- utils/enveomics/Scripts/EBIseq2tax.rb
-- utils/enveomics/Scripts/FastA.N50.pl
-- utils/enveomics/Scripts/FastA.extract.rb
-- utils/enveomics/Scripts/FastA.filter.pl
-- utils/enveomics/Scripts/FastA.filterLen.pl
-- utils/enveomics/Scripts/FastA.filterN.pl
-- utils/enveomics/Scripts/FastA.fragment.rb
-- utils/enveomics/Scripts/FastA.gc.pl
-- utils/enveomics/Scripts/FastA.interpose.pl
-- utils/enveomics/Scripts/FastA.length.pl
-- utils/enveomics/Scripts/FastA.mask.rb
-- utils/enveomics/Scripts/FastA.per_file.pl
-- utils/enveomics/Scripts/FastA.qlen.pl
-- utils/enveomics/Scripts/FastA.rename.pl
-- utils/enveomics/Scripts/FastA.revcom.pl
-- utils/enveomics/Scripts/FastA.sample.rb
-- utils/enveomics/Scripts/FastA.slider.pl
-- utils/enveomics/Scripts/FastA.split.pl
-- utils/enveomics/Scripts/FastA.split.rb
-- utils/enveomics/Scripts/FastA.subsample.pl
-- utils/enveomics/Scripts/FastA.tag.rb
-- utils/enveomics/Scripts/FastA.wrap.rb
-- utils/enveomics/Scripts/FastQ.filter.pl
-- utils/enveomics/Scripts/FastQ.interpose.pl
-- utils/enveomics/Scripts/FastQ.offset.pl
-- utils/enveomics/Scripts/FastQ.split.pl
-- utils/enveomics/Scripts/FastQ.tag.rb
-- utils/enveomics/Scripts/FastQ.test-error.rb
-- utils/enveomics/Scripts/FastQ.toFastA.awk
-- utils/enveomics/Scripts/GFF.catsbj.pl
-- utils/enveomics/Scripts/GenBank.add_fields.rb
-- utils/enveomics/Scripts/HMM.essential.rb
-- utils/enveomics/Scripts/HMM.haai.rb
-- utils/enveomics/Scripts/HMMsearch.extractIds.rb
-- utils/enveomics/Scripts/JPlace.distances.rb
-- utils/enveomics/Scripts/JPlace.to_iToL.rb
-- utils/enveomics/Scripts/M5nr.getSequences.rb
-- utils/enveomics/Scripts/MeTaxa.distribution.pl
-- utils/enveomics/Scripts/MyTaxa.fragsByTax.pl
-- utils/enveomics/Scripts/MyTaxa.seq-taxrank.rb
-- utils/enveomics/Scripts/NCBIacc2tax.rb
-- utils/enveomics/Scripts/Newick.autoprune.R
-- utils/enveomics/Scripts/RAxML-EPA.to_iToL.pl
-- utils/enveomics/Scripts/RecPlot2.compareIdentities.R
-- utils/enveomics/Scripts/RefSeq.download.bash
-- utils/enveomics/Scripts/SRA.download.bash
-- utils/enveomics/Scripts/TRIBS.plot-test.R
-- utils/enveomics/Scripts/TRIBS.test.R
-- utils/enveomics/Scripts/Table.barplot.R
-- utils/enveomics/Scripts/Table.df2dist.R
-- utils/enveomics/Scripts/Table.filter.pl
-- utils/enveomics/Scripts/Table.merge.pl
-- utils/enveomics/Scripts/Table.replace.rb
-- utils/enveomics/Scripts/Table.round.rb
-- utils/enveomics/Scripts/Table.split.pl
-- utils/enveomics/Scripts/Taxonomy.silva2ncbi.rb
-- utils/enveomics/Scripts/VCF.KaKs.rb
-- utils/enveomics/Scripts/VCF.SNPs.rb
-- utils/enveomics/Scripts/aai.rb
-- utils/enveomics/Scripts/ani.rb
-- utils/enveomics/Scripts/clust.rand.rb
-- utils/enveomics/Scripts/gi2tax.rb
-- utils/enveomics/Scripts/in_silico_GA_GI.pl
-- utils/enveomics/Scripts/lib/data/dupont_2012_essential.hmm.gz
-- utils/enveomics/Scripts/lib/data/lee_2019_essential.hmm.gz
-- utils/enveomics/Scripts/lib/enveomics.R
-- utils/enveomics/Scripts/lib/enveomics_rb/enveomics.rb
-- utils/enveomics/Scripts/lib/enveomics_rb/jplace.rb
-- utils/enveomics/Scripts/lib/enveomics_rb/og.rb
-- utils/enveomics/Scripts/lib/enveomics_rb/remote_data.rb
-- utils/enveomics/Scripts/lib/enveomics_rb/seq_range.rb
-- utils/enveomics/Scripts/lib/enveomics_rb/stat.rb
-- utils/enveomics/Scripts/lib/enveomics_rb/vcf.rb
-- utils/enveomics/Scripts/ogs.annotate.rb
-- utils/enveomics/Scripts/ogs.core-pan.rb
-- utils/enveomics/Scripts/ogs.extract.rb
-- utils/enveomics/Scripts/ogs.mcl.rb
-- utils/enveomics/Scripts/ogs.rb
-- utils/enveomics/Scripts/ogs.stats.rb
-- utils/enveomics/Scripts/rbm.rb
-- utils/enveomics/Tests/Makefile
-- utils/enveomics/Tests/Mgen_M2288.faa
-- utils/enveomics/Tests/Mgen_M2288.fna
-- utils/enveomics/Tests/Mgen_M2321.fna
-- utils/enveomics/Tests/Nequ_Kin4M.faa
-- utils/enveomics/Tests/Xanthomonas_oryzae-PilA.tribs.Rdata
-- utils/enveomics/Tests/Xanthomonas_oryzae-PilA.txt
-- utils/enveomics/Tests/Xanthomonas_oryzae.aai-mat.tsv
-- utils/enveomics/Tests/Xanthomonas_oryzae.aai.tsv
-- utils/enveomics/Tests/a_mg.cds-go.blast.tsv
-- utils/enveomics/Tests/a_mg.reads-cds.blast.tsv
-- utils/enveomics/Tests/a_mg.reads-cds.counts.tsv
-- utils/enveomics/Tests/alkB.nwk
-- utils/enveomics/Tests/anthrax-cansnp-data.tsv
-- utils/enveomics/Tests/anthrax-cansnp-key.tsv
-- utils/enveomics/Tests/hiv1.faa
-- utils/enveomics/Tests/hiv1.fna
-- utils/enveomics/Tests/hiv2.faa
-- utils/enveomics/Tests/hiv_mix-hiv1.blast.tsv
-- utils/enveomics/Tests/hiv_mix-hiv1.blast.tsv.lim
-- utils/enveomics/Tests/hiv_mix-hiv1.blast.tsv.rec
-- utils/enveomics/Tests/phyla_counts.tsv
-- utils/enveomics/Tests/primate_lentivirus.ogs
-- utils/enveomics/Tests/primate_lentivirus.rbm/hiv1-hiv1.rbm
-- utils/enveomics/Tests/primate_lentivirus.rbm/hiv1-hiv2.rbm
-- utils/enveomics/Tests/primate_lentivirus.rbm/hiv1-siv.rbm
-- utils/enveomics/Tests/primate_lentivirus.rbm/hiv2-hiv2.rbm
-- utils/enveomics/Tests/primate_lentivirus.rbm/hiv2-siv.rbm
-- utils/enveomics/Tests/primate_lentivirus.rbm/siv-siv.rbm
-- utils/enveomics/build_enveomics_r.bash
-- utils/enveomics/enveomics.R/DESCRIPTION
-- utils/enveomics/enveomics.R/NAMESPACE
-- utils/enveomics/enveomics.R/R/autoprune.R
-- utils/enveomics/enveomics.R/R/barplot.R
-- utils/enveomics/enveomics.R/R/cliopts.R
-- utils/enveomics/enveomics.R/R/df2dist.R
-- utils/enveomics/enveomics.R/R/growthcurve.R
-- utils/enveomics/enveomics.R/R/recplot.R
-- utils/enveomics/enveomics.R/R/recplot2.R
-- utils/enveomics/enveomics.R/R/tribs.R
-- utils/enveomics/enveomics.R/R/utils.R
-- utils/enveomics/enveomics.R/README.md
-- utils/enveomics/enveomics.R/data/growth.curves.rda
-- utils/enveomics/enveomics.R/data/phyla.counts.rda
-- utils/enveomics/enveomics.R/man/cash-enve.GrowthCurve-method.Rd
-- utils/enveomics/enveomics.R/man/cash-enve.RecPlot2-method.Rd
-- utils/enveomics/enveomics.R/man/cash-enve.RecPlot2.Peak-method.Rd
-- utils/enveomics/enveomics.R/man/enve.GrowthCurve-class.Rd
-- utils/enveomics/enveomics.R/man/enve.TRIBS-class.Rd
-- utils/enveomics/enveomics.R/man/enve.TRIBS.merge.Rd
-- utils/enveomics/enveomics.R/man/enve.TRIBStest-class.Rd
-- utils/enveomics/enveomics.R/man/enve.__prune.iter.Rd
-- utils/enveomics/enveomics.R/man/enve.__prune.reduce.Rd
-- utils/enveomics/enveomics.R/man/enve.__tribs.Rd
-- utils/enveomics/enveomics.R/man/enve.barplot.Rd
-- utils/enveomics/enveomics.R/man/enve.cliopts.Rd
-- utils/enveomics/enveomics.R/man/enve.col.alpha.Rd
-- utils/enveomics/enveomics.R/man/enve.col2alpha.Rd
-- utils/enveomics/enveomics.R/man/enve.df2dist.Rd
-- utils/enveomics/enveomics.R/man/enve.df2dist.group.Rd
-- utils/enveomics/enveomics.R/man/enve.df2dist.list.Rd
-- utils/enveomics/enveomics.R/man/enve.growthcurve.Rd
-- utils/enveomics/enveomics.R/man/enve.prune.dist.Rd
-- utils/enveomics/enveomics.R/man/enve.recplot.Rd
-- utils/enveomics/enveomics.R/man/enve.recplot2-class.Rd
-- utils/enveomics/enveomics.R/man/enve.recplot2.ANIr.Rd
-- utils/enveomics/enveomics.R/man/enve.recplot2.Rd
-- utils/enveomics/enveomics.R/man/enve.recplot2.__counts.Rd
-- utils/enveomics/enveomics.R/man/enve.recplot2.__peakHist.Rd
-- utils/enveomics/enveomics.R/man/enve.recplot2.__whichClosestPeak.Rd
-- utils/enveomics/enveomics.R/man/enve.recplot2.changeCutoff.Rd
-- utils/enveomics/enveomics.R/man/enve.recplot2.compareIdentities.Rd
-- utils/enveomics/enveomics.R/man/enve.recplot2.coordinates.Rd
-- utils/enveomics/enveomics.R/man/enve.recplot2.corePeak.Rd
-- utils/enveomics/enveomics.R/man/enve.recplot2.extractWindows.Rd
-- utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.Rd
-- utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__em_e.Rd
-- utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__em_m.Rd
-- utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__emauto_one.Rd
-- utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__mow_one.Rd
-- utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__mower.Rd
-- utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.em.Rd
-- utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.emauto.Rd
-- utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.mower.Rd
-- utils/enveomics/enveomics.R/man/enve.recplot2.peak-class.Rd
-- utils/enveomics/enveomics.R/man/enve.recplot2.seqdepth.Rd
-- utils/enveomics/enveomics.R/man/enve.recplot2.windowDepthThreshold.Rd
-- utils/enveomics/enveomics.R/man/enve.tribs.Rd
-- utils/enveomics/enveomics.R/man/enve.tribs.test.Rd
-- utils/enveomics/enveomics.R/man/enve.truncate.Rd
-- utils/enveomics/enveomics.R/man/growth.curves.Rd
-- utils/enveomics/enveomics.R/man/phyla.counts.Rd
-- utils/enveomics/enveomics.R/man/plot.enve.GrowthCurve.Rd
-- utils/enveomics/enveomics.R/man/plot.enve.TRIBS.Rd
-- utils/enveomics/enveomics.R/man/plot.enve.TRIBStest.Rd
-- utils/enveomics/enveomics.R/man/plot.enve.recplot2.Rd
-- utils/enveomics/enveomics.R/man/summary.enve.GrowthCurve.Rd
-- utils/enveomics/enveomics.R/man/summary.enve.TRIBS.Rd
-- utils/enveomics/enveomics.R/man/summary.enve.TRIBStest.Rd
-- utils/enveomics/globals.mk
-- utils/enveomics/manifest.json
 - utils/find-medoid.R
 - utils/index_metadata.rb
 - utils/mytaxa_scan.R
@@ -545,7 +281,7 @@ homepage: http://enve-omics.ce.gatech.edu/miga
 licenses:
 - Artistic-2.0
 metadata: {}
-post_install_message:
+post_install_message: 
 rdoc_options:
 - lib
 - README.md
@@ -566,8 +302,8 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.1.2
-signing_key:
+rubygems_version: 3.1.4
+signing_key: 
 specification_version: 4
 summary: MiGA
 test_files: []