rbbt-util 5.17.48 → 5.17.49

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 49361db931554a4d261eedceb18ea47bee449862
-  data.tar.gz: e1d042a946e1b2f19402a3e597d761bb2f69fab4
+  metadata.gz: cfd7f56cde2409c43944909047d6345e5a7dddf4
+  data.tar.gz: 32c27e5b110dfa03aec714381aae151ce1ed04bd
 SHA512:
-  metadata.gz: d53621df6c8f379eeb171d26cd7926845052f6086408b8500152566e4e3897d6a25a9d47965d3af1873f11c0f11f6ac138abef641f5ad894d782b63170aa4dab
-  data.tar.gz: f20556bed0086287a5f828b4e5183e8e475022158c0edbe43134545a9711d7205c8e14f177bd0625a882eb687dbf069fc56ba62ede5cbe430ba67e1e658ca511
+  metadata.gz: 0372f20697463b04b0d8b6df2a740a9eeaeb78ef856f127edbaec78cfab003350b6816336fc3f761bfd6b5473e67c034fe41fa92806fbd1920560f3c3350ac1b
+  data.tar.gz: 3bd6af1e63bc28c6e9eb7cf599857f50d527c18a8847a9554fc3f0899ba5ea6717b128187540f938053e8717a0bdb512e2b474fb289156f63751b1bd6800510b

data/etc/app.d/workflows.rb

@@ -1,7 +1,20 @@
 register Sinatra::RbbtRESTWorkflow
 
 Rbbt.etc.workflows.find.read.split("\n").each do |workflow|
+  add = true
+
+  if workflow =~ /(.*)\*$/
+    workflow = $1
+    add = :priority
+  end
+
+  if workflow =~ /(.*)\-$/
+    workflow = $1
+    add = false
+  end
+
+
   next if workflow.empty?
   Workflow.require_workflow workflow
-  add_workflow Kernel.const_get(workflow), true
+  add_workflow Kernel.const_get(workflow), add
 end if Rbbt.etc.workflows.find.exists?

data/lib/rbbt/tsv/manipulate.rb

@@ -548,7 +548,7 @@ module TSV
     all = []
     through :key, field do |k,values|
       values = Array === values ? values.flatten : [values]
-      all.concat value
+      all.concat values
     end
     prepare_entity(all, field, options = {})
   end

data/lib/rbbt/util/R/model.rb

@@ -75,7 +75,7 @@ data = NULL
 
       script = <<-EOF
 model = rbbt.model.load('#{model_file}');
-predict(model, data.frame(#{field} = #{R.ruby2R value}), interval=#{R.ruby2R interval});
+predict(model, data.frame(#{field} = #{R.ruby2R value}), interval=#{R.ruby2R interval}, level=0.90);
       EOF
 
       res = R.eval_a script

data/lib/rbbt/util/misc/omics.rb

@@ -116,6 +116,9 @@ module Misc
     "TGA" => "*",
   }
 
+  def self.correct_mutation(pos, ref, mut_str)
+  end
+
   def self.correct_icgc_mutation(pos, ref, mut_str)
     mut = mut_str
     mut = '-' * (mut_str.length - 1) if mut =~/^-[ACGT]/
@@ -123,6 +126,36 @@ module Misc
     [pos, [mut]]
   end
 
+  def self.correct_mutation(pos, ref, mut_str)
+    muts = mut_str.nil? ? [] : mut_str.split(',')
+    muts.collect!{|m| m == '<DEL>' ? '-' : m }
+
+    ref = '' if ref == '-'
+    while ref.length >= 1 and muts.reject{|m| m[0] == ref[0]}.empty?
+      ref = ref[1..-1]
+      raise "REF nil" if ref.nil?
+      pos = pos + 1
+      muts = muts.collect{|m| m[1..-1]}
+    end
+
+    muts = muts.collect do |m|
+      m = '' if m == '-'
+      case
+      when ref.empty?
+        "+" << m
+      when (m.length < ref.length and (m.empty? or ref.index(m)))
+        "-" * (ref.length - m.length)
+      when (ref.length == 1 and m.length == 1)
+        m
+      else
+        Log.debug{"Cannot understand: #{[ref, m]} (#{ muts })"}
+        '-' * ref.length + m
+      end
+    end
+
+    [pos, muts]
+  end
+
   def self.correct_vcf_mutation(pos, ref, mut_str)
     muts = mut_str.nil? ? [] : mut_str.split(',')
     muts.collect!{|m| m == '<DEL>' ? '-' : m }

data/lib/rbbt/util/misc/pipes.rb

@@ -90,9 +90,9 @@ module Misc
     stream_out1, stream_in1 = Misc.pipe
     stream_out2, stream_in2 = Misc.pipe
 
-    if ConcurrentStream === stream 
-      stream.annotate stream_out1
-    end
+    #if ConcurrentStream === stream 
+    #  stream.annotate stream_out1
+    #end
 
     splitter_thread = Thread.new(Thread.current) do |parent|
       begin
@@ -133,11 +133,11 @@ module Misc
     ConcurrentStream.setup stream_out1, :threads => splitter_thread
     ConcurrentStream.setup stream_out2, :threads => splitter_thread
 
-    stream_out1.callback = stream.callback if stream.respond_to? :callback
-    stream_out1.abort_callback = stream.abort_callback if stream.respond_to? :abort_callback
+    #stream_out1.callback = stream.callback if stream.respond_to? :callback
+    #stream_out1.abort_callback = stream.abort_callback if stream.respond_to? :abort_callback
 
-    stream_out2.callback = stream.callback if stream.respond_to? :callback
-    stream_out2.abort_callback = stream.abort_callback if stream.respond_to? :abort_callback
+    #stream_out2.callback = stream.callback if stream.respond_to? :callback
+    #stream_out2.abort_callback = stream.abort_callback if stream.respond_to? :abort_callback
 
     [stream_out1, stream_out2]
   end

data/lib/rbbt/workflow/step.rb

@@ -226,27 +226,6 @@ class Step
     self
   end
 
-  #def rec_dependencies
-
-  #  # A step result with no info_file means that it was manually
-  #  # placed. In that case, do not consider its dependencies
-  #  return [] if Open.exists?(self.path.to_s) and not Open.exists? self.info_file
-
-  #  return [] if dependencies.nil? or dependencies.empty?
-
-  #  new_dependencies = []
-  #  dependencies.each{|step| 
-  #    new_dependencies.concat step.rec_dependencies
-  #    new_dependencies << step
-  #  }
-  #  new_dependencies.uniq!
-
-  #  dependencies = self.dependencies ? self.dependencies + new_dependencies : new_dependencies
-  #  dependencies.flatten!
-  #  dependencies.uniq!
-  #  dependencies
-  #end
-
   def rec_dependencies
 
     # A step result with no info_file means that it was manually

data/share/rbbt_commands/workflow/server

@@ -47,11 +47,11 @@ app.class_eval do
   eval Rbbt.etc['app.d/finder.rb'].read
 end
 
-WorkflowRest.add_workflow wf, :all
+WorkflowRest.add_workflow wf, :priority
 if options[:workflows]
   options[:workflows].split(/[\s,]+/).each do |name|
     _wf = Workflow.require_workflow name
-    WorkflowRest.add_workflow _wf, :all
+    WorkflowRest.add_workflow _wf, true
   end
 end
 
@@ -60,7 +60,6 @@ if options[:views] and not options[:views].empty?
   Sinatra::RbbtRESTMain.add_resource_path(Path.setup(options[:views]), true)
 end
 
-
 WorkflowRest.port = options[:port] || 4567
 WorkflowRest.bind = options[:bind] || "0.0.0.0"
 WorkflowRest.environment = options[:environment] || "development"

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.17.48
+  version: 5.17.49
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-06-22 00:00:00.000000000 Z
+date: 2015-07-01 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake