rbbt-util 5.2.3 → 5.2.4

checksums.yaml

@@ -0,0 +1,15 @@
+---
+!binary "U0hBMQ==":
+  metadata.gz: !binary |-
+    ZjIwN2RhYmRjNDg2MjMzMWNmYWU4NGQ5ZDUyYjcyNGU4MmExMzJhYw==
+  data.tar.gz: !binary |-
+    NzAyMmUyMjg3ZWRmY2I1N2EwNDk1OGVlNTBmNWUyNmIyNTUxN2QwNg==
+!binary "U0hBNTEy":
+  metadata.gz: !binary |-
+    M2M0OTlkODVmMjY1ZWNjZWIzYjhjMTE2M2MyOGNiNWY5YjZiYjNiNDdkMTQx
+    MjkyNTk0MWRkZGM4ZjU3OTVjOTQ3ODg3YmNhNjVmZjljZDlmZGU3YTI4YWIw
+    MmFkZjcwMTE5OGFlNmI3MjRkZWI0NTQwZDBlZTg3ZTUwMWJhYjY=
+  data.tar.gz: !binary |-
+    ZTIxNTBhZGQyZjg0ZjNiYjhlZjU3MTQ4M2YzMzgyNWNlZWE4MWMxNDg2OWUw
+    MzRlMzQyMzkyZWJiNDM1NjQ3ODljNmUwYjg1ZjJhYzYxOWE3MTZjZjc1ZDM3
+    OTI1ZjMzMTNmZDE4Mzc4OTQ3NDJmY2UyYTQzNWRjZDg0MjhlOWI=

data/bin/rbbt

@@ -1,8 +1,30 @@
 #!/usr/bin/env ruby
 
 require 'rbbt'
+require 'rbbt/util/simpleopt'
 
-$rbbt_command_dir = Rbbt.share.rbbt_commands
+options = SOPT.get("--log* Log level from 0 (debug) 7 (errors):--command_dir* Directory from where to load commands")
+
+if options[:log]
+  Log.severity = options[:log].to_i
+end
+
+if options[:command_dir]
+  $rbbt_command_dir = Path.setup(options[:command_dir])
+else
+  $rbbt_command_dir = Rbbt.share.rbbt_commands
+end
+
+SOPT.synopsys = "rbbt <command> <subcommand> ... -a --arg1 --arg2='value'"
+SOPT.summary = "Ruby bioinformatics toolkit"
+SOPT.description = <<-EOF
+This command controls many aspects of the Rbbt framework, from configuration tasks to running applications. 
+
+Commands are implemented in separate files under the Rbbt path#{
+} '#{$rbbt_command_dir}'. Known locations are: #{
+([$rbbt_command_dir] + $rbbt_command_dir.find_all) * ", "
+}. You can place your own commads at #{$rbbt_command_dir.find(:user)}.
+EOF
 
 def commands(prev)
     rbbt_command_dir = $rbbt_command_dir
@@ -35,6 +57,10 @@ while ARGV.any?
     end
 end
 
+puts SOPT.doc
+
+puts "## COMMANDS"
+puts
 puts "Command:"
 puts 
 puts "  #{File.basename($0)} #{prev * " "}"

data/bin/rbbt_monitor.rb

@@ -50,6 +50,8 @@ def list_jobs(options)
     end
 
     color = case
+            when (not info)
+              Log::SEVERITY_COLOR[3]
             when info[:status] == :error
               Log::SEVERITY_COLOR[3]
             when (info[:pid] and not running? info)
@@ -57,6 +59,8 @@ def list_jobs(options)
             end
 
     case
+    when (not info)
+      print_job file, info, color
     when (not omit_ok)
       print_job file, info, color
     when options[:zombies]
@@ -89,9 +93,9 @@ def clean_jobs(options)
     case
     when options[:all]
       remove_job file
-    when (options[:zombies] and info[:pid] and not running? info)
+    when (options[:errors] and (not info or info[:status] == :error))
       remove_job file
-    when (options[:errors] and info[:status] == :error)
+    when (options[:zombies] and info[:pid] and not running? info)
       remove_job file
     end
 

data/lib/rbbt/persist.rb

@@ -249,11 +249,11 @@ module Persist
 
       else
         if is_persisted?(path, persist_options)
-          Log.debug "Persist up-to-date: #{ path } - #{persist_options.inspect[0..100]}"
+          Log.low "Persist up-to-date: #{ path } - #{persist_options.inspect[0..100]}"
           return nil if persist_options[:no_load]
           return load_file(path, type) 
         else
-          Log.debug "Persist create: #{ path } - #{persist_options.inspect[0..100]}"
+          Log.medium "Persist create: #{ path } - #{persist_options.inspect[0..100]}"
         end
         begin
           res = yield
@@ -262,8 +262,8 @@ module Persist
           end
           res
         rescue
-          Log.high "Error in persist. Erasing '#{ path }'"
-          FileUtils.rm path if File.exists? path
+          Log.high "Error in persist. #{File.exists?(path) ? "Erasing '#{ path }'" : ""}"
+          FileUtils.rm path if File.exists? path 
           raise $!
         end
       end

data/lib/rbbt/persist/tsv.rb

@@ -158,7 +158,7 @@ module Persist
                lock_filename = Persist.persistence_path(path, {:dir => Rbbt.tmp.tsv_open_locks.find})
                return Misc.lock(lock_filename) do open_tokyocabinet(path, false); end
              else
-               Log.debug "TSV persistence creating: #{ path }"
+               Log.medium "TSV persistence creating: #{ path }"
              end
 
              FileUtils.rm path if File.exists? path

data/lib/rbbt/tsv/attach.rb

@@ -48,13 +48,16 @@ module TSV
   end
 
   # Merge two files with the same keys and different fields
-  def self.merge_different_fields(file1, file2, output, sep = "\t")
+  def self.merge_different_fields(file1, file2, output, sep = "\t", monitor = false)
     case
     when (String === file1 and not file1 =~ /\n/ and file1.length < 250 and File.exists?(file1))
+      size = CMD.cmd("wc -l '#{file1}'").read.to_f if monitor
       file1 = CMD.cmd("sort -k1,1 -t'#{sep}' #{ file1 } | grep -v '^#{sep}' ", :pipe => true)
     when (String === file1 or StringIO === file1)
+      size = file1.length if monitor
       file1 = CMD.cmd("sort -k1,1 -t'#{sep}' | grep -v '^#{sep}'", :in => file1, :pipe => true)
     when TSV === file1
+      size = file1.size if monitor
       file1 = CMD.cmd("sort -k1,1 -t'#{sep}' | grep -v '^#{sep}'", :in => file1.to_s(:sort, true), :pipe => true)
     end
 
@@ -88,6 +91,8 @@ module TSV
       cols2 = parts2.length
     end
 
+    progress_monitor = Progress::Bar.new(size, 0, 100, "Merging fields") if monitor
+
     key = key1 < key2 ? key1 : key2
     parts = [""] * (cols1 + cols2)
     while not (done1 and done2)
@@ -99,6 +104,7 @@ module TSV
         while key1.nil? and not done1
           if file1.eof?; done1 = true; else key1, *parts1 = file1.gets.sub("\n",'').split(sep, -1) end
         end
+        progress_monitor.tick if monitor
       end
       while (not done2 and key2 == key)
         parts2.each_with_index do |part, i|
@@ -151,7 +157,7 @@ module TSV
     end
 
     other_filename = other.respond_to?(:filename) ? other.filename : other.inspect
-    Log.medium("Attaching fields:#{fields.inspect} from #{other_filename}.")
+    Log.low("Attaching fields:#{fields.inspect} from #{other_filename}.")
 
     case
     when key_field == other.key_field

data/lib/rbbt/tsv/attach/util.rb

@@ -229,7 +229,7 @@ module TSV
 
     traversal_ids = path.collect{|p| p.first}
 
-    Log.low "Found Traversal: #{traversal_ids * " => "}"
+    Log.debug "Found Traversal: #{traversal_ids * " => "}"
 
     data_key, data_file = path.shift
     data_index = if data_key == data_file.key_field

data/lib/rbbt/util/log.rb

@@ -25,7 +25,7 @@ module Log
   #  @severity
   #end
 
-  SEVERITY_COLOR = ["0;37m", "0;32m", "0;33m", "0;31m", "1;0m" ].collect{|e| "\033[#{e}"}
+  SEVERITY_COLOR = ["0;37m", "0;32m", "0;33m", "0;31m","0;37m", "0;32m", "0;33m"].collect{|e| "\033[#{e}"}
 
   def self.log(message, severity = MEDIUM)
     message ||= ""

data/lib/rbbt/util/misc.rb

@@ -19,6 +19,38 @@ end
 module Misc
   class FieldNotFoundError < StandardError;end
 
+  def self.correct_icgc_mutation(pos, ref, mut_str)
+    mut = mut_str
+    mut = '-' * (mut_str.length - 1) if mut =~/^-[ACGT]/
+    [pos, [mut]]
+  end
+
+  def self.correct_vcf_mutation(pos, ref, mut_str)
+    muts = mut_str.nil? ? [] : mut_str.split(',')
+
+    while ref.length >= 1 and muts.reject{|m| m[0] == ref[0]}.empty?
+      ref = ref[1..-1]
+      pos = pos + 1
+      muts = muts.collect{|m| m[1..-1]}
+    end
+
+    muts = muts.collect do |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.pid_exists?(pid)
     return false if pid.nil?
     begin

data/lib/rbbt/util/simpleopt.rb

@@ -1,17 +1,178 @@
 module SOPT
+  class << self
+    attr_accessor :command, :summary, :synopsys, :description
+    attr_accessor :inputs, :input_shortcuts, :input_types, :input_descriptions, :input_defaults
+
+    def command
+      @command ||= File.basename($0)
+    end
+
+    def summary
+      @summary ||= ""
+    end
+
+    def synopsys
+      @synopsys ||= begin
+                      "#{command} " <<
+                      inputs.collect{|name|
+                        "[" << input_format(name, input_types[name] || :string, input_defaults[name], input_shortcuts[name]).sub(/:$/,'') << "]"
+                      } * " "
+                    end
+    end
+
+    def description
+      @description ||= "Missing"
+    end
+
+
+    def shortcuts
+      @shortcuts ||= []
+    end
+
+    def all
+      @all ||= {}
+    end
+    
+    def inputs 
+      @inputs ||= []
+    end
+  
+    def input_shortcuts 
+      @input_shortcuts ||= {}
+    end
+
+    def input_types 
+      @input_types ||= {}
+    end
+ 
+    def input_descriptions 
+      @input_descriptions ||= {}
+    end
+ 
+    def input_defaults 
+      @input_defaults ||= {}
+    end
+
+
+    def reset
+      @shortcuts = []
+      @all = {}
+    end
+
+    def record(info)
+      input = info[:long].sub("--", '')
+      inputs << input
+      input_types[input] = info[:arg] ? :string : :boolean
+      input_descriptions[input] = info[:description]
+      input_defaults[input] = info[:default]
+      input_shortcuts[input] = info[:short]? info[:short].sub("-",'') : nil
+    end
+  end
+
+
+  def self.short_for(name)
+    short = []
+    chars = name.to_s.chars.to_a
+
+    short << chars.shift 
+    shortcuts = input_shortcuts.values.compact.flatten
+    while shortcuts.include? short * "" and chars.any?
+      short << chars.shift 
+    end
+    return nil if chars.empty?
+
+    short * ""
+  end
+
+  def self.input_format(name, type = nil, default = nil, short = "")
+    short = short_for(name) if not short.nil? and short.empty?
+
+    input_str = short.nil? ? "--#{name}" : "-#{short}, --#{name}"
+    input_str << case type
+    when nil
+      "#{default != nil ? " (default '#{default}')" : ""}:"
+    when :boolean
+      "[=false]#{default != nil ? " (default '#{default}')" : ""}:"
+    when :tsv, :text
+      "=<filename.#{type}|->#{default != nil ? " (default '#{default}')" : ""}; Use '-' for STDIN:"
+    when :array
+      "=<string[,string]*|filename.list|->#{default != nil ? " (default '#{default}')" : ""}; Use '-' for STDIN:"
+    else
+      "=<#{ type }>#{default != nil ? " (default '#{default}')" : ""}:"
+    end
+  end
+
+  def self.input_doc(inputs, input_types = nil, input_descriptions = nil, input_defaults = nil, input_shortcuts = nil)
+    type = description = default = nil
+    shortcut = ""
+    inputs.collect do |name|
+
+      type = input_types[name] unless input_types.nil?
+      description = input_descriptions[name] unless input_descriptions.nil?
+      default = input_defaults[name] unless input_defaults.nil?
+      shortcut = input_shortcuts[name] unless input_shortcuts.nil?
+
+      type = :string if type.nil?
+
+      str  = "  * " << SOPT.input_format(name, type.to_sym, default, shortcut) << "\n"
+      str << "    " << description << "\n" if description and not description.empty?
+      str
+    end * "\n"
+  end
+
+  def self.doc
+    doc = <<-EOF
+#{command}(1) -- #{summary}
+#{"=" * (command.length + summary.length + 7)}
+
+## SYNOPSYS
+
+#{synopsys}
+
+## DESCRIPTION
+
+#{description}
+
+## OPTIONS
+
+#{input_doc(inputs, input_types, input_descriptions, input_defaults, input_shortcuts)}
+    EOF
+  end
+
   def self.name(info)
     (info[:long] || info[:short]).sub(/^-*/,'')
   end
 
   def self.parse(opts)
     info = {}
+
     opts.split(/:/).each do |opt|
-      short, long = opt.sub(/\*$/,'').split('--').values_at(0,1)
-      i= {
-        :arg => !!opt.match(/\*$/),
-      }
-      i[:short] = short unless short.nil? || short.empty?
-      i[:long] = '--' + long unless long.nil? || long.empty?
+      next if opt.strip.empty?
+
+      short, long = opt.strip.sub(/(^[^\s]*)\*/,'\1').split('--').values_at(0,1)
+      long, short = short, nil if long.nil?
+
+      if long.index(" ")
+        long, description = long.match(/^([^\s]+)\s+(.*)/).values_at 1, 2
+      else
+        description = nil
+      end
+      
+      i= { :arg => !!opt.match(/^[^\s]*\*/) }
+
+      i[:short]       = short unless short.nil? || short.empty?
+      i[:long]        = '--' + long unless long.nil? || long.empty?
+      i[:description] = description unless description.nil? || description.empty?
+
+      if shortcuts.include? short
+        i[:short] = short_for(i[:long])
+        Log.debug("Short for #{ long } is taken. Changed to #{i[:short]}")
+      else
+        shortcuts << i[:short] if short
+      end
+
+      record(i)
+
       info[name(i)] = i
     end
 
@@ -51,7 +212,7 @@ module SOPT
           end
           options[name.to_sym] = value
         else
-          options[name.to_sym] = true
+          options[name.to_sym] = value == "false" ? false : true
         end
       else
         rest << orig_arg

data/lib/rbbt/workflow.rb

@@ -41,14 +41,14 @@ module Workflow
       when ((File.exists?(wf_name.find) and not File.directory?(wf_name.find)) or File.exists?(wf_name.find + '.rb')) 
         $LOAD_PATH.unshift(File.join(File.expand_path(File.dirname(wf_name.find)), 'lib'))
         require wf_name.find
-        Log.debug "Workflow loaded from file: #{ wf_name }"
+        Log.medium "Workflow loaded from file: #{ wf_name }"
         return true
 
         # Points to workflow dir
       when (File.exists?(wf_name.find) and File.directory?(wf_name.find) and File.exists?(File.join(wf_name.find, 'workflow.rb')))
         $LOAD_PATH.unshift(File.join(File.expand_path(wf_name.find), 'lib'))
         require File.join(wf_name.find, 'workflow.rb')
-        Log.debug "Workflow loaded from directory: #{ wf_name }"
+        Log.medium "Workflow loaded from directory: #{ wf_name }"
         return true
 
       else
@@ -61,7 +61,7 @@ module Workflow
       when ((File.exists?(wf_name) and not File.directory?(wf_name)) or File.exists?(wf_name + '.rb')) 
         $LOAD_PATH.unshift(File.join(File.expand_path(File.dirname(wf_name)), 'lib'))
         require wf_name
-        Log.debug "Workflow loaded from file: #{ wf_name }"
+        Log.medium "Workflow loaded from file: #{ wf_name }"
         return true
 
       when (defined?(Rbbt) and Rbbt.etc.workflow_dir.exists?)
@@ -69,21 +69,21 @@ module Workflow
         dir = File.join(dir, wf_name)
         $LOAD_PATH.unshift(File.join(File.expand_path(dir), 'lib'))
         require File.join(dir, 'workflow.rb')
-        Log.debug "Workflow #{wf_name} loaded from workflow_dir: #{ dir }"
+        Log.medium "Workflow #{wf_name} loaded from workflow_dir: #{ dir }"
         return true
 
       when defined?(Rbbt)
         path = Rbbt.workflows[wf_name].find
         $LOAD_PATH.unshift(File.join(File.expand_path(path), 'lib'))
         require File.join(path, 'workflow.rb')
-        Log.debug "Workflow #{wf_name} loaded from Rbbt.workflows: #{ path }"
+        Log.medium "Workflow #{wf_name} loaded from Rbbt.workflows: #{ path }"
         return true
 
       else
         path = File.join(ENV['HOME'], '.workflows', wf_name)
         $LOAD_PATH.unshift(File.join(File.expand_path(path), 'lib'))
         require File.join(path, 'workflow.rb')
-        Log.debug "Workflow #{wf_name} loaded from .workflows: #{ path }"
+        Log.medium "Workflow #{wf_name} loaded from .workflows: #{ path }"
         return true
       end
     end
@@ -211,6 +211,7 @@ module Workflow
     path = File.join(workdir, id)
     task = task_for path
     step = Step.new path, tasks[task.to_sym]
+    step.info
     if step.info.include? :dependencies
       step.dependencies = step.info[:dependencies].collect do |task, job|
         load_id(File.join(task.to_s, job))

data/lib/rbbt/workflow/step.rb

@@ -68,16 +68,14 @@ class Step
 
   def join
     if @pid.nil?
-      while not done? do
-        sleep 5
-      end
+      self
     else
-      Log.debug "Waiting for pid: #{@pid}"
       begin
-        Process.waitpid @pid
+        Log.debug "Waiting for pid: #{@pid}"
+        Process.waitpid @pid 
       rescue Errno::ECHILD
         Log.debug "Process #{ @pid } already finished: #{ path }"
-      end
+      end if Misc.pid_exists? @pid
       @pid = nil
     end
     self
@@ -108,7 +106,8 @@ class Step
         end
       }
       
-      log(:started, "Starting task #{task.name || ""} [#{Process.pid}]")
+      Log.medium("Starting task #{task.name || ""} [#{Process.pid}]: #{ path }")
+      set_info :status, :started
 
       set_info :started, Time.now
       
@@ -147,6 +146,8 @@ class Step
             end
 
       set_info :status, :done
+      set_info :done, Time.now
+      Log.medium("Completed task #{task.name || ""} [#{Process.pid}]: #{ path }")
       res
     end
 
@@ -164,6 +165,12 @@ class Step
       FileUtils.mkdir_p File.dirname(path) unless File.exists? File.dirname(path)
       begin
         run
+      rescue Exception
+        Log.debug("Exception caught on forked process: #{$!.message}")
+        exit -1
+      end
+
+      begin
         children_pids = info[:children_pids]
         if children_pids
           children_pids.each do |pid|
@@ -177,7 +184,7 @@ class Step
           end
         end
       rescue Exception
-        Log.debug("Exception caught on forked process: #{$!.message}")
+        Log.debug("Exception waiting for children: #{$!.message}")
         exit -1
       end
       set_info :pid, nil

data/lib/rbbt/workflow/usage.rb

@@ -1,28 +1,11 @@
+require 'rbbt/util/simpleopt'
 
 module Task
   def doc(deps = nil)
-
     puts "## #{ name }:"
     puts "\n" << description if description and not description.empty?
-    puts 
-
-    inputs.each do |name|
-      short = name.to_s.chars.first
-
-      description = input_descriptions[name]
-      default = input_defaults[name]
-      type = input_types[name]
-
-
-      if type.to_sym == :boolean
-        puts "  * -#{short}, --#{name}[=<true|false>]#{default != nil ? " (default: #{default})" : ""}:"
-      else
-        puts "  * -#{short}, --#{name}=<#{ type }>#{default != nil ? " (default: #{default})" : ""}:"
-      end
-
-      puts "    " << description if description and not description.empty?
-      puts
-    end
+    puts
+    puts SOPT.input_doc(inputs, input_types, input_descriptions, input_defaults)
 
     if deps and deps.any?
       puts
@@ -31,22 +14,7 @@ module Task
       deps.each do |dep|
         puts "  #{dep.name}:"
         puts
-        dep.inputs.each do |name|
-          short = name.to_s.chars.first
-
-          description = dep.input_descriptions[name]
-          default = dep.input_defaults[name]
-          type = dep.input_types[name]
-
-          if type.to_sym == :boolean
-            puts "  * -#{short}, --#{name}[=<true|false>]#{default != nil ? " (default: #{default})" : ""}:"
-          else
-            puts "  * -#{short}, --#{name}=<#{ type }>#{default != nil ? " (default: #{default})" : ""}:"
-          end
-
-          puts "    " << description if description and not description.empty?
-          puts
-        end
+        puts SOPT.input_doc(dep.inputs, dep.input_types, dep.input_descriptions, dep.input_defaults)
       end
     end
   end

data/share/rbbt_commands/app/start

@@ -14,5 +14,6 @@ app_dir = app_dir[app]
 server = options[:server] || 'thin'
 
 Misc.in_dir(app_dir) do
-  `#{options.include?(:environment)? "env RACK_ENV=#{options[:environment]}" : ""} #{server} start -p #{options[:port]} #{ARGV.collect{|a| "'#{a}'"} * " "}`
+  `env RBBT_LOG=#{Log.severity} #{options.include?(:environment)? "env RACK_ENV=#{options[:environment]}" : ""} \
+  #{server} start -p #{options[:port]} #{ARGV.collect{|a| "'#{a}'"} * " "}`
 end

data/share/rbbt_commands/workflow/task

@@ -5,6 +5,9 @@ require 'rbbt/workflow'
 require 'rbbt/workflow/usage'
 
 def usage(workflow = nil, task = nil)
+  puts SOPT.doc
+  puts "## WORKFLOW"
+  puts
   if workflow.nil?
     puts "No workflow specified"
     exit -1 
@@ -14,6 +17,9 @@ def usage(workflow = nil, task = nil)
     workflow.load_tasks if workflow.respond_to? :load_tasks
     workflow.doc
   else
+    puts workflow.to_s
+    puts "=" * workflow.to_s.length
+    puts
     workflow.doc(task)
   end
 
@@ -94,7 +100,14 @@ def fix_options(workflow, task, job_options)
   job_options_cleaned
 end
 
-options = SOPT.get "-t--task*:--profile:-l--log*:-h--help:-n--name*:-cl--clean:-rcl-recursive_clean:-pn--printname:-as--array_separator*"
+options = SOPT.get <<EOF
+-h--help Show this help:
+-as--array_separator* Change the character that separates elements of Arrays, ',', '|', or '\\n' by default:
+-cl--clean Clean the last step of the job so that it gets recomputed:
+-rcl--recursive_clean Clean the last step and its dependencies to recompute the job completely:
+-n--name* Job name to use. The name 'Default' is used by default:
+-pn--printname Print the name of the job and exit without starting it:
+EOF
 
 workflow = ARGV.shift
 usage if workflow.nil?
@@ -103,9 +116,9 @@ task     = ARGV.shift
 
 
 # Set log, fork, clean, recursive_clean and help
-Log.severity = options[:log].to_i if options.include? :log
 help = !!options.delete(:help)
 do_fork = !!options.delete(:fork)
+do_exec = !!options.delete(:exec)
 clean = !!options.delete(:clean)
 recursive_clean = !!options.delete(:recursive_clean)
 $array_separator = options.delete(:array_separator)
@@ -155,7 +168,7 @@ job_options = fix_options(workflow, task, job_options)
 job = workflow.job(task.name, name, job_options)
 
 # clean job
-if clean and job.done?
+if clean and job.done? != false
   job.clean 
   sleep 1
   job = workflow.job(task.name, name, job_options)
@@ -168,6 +181,21 @@ if recursive_clean and job.done?
 end
 
 # run
+if do_exec
+  res = job.exec
+  case
+  when Array === res
+    puts res * "\n"
+  when TSV === res
+    puts res
+  when Hash === res
+    puts res.to_yaml
+  else
+    puts res
+  end
+  exit 0
+end
+
 if do_fork
   job.fork
   while not job.done?
@@ -175,30 +203,21 @@ if do_fork
     sleep 2
   end
   raise job.messages.last if job.error?
-  if $array_separator
-    res = job.load(:sep2 => $array_separator)
-  else
-    res = job.load
-  end
 else
-  res = job.run
+  res = job.run(true)
 end
 
 if options.delete(:printname)
   puts job.name
-  exit
+  exit 0
 else
   Log.low "Job name: #{job.name}" 
 end
 
-case
-when Array === res
-  puts res * "\n"
-when TSV === res
-  puts res
-when Hash === res
-  puts res.to_yaml
+if Step === res
+  puts Open.read(res.path)
 else
   puts res
 end
 
+exit 0

data/test/rbbt/test_tsv.rb

@@ -420,6 +420,22 @@ row2   b  bbb bbbb bb
     end
   end
 
+  def test_flat_key
+    content =<<-EOF
+#Id    ValueA 
+row1   a   aa   aaa
+row2   b  bbb bbbb bb aa
+    EOF
+
+    TmpFile.with_file(content) do |filename|
+      tsv = TSV.open(filename, :sep => /\s+/, :merge => true, :type => :flat, :key_field => "ValueA")
+      assert_equal ["row1"], tsv["a"]
+      assert_equal ["row1", "row2"], tsv["aa"]
+    end
+  end
+
+
+
   def test_zipped
     content =<<-EOF
 #Id    ValueA    ValueB

data/test/rbbt/util/test_misc.rb

@@ -220,4 +220,8 @@ class TestMisc < Test::Unit::TestCase
     assert_equal "ACRONIM_test", Misc.snake_case(str1)
     assert_equal "ACRONIM_test", Misc.snake_case(str2)
   end
+
+  def test_correct_vcf_mutations
+    assert_equal [737407, ["-----", "-----G", "-----GTTAAT"]], Misc.correct_vcf_mutation(737406, "GTTAAT", "G,GG,GGTTAAT")
+  end
 end

metadata

@@ -1,20 +1,18 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.2.3
-  prerelease: 
+  version: 5.2.4
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-05-22 00:00:00.000000000 Z
+date: 2013-05-27 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ! '>='
       - !ruby/object:Gem::Version
@@ -22,7 +20,6 @@ dependencies:
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ! '>='
       - !ruby/object:Gem::Version
@@ -30,7 +27,6 @@ dependencies:
 - !ruby/object:Gem::Dependency
   name: spreadsheet
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ! '>='
       - !ruby/object:Gem::Version
@@ -38,7 +34,6 @@ dependencies:
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ! '>='
       - !ruby/object:Gem::Version
@@ -46,7 +41,6 @@ dependencies:
 - !ruby/object:Gem::Dependency
   name: ruby-prof
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ! '>='
       - !ruby/object:Gem::Version
@@ -54,7 +48,6 @@ dependencies:
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ! '>='
       - !ruby/object:Gem::Version
@@ -62,7 +55,6 @@ dependencies:
 - !ruby/object:Gem::Dependency
   name: tokyocabinet
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ! '>='
       - !ruby/object:Gem::Version
@@ -70,7 +62,6 @@ dependencies:
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ! '>='
       - !ruby/object:Gem::Version
@@ -78,7 +69,6 @@ dependencies:
 - !ruby/object:Gem::Dependency
   name: progress-monitor
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ! '>='
       - !ruby/object:Gem::Version
@@ -86,7 +76,6 @@ dependencies:
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ! '>='
       - !ruby/object:Gem::Version
@@ -94,7 +83,6 @@ dependencies:
 - !ruby/object:Gem::Dependency
   name: lockfile
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ! '>='
       - !ruby/object:Gem::Version
@@ -102,7 +90,6 @@ dependencies:
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ! '>='
       - !ruby/object:Gem::Version
@@ -110,7 +97,6 @@ dependencies:
 - !ruby/object:Gem::Dependency
   name: RubyInline
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ! '>='
       - !ruby/object:Gem::Version
@@ -118,7 +104,6 @@ dependencies:
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ! '>='
       - !ruby/object:Gem::Version
@@ -126,7 +111,6 @@ dependencies:
 - !ruby/object:Gem::Dependency
   name: narray
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ! '>='
       - !ruby/object:Gem::Version
@@ -134,7 +118,6 @@ dependencies:
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ! '>='
       - !ruby/object:Gem::Version
@@ -142,7 +125,6 @@ dependencies:
 - !ruby/object:Gem::Dependency
   name: simplews
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ! '>='
       - !ruby/object:Gem::Version
@@ -150,7 +132,6 @@ dependencies:
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ! '>='
       - !ruby/object:Gem::Version
@@ -158,7 +139,6 @@ dependencies:
 - !ruby/object:Gem::Dependency
   name: highline
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ! '>='
       - !ruby/object:Gem::Version
@@ -166,7 +146,6 @@ dependencies:
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ! '>='
       - !ruby/object:Gem::Version
@@ -286,27 +265,26 @@ files:
 - bin/rbbt_dangling_locks.rb
 homepage: http://github.com/mikisvaz/rbbt-util
 licenses: []
+metadata: {}
 post_install_message: 
 rdoc_options: []
 require_paths:
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement
-  none: false
   requirements:
   - - ! '>='
     - !ruby/object:Gem::Version
       version: '0'
 required_rubygems_version: !ruby/object:Gem::Requirement
-  none: false
   requirements:
   - - ! '>='
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 1.8.24
+rubygems_version: 2.0.3
 signing_key: 
-specification_version: 3
+specification_version: 4
 summary: Utilities for the Ruby Bioinformatics Toolkit (rbbt)
 test_files:
 - test/rbbt/tsv/test_accessor.rb