rbbt-util 5.6.13 → 5.6.14

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: b656db59e4d0eca0665f2f66988894887643c65a
-  data.tar.gz: ad90d4cf34155c405e418306f9376716c514db4e
+  metadata.gz: 4e0c8c6ded43303be8e60d1b3f296c01a7eb71d9
+  data.tar.gz: 16641eeaa05112c42e6d4cbf19225a241f838910
 SHA512:
-  metadata.gz: bd6c1cf896bcbd16e00f35064b764789a0d35e6e5ef3db98d93bbe86ab55a1de92a5a72fe2c5559cfeba9cd06c645d20ec5f1a62cd4dca482a3f8f2aa9ff8678
-  data.tar.gz: 2909d49e91db24d697b445256475b6066bf807018394eb1560f1161fd8fd1966483db16f7c222bde72cfc54b90869a1bdf794e662bd4dd73f29ecafd3516d793
+  metadata.gz: 8cbac69ebc91242fb6a0343a082a7e90d4bb1746b93b2af1b750e71a14745f77256351f539223da2ffc3918a1270410c8bdd4d5efaa590e83fbcbff60fe19742
+  data.tar.gz: de45c205481873a3d514e160275fa22a6182d2862796d09c1cb6e54009645ee29dc8d132dc739282fb09adc45bfb0f6ce089047f61089876db5d57b34e9565ba

data/bin/rbbt

@@ -33,13 +33,19 @@ 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)
+def prev_dir(prev)
     rbbt_command_dir = $rbbt_command_dir
 
     prev.each do |previous_command|
         rbbt_command_dir = rbbt_command_dir[previous_command]
     end
 
+    rbbt_command_dir
+end
+
+def commands(prev)
+    rbbt_command_dir = prev_dir(prev)
+
     command_file_dirs = rbbt_command_dir.find_all
     command_files = command_file_dirs.collect{|d| d.glob('*') }.flatten
     command_files.collect{|p| File.basename(p) }.uniq.reject{|p| p =~ /\.desc$/}.sort
@@ -59,8 +65,14 @@ def rbbt_usage(prev = nil)
     puts 
     puts Log.color :magenta, "Subcommands:"
     puts 
+    prev_dir = prev_dir(prev)
     commands(prev).each do |command|
-      puts "  " << command
+      directory = File.directory? prev_dir[command].find
+      if directory
+        puts "  " << Log.color(:blue, command)
+      else
+        puts "  " << command
+      end
     end
   end
   puts

data/lib/rbbt/util/misc.rb

@@ -917,15 +917,32 @@ end
     html
   end
 
+  #def self.path_relative_to(basedir, path)
+  #  path = File.expand_path(path) unless path[0] == "/"
+  #  basedir = File.expand_path(basedir) unless basedir[0] == "/"
+
+  #  basedir << "/" unless basedir[-1] == "/"
+  #  case
+  #  when path == basedir
+  #    "."
+  #  #when path =~ /#{Regexp.quote basedir}\/(.*)/
+  #  when path.index(basedir) == 0
+  #    return path[basedir.length..-1]
+  #  else
+  #    return nil
+  #  end
+  #end
+
   def self.path_relative_to(basedir, path)
-    path = File.expand_path(path)
-    basedir = File.expand_path(basedir)
+    path = File.expand_path(path) unless path[0] == "/"
+    basedir = File.expand_path(basedir) unless basedir[0] == "/"
 
-    case
-    when path == basedir
-      "."
-    when path =~ /#{Regexp.quote basedir}\/(.*)/
-      return $1
+    if path.index(basedir) == 0
+      if basedir[-1] == "/"
+        return path[basedir.length..-1]
+      else
+        return path[basedir.length+1..-1]
+      end
     else
       return nil
     end

data/lib/rbbt/util/simpleopt/parse.rb

@@ -7,14 +7,14 @@ module SOPT
     current = [chars.shift]
     short = current * ""
 
-    if shortcuts.include? short and long.index "-" or long.index "_"
+    if (shortcuts.include?(short) and not shortcuts[short] == long) and long.index "-" or long.index "_"
       parts = long.split(/[_-]/)
       acc = parts.collect{|s| s[0] } * ""
       return acc unless shortcuts.include? acc
     end
 
-    while shortcuts.include? short
-      while shortcuts[short].index current * ""
+    while shortcuts.include?(short) and not shortcuts[short] == long
+      while (long.length - current.length > 2) and shortcuts[short].index current * ""
         next_letter = chars.shift
         return nil if next_letter.nil?
         current << next_letter

data/lib/rbbt/workflow.rb

@@ -259,8 +259,8 @@ module Workflow
   end
 
   def jobs(taskname, query = nil)
-    task_dir = File.join(workdir.find, taskname.to_s)
-    pattern = File.join(task_dir, '**/*')
+    task_dir = File.join(File.expand_path(workdir.find), taskname.to_s)
+    pattern = File.join(File.expand_path(task_dir), '**/*')
     job_info_files = Dir.glob(Step.info_file(pattern)).collect{|f| Misc.path_relative_to task_dir, f }
     job_info_files = job_info_files.select{|f| f.index(query) == 0 } if query
     job_info_files.collect{|f|

data/share/rbbt_commands/tsv/change_id

@@ -2,14 +2,50 @@
 
 require 'rbbt-util'
 require 'rbbt/util/simpleopt'
+require 'rbbt/sources/organism'
 
+options = SOPT.get("-f--file* File to process:-f--field* Field to change:-t--target* Target format:-i--identifiers* Identifier file to use")
 
-file = ARGV.shift
-identifiers = ARGV.shift
-format = ARGV.shift
+raise ParameterException, "No file given" unless file = options[:file]
+raise ParameterException, "No field given" unless field = options[:field]
+raise ParameterException, "No target given" unless target = options[:target]
 
+identifiers = options[:identifiers] || Organism.identifiers("Hsa").find
 
-tsv = TSV.open(file).attach identifiers, :fields => [format]
+begin
+  index = TSV.index(identifiers, :persist => true, :target => target, :merge => true)
+rescue
+  raise ParameterException, "Could not build index for '#{target}': #{ identifiers }"
+end
 
-puts tsv.reorder(format, tsv.fields - [format])
+tsv = TSV.open file
 
+tsv.process field do |value|
+  if Array === value
+    index.values_at *value
+  else
+    index[value]
+  end
+end
+
+tsv.fields = tsv.fields.collect{|f| f == field ? target : f}
+
+puts tsv
+
+exit
+
+#stream = Open.open file
+#header = TSV.parse_header stream
+#field_pos = header.all_fields.index field
+#raise ParameterException, "Unknown field: #{ field }" unless field_pos
+#
+#out = STDOUT
+#out.puts TSV.header_lines :fields => header.fields, :key_field =
+#while line = stream.gets do
+#  if line =~ /^#/
+#    out.puts line
+#    next
+#  else
+#  end
+#end
+#

data/share/rbbt_commands/workflow/jobs

@@ -0,0 +1,15 @@
+#!/usr/bin/env ruby
+
+require 'rbbt/workflow'
+
+dir = ARGV.shift || '.'
+
+all_files = Dir.glob(File.join(dir, '*'))
+info_files = Dir.glob(File.join(dir, Step.info_file('*')))
+file_dirs = Dir.glob(File.join(dir, Step.files_dir('*')))
+
+jobs = (all_files - info_files - file_dirs)
+
+jobs.reject!{|j| j =~ /\.lock/ }
+
+puts jobs * "\n"

data/share/rbbt_commands/workflow/task

@@ -84,7 +84,7 @@ def fix_options(workflow, task, job_options)
               value.to_f
             when :integer
               value.to_i
-            when :string, :text
+            when :text
               case
               when value == '-'
                 STDIN.read

data/test/rbbt/util/test_misc.rb

@@ -6,12 +6,12 @@ require 'rbbt/entity'
 
 class TestMisc < Test::Unit::TestCase
 
-  def test_parse_cmd_params
+  def _test_parse_cmd_params
     ddd Misc.parse_cmd_params("workflow task Translation translate -f 'Associated Gene Name' -l -")
   end
 
 
-  def test_fixutf8
+  def _test_fixutf8
     string = "abc\xffdef"
     string = string.force_encoding("UTF-8") if string.respond_to? :force_encoding
     assert(! string.valid_encoding?) if string.respond_to? :valid_encoding?
@@ -20,37 +20,37 @@ class TestMisc < Test::Unit::TestCase
     assert( Misc.fixutf8(string).valid_encoding) if string.respond_to? :valid_encoding
   end
 
-  def test_colors_for
+  def _test_colors_for
     colors, used = Misc.colors_for([1,2,2,1,2,1,2,2,3,3,2,3,2])
     assert_equal Misc::COLOR_LIST[1], used[2]
   end
 
-  def test_total_length
+  def _test_total_length
     ranges = [(0..100), (50..150), (120..160)]
     ranges = [(0..100), (50..150), (120..160), (51..70)]
     assert_equal 161, Misc.total_length(ranges)
   end
 
-  def test_id_filename?
+  def _test_id_filename?
     TmpFile.with_file("") do |file|
       assert Misc.is_filename?(file)
       assert ! Misc.is_filename?("TEST STRING")
     end
   end
 
-  def test_merge_sorted_arrays
+  def _test_merge_sorted_arrays
     assert_equal [1,2,3,4], Misc.merge_sorted_arrays([1,3], [2,4])
   end
 
-  def test_intersect_sorted_arrays
+  def _test_intersect_sorted_arrays
     assert_equal [2,4], Misc.intersect_sorted_arrays([1,2,3,4], [2,4])
   end
 
-  def test_sorted_array_matches
+  def _test_sorted_array_matches
     assert_equal [1,3], Misc.sorted_array_hits(%w(a b c d e), %w(b d))
   end
 
-  def test_binary_include?
+  def _test_binary_include?
     a = %w(a b c d e).sort
     assert Misc.binary_include?(a, "a")
     assert(!Misc.binary_include?(a, "z"))
@@ -59,24 +59,24 @@ class TestMisc < Test::Unit::TestCase
     assert(Misc.binary_include?(a, "d"))
   end
 
-  def test_process_to_hash
+  def _test_process_to_hash
     list = [1,2,3,4]
     assert_equal 4, Misc.process_to_hash(list){|l| l.collect{|e| e * 2}}[2]
   end
 
-#  def test_pdf2text_example
+#  def _test_pdf2text_example
 #    assert PDF2Text.pdf2text(datafile_test('example.pdf')).read =~ /An Example Paper/i
 #  end
 #
-#  def test_pdf2text_EPAR
+#  def _test_pdf2text_EPAR
 #    assert PDF2Text.pdf2text("http://www.ema.europa.eu/docs/en_GB/document_library/EPAR_-_Scientific_Discussion/human/000402/WC500033103.pdf").read =~ /Tamiflu/i
 #  end
 #
-#  def test_pdf2text_wrong
+#  def _test_pdf2text_wrong
 #    assert_raise CMD::CMDError do PDF2Text.pdf2text("http://www.ema.europa.eu/docs/en_GB#").read end
 #  end
 
-  def test_string2hash
+  def _test_string2hash
     assert(Misc.string2hash("--user-agent=firefox").include? "--user-agent")
     assert_equal(true, Misc.string2hash(":true")[:true])
     assert_equal(true, Misc.string2hash("true")["true"])
@@ -87,17 +87,23 @@ class TestMisc < Test::Unit::TestCase
     assert_equal(:j, Misc.string2hash("a=b#c=d#:h=:j")[:h])
   end
   
-  def test_named_array
+  def _test_named_array
     a = NamedArray.setup([1,2,3,4], %w(a b c d))
     assert_equal(1, a['a'])
   end
 
-#  def test_path_relative_to
-#    assert_equal "test/foo", Misc.path_relative_to('test/test/foo', 'test')
-#  end
+  def test_path_relative_to
+    assert_equal "test/foo", Misc.path_relative_to('/test', '/test/test/foo')
+
+    Misc.profile do
+    Misc.benchmark(45_000) do
+      Misc.path_relative_to('/test', '/test/test/foo')
+    end
+    end
+  end
 
-#  def test_chunk
-#    test =<<-EOF
+#  def _test_chunk
+#    _test =<<-EOF
 #This is an example file. Entries are separated by Entry
 #-- Entry
 #1
@@ -112,7 +118,7 @@ class TestMisc < Test::Unit::TestCase
 #    assert_equal "1\n2\n3", Misc.chunk(test, /^-- Entry/).first.strip
 #  end
 
-  def test_hash2string
+  def _test_hash2string
     hash = {}
     assert_equal hash, Misc.string2hash(Misc.hash2string(hash))
 
@@ -130,14 +136,14 @@ class TestMisc < Test::Unit::TestCase
  
   end
 
-  def test_merge
+  def _test_merge
     a = [[1],[2]]
     a = NamedArray.setup a, %w(1 2)
     a.merge [3,4]
     assert_equal [1,3], a[0]
   end
 
-  def test_indiferent_hash
+  def _test_indiferent_hash
     a = {:a => 1, "b" => 2}
     a.extend IndiferentHash
 
@@ -147,7 +153,7 @@ class TestMisc < Test::Unit::TestCase
     assert_equal 2, a[:b]
   end
 
-  def test_lockfile
+  def _test_lockfile
 
     TmpFile.with_file do |tmpfile|
       pids = []
@@ -171,7 +177,7 @@ class TestMisc < Test::Unit::TestCase
     end
   end
 
-  def test_positions2hash
+  def _test_positions2hash
     inputs = Misc.positional2hash([:one, :two, :three], 1, :two => 2, :four => 4)
     assert_equal 1, inputs[:one]
     assert_equal 2, inputs[:two]
@@ -179,7 +185,7 @@ class TestMisc < Test::Unit::TestCase
     assert_equal nil, inputs[:four]
   end
 
-  def test_mean
+  def _test_mean
     assert_equal 2, Misc.mean([1,2,3])
     assert_equal 3, Misc.mean([1,2,3,4,5])
   end
@@ -188,32 +194,32 @@ class TestMisc < Test::Unit::TestCase
     assert_equal Math.sqrt(2), Misc.sd([1,3])
   end
 
-  def test_align_small
+  def _test_align_small
     reference = "AABCDEBD"
     sequence  = "ABCD"
     assert_equal '-ABCD---', Misc.fast_align(reference, sequence).last
   end
 
-  def test_align_real
+  def _test_align_real
     reference = "SGNECNKAIDGNKDTFWHTFYGANGDPKPPPHTYTIDMKTTQNVNGLSMLPRQDGNQNGWIGRHEVYLSSDGTNW"
     sequence  = "TYTIDMKTTQNVNGLSML"
     assert_equal "--------------------------------TYTIDMKTTQNVNGLSML-------------------------", Misc.fast_align(reference, sequence).last
   end
 
-  def test_divide
+  def _test_divide
     assert_equal 2, Misc.divide(%w(1 2 3 4 5 6 7 8 9),2).length
   end
 
-  def test_ordered_divide
+  def _test_ordered_divide
     assert_equal 5, Misc.ordered_divide(%w(1 2 3 4 5 6 7 8 9),2).length
   end
 
-  def test_collapse_ranges
+  def _test_collapse_ranges
     ranges = [(0..100), (50..150), (51..61),(200..250), (300..324),(320..350)]
     assert_equal [(0..150),(200..250), (300..350)], Misc.collapse_ranges(ranges)
   end
 
-  def test_humanize
+  def _test_humanize
     str1 = "test_string"
     str2 = "TEST_string"
     str3 = "test"
@@ -225,22 +231,22 @@ class TestMisc < Test::Unit::TestCase
     assert_equal "mutation_enrichment", Misc.snake_case("MutationEnrichment")
   end
 
-  def test_snake_case
+  def _test_snake_case
     str1 = "ACRONIMTest"
     str2 = "ACRONIM_test"
     assert_equal "ACRONIM_test", Misc.snake_case(str1)
     assert_equal "ACRONIM_test", Misc.snake_case(str2)
   end
 
-  def test_correct_vcf_mutations
+  def _test_correct_vcf_mutations
     assert_equal [737407, ["-----", "-----G", "-----GTTAAT"]], Misc.correct_vcf_mutation(737406, "GTTAAT", "G,GG,GGTTAAT")
   end
 
-  def test_fingerprint
+  def _test_fingerprint
     assert_equal '{a=>1}', Misc.fingerprint({:a => 1})
   end
 
-  def test_tarize
+  def _test_tarize
     path = File.expand_path('/home/mvazquezg/git/rbbt-util/lib')
     stream = Misc.tarize(path)
     TmpFile.with_file do |res|
@@ -250,7 +256,7 @@ class TestMisc < Test::Unit::TestCase
     end
   end
 
-  def test_camel_case
+  def _test_camel_case
     assert_equal "DbSNP", Misc.camel_case("db_SNP")
     assert_equal "D3Js", Misc.camel_case("D3Js")
     assert_equal "Structure", Misc.camel_case("Structure")
@@ -258,7 +264,7 @@ class TestMisc < Test::Unit::TestCase
     assert_equal "COSMIC", Misc.camel_case("COSMIC")
   end
 
-  def test_pipe
+  def _test_pipe
     t = 5
     stream = Misc.open_pipe do |sin|
       t.times do |i|

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.6.13
+  version: 5.6.14
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-02-27 00:00:00.000000000 Z
+date: 2014-02-28 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
@@ -228,6 +228,7 @@ files:
 - share/rbbt_commands/workflow/cmd
 - share/rbbt_commands/workflow/example
 - share/rbbt_commands/workflow/install
+- share/rbbt_commands/workflow/jobs
 - share/rbbt_commands/workflow/list
 - share/rbbt_commands/workflow/monitor
 - share/rbbt_commands/workflow/provenance