rbbt-util 3.2.0 → 3.2.1

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Files changed (32) hide show
  1. data/bin/run_workflow.rb +118 -0
  2. data/lib/rbbt-util.rb +0 -3
  3. data/lib/rbbt/util/fix_width_table.rb +7 -0
  4. data/lib/rbbt/util/misc.rb +20 -4
  5. data/lib/rbbt/util/persistence.rb +51 -28
  6. data/lib/rbbt/util/resource.rb +1 -0
  7. data/lib/rbbt/util/task.rb +11 -0
  8. data/lib/rbbt/util/task/job.rb +3 -1
  9. data/lib/rbbt/util/tc_hash.rb +89 -20
  10. data/lib/rbbt/util/tsv.rb +23 -8
  11. data/lib/rbbt/util/tsv/accessor.rb +8 -5
  12. data/lib/rbbt/util/tsv/filters.rb +68 -20
  13. data/lib/rbbt/util/tsv/index.rb +115 -92
  14. data/lib/rbbt/util/tsv/manipulate.rb +10 -13
  15. data/lib/rbbt/util/tsv/parse.rb +1 -1
  16. data/lib/rbbt/util/tsv/resource.rb +8 -0
  17. data/lib/rbbt/util/workflow.rb +26 -8
  18. data/share/lib/R/util.R +71 -1
  19. data/test/rbbt/util/test_misc.rb +17 -0
  20. data/test/rbbt/util/test_persistence.rb +32 -0
  21. data/test/rbbt/util/test_resource.rb +1 -0
  22. data/test/rbbt/util/test_task.rb +14 -0
  23. data/test/rbbt/util/test_tc_hash.rb +16 -0
  24. data/test/rbbt/util/tsv/test_accessor.rb +0 -1
  25. data/test/rbbt/util/tsv/test_filters.rb +26 -0
  26. data/test/rbbt/util/tsv/test_index.rb +78 -26
  27. data/test/rbbt/util/tsv/test_manipulate.rb +1 -1
  28. metadata +10 -14
  29. data/bin/workflow.rb +0 -24
  30. data/lib/rbbt/util/bed.rb +0 -325
  31. data/lib/rbbt/util/cachehelper.rb +0 -100
  32. data/test/rbbt/util/test_bed.rb +0 -136
data/test/rbbt/util/test_bed.rb DELETED
@@ -1,136 +0,0 @@
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- require File.join(File.expand_path(File.dirname(__FILE__)), '../..', 'test_helper.rb')
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- require 'rbbt/util/bed'
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- require 'rbbt/util/tmpfile'
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-
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- class TestBed < Test::Unit::TestCase
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- def load_data(data)
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- Log.debug("Data:\n#{Open.read(data)}")
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- tsv = TSV.new(data, :list, :sep=>":", :cast => proc{|e| e =~ /(\s*)(_*)/; ($1.length..($1.length + $2.length - 1))})
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- tsv.add_field "Start" do |key, values|
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- values["Range"].first
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- end
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- tsv.add_field "End" do |key, values|
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- values["Range"].last
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- end
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-
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- tsv
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- end
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-
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- def test_point
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- data =<<-EOF
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- #ID Pos
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- a 1
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- b 10
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- c 20
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- d 12
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- e 26
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- f 11
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- g 25
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- EOF
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-
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- TmpFile.with_file(data) do |f|
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- bed = Bed.new TSV.new(f, :list, :sep=>" "), :key => "Pos" , :value => "ID"
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-
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- assert_equal %w(), bed[0].sort
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- assert_equal %w(b), bed[10].sort
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- assert_equal %w(a b c d f), bed[(0..20)].sort
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- end
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- end
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-
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- def test_range
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- data =<<-EOF
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- #ID:Range
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- #:012345678901234567890
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- a: ______
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- b: ______
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- c: _______
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- d: ____
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- e: ______
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- f: ___
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- g: ____
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- EOF
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-
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- TmpFile.with_file(data) do |f|
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- bed = Bed.new load_data(f), :range => ["Start" , "End"], :value => "ID"
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-
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- assert_equal %w(), bed[0].sort
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- assert_equal %w(b), bed[1].sort
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- assert_equal %w(), bed[20].sort
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- assert_equal %w(), bed[(20..100)].sort
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- assert_equal %w(a b d), bed[3].sort
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- assert_equal %w(a b c d e), bed[(3..4)].sort
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- end
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- end
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-
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- def test_format
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- entry = Bed::Entry.new "Hola", 0, 10, nil
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- format = Bed::FixWidthTable.format(entry,1, 100)
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- assert_equal entry, Bed::FixWidthTable.unformat(format, 100)
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- end
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-
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- def test_table
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- TmpFile.with_file do |f|
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- table = Bed::FixWidthTable.new(f, 100, false)
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- table.add Bed::Entry.new("Entry1", 0, 10, nil), 0
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- table.add Bed::Entry.new("Entry2", 10, 20, nil), 10
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- table.add Bed::Entry.new("Entry3", 10, 20, nil), 10
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-
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- table.read
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-
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- assert_equal "Entry1", table[0].value
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- assert_equal "Entry2", table[1].value
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- assert_equal "Entry3", table[2].value
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- end
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-
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- end
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-
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- def test_range_point
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- data =<<-EOF
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- #ID Pos
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- a 1
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- b 10
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- c 20
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- d 12
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- e 26
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- f 11
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- g 25
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- EOF
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-
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- TmpFile.with_file(data) do |f|
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- bed = Bed.new TSV.new(f,:list, :sep=>" "), :key => "Pos" , :value => "ID", :persistence => true
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-
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- bed = Bed.new TSV.new(f,:list, :sep=>" "), :key => "Pos" , :value => "ID", :persistence => true
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-
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- assert_equal %w(), bed[0].sort
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- assert_equal %w(a b c d f), bed[(0..20)].sort
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- assert_equal %w(b), bed[10].sort
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- end
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- end
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-
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- def test_range_persistence
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- data =<<-EOF
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- #ID:Range
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- #:012345678901234567890
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- a: ______
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- b: ______
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- c: _______
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- d: ____
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- e: ______
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- f: ___
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- g: ____
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- EOF
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-
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- TmpFile.with_file(data) do |f|
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- bed = Bed.new load_data(f), :range => ["Start" , "End"], :value => "ID", :persistence => true
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-
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- bed = Bed.new load_data(f), :range => ["Start" , "End"], :value => "ID", :persistence => true
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-
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- assert_equal %w(), bed[0].sort
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- assert_equal %w(b), bed[1].sort
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- assert_equal %w(), bed[20].sort
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- assert_equal %w(), bed[(20..100)].sort
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- assert_equal %w(a b d), bed[3].sort
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- assert_equal %w(a b c d e), bed[(3..4)].sort
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- end
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- end
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- end