htsworkflow/submission/test/test_daf.py

   1 import unittest
   2
   3 from htsworkflow.submission import daf
   4
   5 test_daf = """# Lab and general info
   6 grant             Hardison
   7 lab               Caltech-m
   8 dataType          ChipSeq
   9 variables         cell, antibody,sex,age,strain,control
  10 compositeSuffix   CaltechHistone
  11 assembly          mm9
  12 dafVersion        2.0
  13 validationSettings validateFiles.bam:mismatches=2,bamPercent=99.9;validateFiles.fastq:quick=1000
  14
  15 # Track/view definition
  16 view             Peaks
  17 longLabelPrefix  Caltech Histone Peaks
  18 type             narrowPeak
  19 hasReplicates    yes
  20 required         no
  21
  22 view             Signal
  23 longLabelPrefix  Caltech Histone Signal
  24 type             bigWig
  25 hasReplicates    yes
  26 required         no
  27 """
  28
  29 class TestDAF(unittest.TestCase):
  30     def test_parse(self):
  31
  32         parsed = daf.fromstring(test_daf)
  33
  34         self.failUnlessEqual(parsed['assembly'], 'mm9')
  35         self.failUnlessEqual(parsed['grant'], 'Hardison')
  36         self.failUnlessEqual(len(parsed['variables']), 6)
  37         self.failUnlessEqual(len(parsed['views']), 2)
  38         self.failUnlessEqual(len(parsed['views']['Peaks']), 5)
  39         self.failUnlessEqual(len(parsed['views']['Signal']), 5)
  40         signal = parsed['views']['Signal']
  41         self.failUnlessEqual(signal['required'], False)
  42         self.failUnlessEqual(signal['longLabelPrefix'],
  43                              'Caltech Histone Signal')
  44
  45     def test_rdf(self):
  46         try:
  47             import RDF
  48
  49             parsed = daf.fromstring(test_daf)
  50             #mem = RDF.Storage(storage_name='hashes',
  51             #                  options_string='hash-type="memory"'),
  52             mem = RDF.MemoryStorage()
  53             model = RDF.Model(mem)
  54
  55             daf.add_to_model(model, parsed)
  56
  57             writer = RDF.Serializer(name='turtle')
  58             print writer.serialize_model_to_string(model)
  59
  60         except ImportError, e:
  61             print "Skipped test_rdf"
  62
  63 def suite():
  64     return unittest.makeSuite(TestDAF, 'test')
  65
  66 if __name__ == "__main__":
  67     unittest.main(defaultTest='suite')