def test_isBarcoded(self): empty = upstreamdata.getEmptyBam() nonempty = ('/pbi/dept/secondary/siv/testdata/' 'pblaa-unittest/Sequel/Phi29/m54008_160219_003234' '.tiny.subreadset.xml') # One empty one non empty sset = SubreadSet(nonempty, empty, skipMissing=True) self.assertTrue(sset.isBarcoded) # Just nonempty sset = SubreadSet(nonempty, skipMissing=True) self.assertEqual(len(sset), 15133) self.assertTrue(sset.isBarcoded) # Just empty # This is crazy, the pbi must be out of date: sset = SubreadSet(empty) self.assertEqual(len(sset), 0) self.assertTrue(sset.isBarcoded) # To confirm current behavior, I will regenerate the pbi with a # current pbindex: efn = tempfile.NamedTemporaryFile(suffix=".subreadset.xml").name log.info("Copying to {}".format(efn)) sset.copyTo(efn) sset.induceIndices(force=True) self.assertFalse(sset.isBarcoded)
def test_empty_bam(self): fn = data.getEmptyBam() bam = IndexedBamReader(fn) EQ(len(bam), 0)
def test_empty_bam(self): fn = data.getEmptyBam() bam = IndexedBamReader(fn) assert len(bam) == 0
def test_empty_bam(self): fn = data.getEmptyBam() bam = IndexedBamReader(fn) EQ(len(bam), 0)