def test_barcodegroup_add(self):
"""BarcodeGroup: check adding a sequence to the group
"""
# Add sequences to a BarcodeGroup
grp = BarcodeGroup("CTAAGCCT",2894178)
grp.add("CTAAGCCA",92417)
self.assertEqual(grp.reference,"CTAAGCCT")
self.assertEqual(grp.sequences,["CTAAGCCT","CTAAGCCA"])
self.assertEqual(grp.counts,2986595)
self.assertEqual(len(grp),2)
def test_barcodegroup_add(self):
"""BarcodeGroup: check adding a sequence to the group
"""
# Add sequences to a BarcodeGroup
grp = BarcodeGroup("CTAAGCCT",2894178)
grp.add("CTAAGCCA",92417)
self.assertEqual(grp.reference,"CTAAGCCT")
self.assertEqual(grp.sequences,["CTAAGCCT","CTAAGCCA"])
self.assertEqual(grp.counts,2986595)
self.assertEqual(len(grp),2)
def test_barcodegroup(self):
"""BarcodeGroup: check making a new instance
"""
# Create a new BarcodeGroup
grp = BarcodeGroup("CTAAGCCT",2894178)
self.assertEqual(grp.reference,"CTAAGCCT")
self.assertEqual(grp.sequences,["CTAAGCCT"])
self.assertEqual(grp.counts,2894178)
self.assertEqual(len(grp),1)
def test_barcodegroup_match(self):
"""BarcodeGroup: check matching sequences against the reference
"""
# Match sequence against the group
grp = BarcodeGroup("CTAAGCCT",2894178)
# 1 mismatch allowed
self.assertTrue(grp.match("CTAAGCCA",mismatches=1))
self.assertFalse(grp.match("CGAAGCCA",mismatches=1))
self.assertFalse(grp.match("CGATGCCA",mismatches=1))
# Default (2 mismatches)
self.assertTrue(grp.match("CTAAGCCA"))
self.assertTrue(grp.match("CGAAGCCA"))
self.assertFalse(grp.match("CGATGCCA"))
# Differing lengths of barcode
# -- Too short
self.assertFalse(grp.match("CGATGCC"))
# -- Too long
self.assertFalse(grp.match("CGATGCCGG"))
def test_barcodegroup_match(self):
"""BarcodeGroup: check matching sequences against the reference
"""
# Match sequence against the group
grp = BarcodeGroup("CTAAGCCT",2894178)
# 1 mismatch allowed
self.assertTrue(grp.match("CTAAGCCA",mismatches=1))
self.assertFalse(grp.match("CGAAGCCA",mismatches=1))
self.assertFalse(grp.match("CGATGCCA",mismatches=1))
# Default (2 mismatches)
self.assertTrue(grp.match("CTAAGCCA"))
self.assertTrue(grp.match("CGAAGCCA"))
self.assertFalse(grp.match("CGATGCCA"))
# Differing lengths of barcode
# -- Too short
self.assertFalse(grp.match("CGATGCC"))
# -- Too long
self.assertFalse(grp.match("CGATGCCGG"))