def test_empty_counter(self):
"""BarcodeCounter: check empty counter
"""
# Initialise counter object
bc = BarcodeCounter()
self.assertEqual(bc.barcodes(),[])
self.assertEqual(bc.lanes,[])
self.assertEqual(bc.filter_barcodes(),[])
self.assertEqual(bc.counts("AGGCAGAATCTTACGC"),0)
self.assertEqual(bc.counts("AGGCAGAATCTTACGC",lane=1),0)
self.assertEqual(bc.counts_all("AGGCAGAATCTTACGC"),0)
self.assertEqual(bc.nreads(),0)
self.assertEqual(bc.nreads(1),0)
def test_empty_counter(self):
"""BarcodeCounter: check empty counter
"""
# Initialise counter object
bc = BarcodeCounter()
self.assertEqual(bc.barcodes(),[])
self.assertEqual(bc.lanes,[])
self.assertEqual(bc.filter_barcodes(),[])
self.assertEqual(bc.counts("AGGCAGAATCTTACGC"),0)
self.assertEqual(bc.counts("AGGCAGAATCTTACGC",lane=1),0)
self.assertEqual(bc.counts_all("AGGCAGAATCTTACGC"),0)
self.assertEqual(bc.nreads(),0)
self.assertEqual(bc.nreads(1),0)
def test_filter_barcodes(self):
"""BarcodeCounter: check filtering by lane and cutoff
"""
bc = BarcodeCounter()
bc.count_barcode("TATGCGCGGTA",lane=1,incr=285302)
bc.count_barcode("TATGCGCGGTG",lane=1,incr=532)
bc.count_barcode("ACCTACCGGTA",lane=1,incr=315)
bc.count_barcode("CCCTTATGCGA",lane=1,incr=22)
bc.count_barcode("ACCTAGCGGTA",lane=2,incr=477)
bc.count_barcode("ACCTCTATGCT",lane=2,incr=368)
self.assertEqual(bc.barcodes(),["TATGCGCGGTA",
"TATGCGCGGTG",
"ACCTAGCGGTA",
"ACCTCTATGCT",
"ACCTACCGGTA",
"CCCTTATGCGA"])
# No filtering
self.assertEqual(bc.filter_barcodes(),["TATGCGCGGTA",
"TATGCGCGGTG",
"ACCTAGCGGTA",
"ACCTCTATGCT",
"ACCTACCGGTA",
"CCCTTATGCGA"])
# Filter by lane
self.assertEqual(bc.filter_barcodes(lane=1),["TATGCGCGGTA",
"TATGCGCGGTG",
"ACCTACCGGTA",
"CCCTTATGCGA"]),
self.assertEqual(bc.filter_barcodes(lane=2),["ACCTAGCGGTA",
"ACCTCTATGCT"])
# Filter by cutoff
self.assertEqual(bc.filter_barcodes(cutoff=0.5),
["TATGCGCGGTA",])
self.assertEqual(bc.filter_barcodes(cutoff=0.0015,lane=1),
["TATGCGCGGTA","TATGCGCGGTG"])
self.assertEqual(bc.filter_barcodes(cutoff=0.5,lane=2),
["ACCTAGCGGTA",])
def test_filter_barcodes(self):
"""BarcodeCounter: check filtering by lane and cutoff
"""
bc = BarcodeCounter()
bc.count_barcode("TATGCGCGGTA",lane=1,incr=285302)
bc.count_barcode("TATGCGCGGTG",lane=1,incr=532)
bc.count_barcode("ACCTACCGGTA",lane=1,incr=315)
bc.count_barcode("CCCTTATGCGA",lane=1,incr=22)
bc.count_barcode("ACCTAGCGGTA",lane=2,incr=477)
bc.count_barcode("ACCTCTATGCT",lane=2,incr=368)
self.assertEqual(bc.barcodes(),["TATGCGCGGTA",
"TATGCGCGGTG",
"ACCTAGCGGTA",
"ACCTCTATGCT",
"ACCTACCGGTA",
"CCCTTATGCGA"])
# No filtering
self.assertEqual(bc.filter_barcodes(),["TATGCGCGGTA",
"TATGCGCGGTG",
"ACCTAGCGGTA",
"ACCTCTATGCT",
"ACCTACCGGTA",
"CCCTTATGCGA"])
# Filter by lane
self.assertEqual(bc.filter_barcodes(lane=1),["TATGCGCGGTA",
"TATGCGCGGTG",
"ACCTACCGGTA",
"CCCTTATGCGA"]),
self.assertEqual(bc.filter_barcodes(lane=2),["ACCTAGCGGTA",
"ACCTCTATGCT"])
# Filter by cutoff
self.assertEqual(bc.filter_barcodes(cutoff=0.5),
["TATGCGCGGTA",])
self.assertEqual(bc.filter_barcodes(cutoff=0.0015,lane=1),
["TATGCGCGGTA","TATGCGCGGTG"])
self.assertEqual(bc.filter_barcodes(cutoff=0.5,lane=2),
["ACCTAGCGGTA",])
