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",])