def test_no_alligned_reads_no_bc(self): inBam = tests.get_file("no_mapped_reads.bam") outBam = tests.get_file("test_barcode_collapse.bc.bam") total_count, removed_count = barcode_collapse.barcode_collapse(inBam, outBam, False, em=True)
def test_barcode_collapse_not_barcoded(self): """ Tests duplicate removal for non barcoded samples """ inBam = tests.get_file("test_barcode_collapse.bam") outBam = tests.get_file("test_barcode_collapse.bc.bam") total_count, removed_count = barcode_collapse.barcode_collapse( inBam, outBam, False) true_total_count = {"total": 7} true_removed_count = {"total": 5} self.assertDictEqual(true_total_count, total_count) self.assertDictEqual(true_removed_count, removed_count)
def test_barcode_collapse_bacoded(self): """ Tests on duplciate removal for barcoded samples """ inBam = tests.get_file("test_barcode_collapse.bam") outBam = tests.get_file("test_barcode_collapse.bc.bam") total_count, removed_count = barcode_collapse.barcode_collapse( inBam, outBam, True) true_total_count = {"AAGGGTCGC": 3, "AAGGGTCGT": 4} true_removed_count = {"AAGGGTCGC": 1, "AAGGGTCGT": 2} self.assertDictEqual(true_total_count, total_count) self.assertDictEqual(true_removed_count, removed_count)
def test_barcode_collapse_not_barcoded(self): """ Tests duplicate removal for non barcoded samples """ inBam = tests.get_file("test_barcode_collapse.bam") outBam = tests.get_file("test_barcode_collapse.bc.bam") total_count, removed_count = barcode_collapse.barcode_collapse(inBam, outBam, False) true_total_count = {"total": 7} true_removed_count = {"total": 5} self.assertDictEqual(true_total_count, total_count) self.assertDictEqual(true_removed_count, removed_count)
def test_barcode_collapse_bacoded(self): """ Tests on duplciate removal for barcoded samples """ inBam = tests.get_file("test_barcode_collapse.bam") outBam = tests.get_file("test_barcode_collapse.bc.bam") total_count, removed_count = barcode_collapse.barcode_collapse(inBam, outBam, True) true_total_count = {"AAGGGTCGC": 3, "AAGGGTCGT": 4} true_removed_count = {"AAGGGTCGC": 1, "AAGGGTCGT": 2} self.assertDictEqual(true_total_count, total_count) self.assertDictEqual(true_removed_count, removed_count)