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)
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)
