def test_write_gap_file(self):
original_read_len = 50
delimiter = "|"
additional_header_lines=["hoopy", "frood"]
gaps = [MockGap("foo"), MockGap("bar")]
writer = MockWriter()
GapUtility(original_read_len, delimiter, MockLogger()).write_gap_file(gaps, writer, additional_header_lines)
actual_lines = writer.lines()
self.assertEqual(["#hoopy", "#frood", Gap.header("|"), "foo", "bar"], actual_lines)
def test_format(self):
gap = Gap("sampleName", "split-read-name-L-13", "chromosome", 0, 4, 16, 64)
self.assertEqual("chromosome|-1|sampleName|4|16|12|0|64|64|split-read-name-L-13|split-read-name", gap.format("|"))
gap.cluster = "42"
self.assertEqual("chromosome|42|sampleName|4|16|12|0|64|64|split-read-name-L-13|split-read-name", gap.format("|"))
def test_header(self):
self.assertEqual("#chromosome|cluster|sample_name|gap_start|gap_end|gap_width|read_start|read_end|read_width|split_read_name|original_read_name", Gap.header("|"))
def test_additional_sam_tags(self):
gap = Gap("sampleName", "split-read-name-L-13", "chromosome", 0, 4, 16, 64)
gap.cluster = 42
self.assertEqual("XC:i:42|XR:Z:split-read-name", gap.additional_sam_tags("|"))
