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"""
Tests for `bx.align.lav`.
"""
import unittest
import bx.align.lav as lav
test_lav = "test_data/lav_tests/apple_orange.lav"
class lavTestCase(unittest.TestCase):
def testReader(self):
reader = lav.Reader(open(test_lav))
a = next(reader)
assert a.score == 10286, f"a.score is wrong: {a.score}"
assert len(a.components) == 2
check_component(
a.components[0],
"apple",
106,
252,
"+",
411,
"GTCCGGCCGGCTGAGAGCTACAATACACATGCACGCAGTTTGGCCACTCACATTAAGTATATGAGGAAGGGTTAGCATGAGTTGTACTATAAGGCAGCGGATAGCAGGTTGTGGAAAAATATCCTCCCGATTCAAATCCCCAGGTGCCTAAA----------------GTAGGGCCGGTAGTTGAATGCTTGCCTGTCAGACTGGATGACCAAGTTCAGTATCAACACAATATAGTGCCAGGAGCTAATTGTTCCCCAGCAGCGTGAC",
)
check_component(
a.components[1],
"lav_tests.orange",
53,
252,
"+",
361,
"GTCCGGCCGGCTGTGTGCTACAATACACGTTCACGCAGTTTGGCCAATCACTTTAAGTATATACGAAATGGTTACCATGAGTTGTACTGTAAGGCAGCGGAAAGC---TTGTTAA--------CTCCTGGGCGACATT----GGGGCTGCAACATCGTTTATCCTCCTCTACAACCAATAGCTG-TTGCTTCTTGGTTCAAGTATATCCCATGGATTAGTATCAACACGATATAGTGTCAGGAGCTAATTGTTCCCCAGCAGCGTGAC",
)
a = next(reader)
assert a.score == 3586, f"a.score is wrong: {a.score}"
assert len(a.components) == 2
check_component(
a.components[0],
"apple",
52,
72,
"+",
411,
"TGCATATCGACTATTACAGCCACGCGAGTTACATTCCTCTTTTTTTTTGCTGGCGTCCGGCCGGCTGAGAGC",
)
check_component(
a.components[1],
"lav_tests.orange",
2,
72,
"-",
361,
"TGCATATCGACTAGTACAGCCTCTCGAGTTACCCCCCCCATTCCTCTTGCTGACGTCACGCTGCTGGGGAAC",
)
a = next(reader)
assert a is None
reader.close()
def check_component(c, src, start, size, strand, src_size, text):
# ..print "\"%s\" == \"%s\"" % (c.src,src)
assert c.src == src, f"c.src = {c.src} (expected {src})"
assert c.start == start, f"c.start = {c.start} (expected {start})"
assert c.size == size, f"c.size = {c.size} (expected {size})"
assert c.strand == strand, f"c.strand = {c.strand} (expected {strand})"
assert c.src_size == src_size, f"c.src_size = {c.src_size} (expected {src_size})"
assert c.text == text, f'c.text = "{c.text}" (expected "{text}")'
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