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"""
Tests for `bx.align.score`.
"""
import unittest
from io import StringIO
from numpy import (
allclose,
array,
cumsum,
)
import bx.align.maf
import bx.align.score
aligns = [
(
"CCACTAGTTTTTAAATAATCTACTATCAAATAAAAGATTTGTTAATAATAAATTTTAAATCATTAACACTT",
"CCATTTGGGTTCAAAAATTGATCTATCA----------TGGTGGATTATTATTTAGCCATTAAGGACAAAT",
-111,
),
(
"CCACTAGTTTTTAAATAATCTAC-----AATAAAAGATTTGTTAATAAT---AAATTTTAAATCATTAA-----CACTT",
"CCATTTGGGTTCAAAAATTGATCTATCA----------TGGTGGAT---TATTATTT-----AGCCATTAAGGACAAAT",
-3626,
),
("CCACTAGTTTTTGATTC", "CCATTTGGGTTC-----", -299),
("CTTAGTTTTTGATCACC", "-----CTTGGGTTTACC", -299),
(
"gggaattgaacaatgagaacacatggacacaggaaggggaacatcacacacc----------ggggcctgttgtggggtggggggaag",
"ggaactagaacaagggagacacatacaaacaacaacaacaacaacacagcccttcccttcaaagagcttatagtctgatggaggagag",
1690,
),
]
mafs = """##maf
a score=2883.0
s hg17.chr1 6734 30 + 245522847 CTACCTCAGTGTGGAAGGTGGGCAGTTCTG
s rheMac1.SCAFFOLD71394 9319 30 - 13789 CTACCTCAGTGTGGAAGGTGGGCAGTTCTG
a score=8167.0
s hg17.chr1 41401 40 + 245522847 TGTGTGATTAATGCCTGAGACTGTGTGAAGTAAGAGATGG
s panTro1.chr1 49673 40 + 229575298 TGCGTGATTAATGCCTGAGATTGTGTGAAGTAAAAGATGG
s rheMac1.SCAFFOLD45837 26063 33 - 31516 TGTGTGATTAATGCCTGAGATTGTGTGAAGTAA-------
"""
nonsymm_scheme = bx.align.score.build_scoring_scheme(
""" A C G T
91 0 -31 -123
-114 100 -125 -31
-31 -125 100 -114
-123 -31 -114 91 """,
400,
30,
)
aligns_for_nonsymm_scheme = [("AAAACCCCGGGGTTTT", "ACGTACGTACGTACGT", -580)]
asymm_scheme = bx.align.score.build_scoring_scheme(
""" 01 02 A C G T
01 200 -200 -50 100 -50 100
02 -200 200 100 -50 100 -50 """,
0,
0,
gap1="\x00",
)
aligns_for_asymm_scheme = [("\x01\x01\x01\x01\x01\x01", "ACGT\x01\x02", 100)]
class BasicTests(unittest.TestCase):
def test_scoring_text(self):
ss = bx.align.score.hox70
for t1, t2, score in aligns:
self.assertEqual(bx.align.score.score_texts(ss, t1, t2), score)
def test_align(self):
ss = bx.align.score.hox70
for block in bx.align.maf.Reader(StringIO(mafs)):
self.assertEqual(bx.align.score.score_alignment(ss, block), float(block.score))
def test_accumulate(self):
ss = bx.align.score.hox70
self.assertTrue(
allclose(
bx.align.score.accumulate_scores(ss, "-----CTTT", "CTTAGTTTA"),
cumsum(array([-430, -30, -30, -30, -30, -31, 91, 91, -123])),
)
)
self.assertTrue(
allclose(
bx.align.score.accumulate_scores(ss, "-----CTTT", "CTTAGTTTA", skip_ref_gaps=True),
cumsum(array([-581, 91, 91, -123])),
)
)
def test_nonsymm_scoring(self):
ss = nonsymm_scheme
for t1, t2, score in aligns_for_nonsymm_scheme:
self.assertEqual(bx.align.score.score_texts(ss, t1, t2), score)
def test_asymm_scoring(self):
ss = asymm_scheme
for t1, t2, score in aligns_for_asymm_scheme:
self.assertEqual(bx.align.score.score_texts(ss, t1, t2), score)
|
