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"""
Tests for `bx.seqmapping`.
"""
import unittest
from io import StringIO
from numpy import (
allclose,
array,
)
import bx.seqmapping
class CharMappingTests(unittest.TestCase):
__test__ = False
def test_DNA(self):
assert allclose(bx.seqmapping.DNA.translate("ACGTacgt-?X"), [0, 1, 2, 3, 0, 1, 2, 3, 4, -1, -1])
def test_DNA_list(self):
assert allclose(
bx.seqmapping.DNA.translate_list(["ACGTA", "TGCAX"]), [0 + 3 * 6, 1 + 2 * 6, 2 + 1 * 6, 3 + 0 * 6, -1]
)
def test_other(self):
m = bx.seqmapping.CharToIntArrayMapping()
m.set_mapping("A", 0)
m.set_mapping("B", 7)
assert allclose(m.translate("ABCCBA"), [0, 7, -1, -1, 7, 0])
class IntMappingTests(unittest.TestCase):
__test__ = False
def test_simple(self):
m = bx.seqmapping.IntToIntMapping(4)
m.set_mapping(0, 0)
m.set_mapping(2, 0)
m.set_mapping(1, 1)
m.set_mapping(3, 1)
assert allclose(m.translate(array([0, 1, 2, 3, 4], "i")), array([0, 1, 0, 1, -1]))
eight_species_mapping = """TTTTTTTT 0
CCCCCCCC 4
AAAAAAAA 1
GGGGGGGG 5
AAAAA*AA 2
TTTTT*TT 0
GGGGG*GG 5
CCCCC*CC 4
GGGG*GGG 5
TTTT*TTT 2
GGGAAGGG 5
AAAA*AAA 2
TTTTT*T* 2
CCCCC*C* 4
CCCTTCCC 4
CCCC*CCC 4
TTTT**TT 2
AAAA**AA 2
AAAAA*A* 2
GGGGG*G* 5
AAAAAGAA 2
TTTTTCTT 2
GGGAA*GG 5
TTTT**T* 2
TTTCCTTT 0
AAAAAAA* 1
CCCTT*CC 3
TTTTTTT* 2
CC*CC*CC 3
AAAGGAAA 2
------G- 2
"""
rows = [
"AAATTGT-----ATGTCCATCCTTTAAAGGTCATTCCTTTAATGGTCTTTTCTGGACACCACTAGGGGTCAGAAGTAGTTCATCAAAC-----------------TTTCTTCCCTCCC-TACTTCAGTG",
"AAATTGT-----ATGTCCATCCTTTAAAGGTCATTCCTTTAATGGTCTTTTCTGGACACCACTAGGGGTCAGAAGTAGTTCATCAAAC-----------------TTTCTTCCCTCCC-TACTTCAGTG",
"AAATTTT-----ATGTCTATCCTTTAAAGGTCATTCCTCTAATAGTCTTTTCTGGACACCACTAGGGGTCAGAAGTAGTTCATTAAAC-----------------TTTCTTCCCTCCC-TACCTCAGTG",
"AAACTGT-----ATCACCACCTTTTTAAGGTCATTTCTCTAATGATCCTGTT-GCATACCAGTAGGGGGCAGAAGTGTTCCGCTGATTTCCGCCCTCCTCCCCACCCCCCCACCCCCC-TTATTCAAAG",
"*********************************************************************************************************************************",
"-TATTAT-----ATGGCCATGTTCAAAAGGTTGTTTCTCTAATGATTCCTTC-TGATACCAGTAGGGGTCAGAAGTGGTCCATTGATT---------------------CTTTTCCTC-TGATTC-AAG",
"AAATTGA--AAGATCTCACTCTTTGCCAGGTAGTCCATCTAAGGGTCACATATGGATACCAGCAGGGCCT-GAAGAAGCCCATTGAAT------------------------TTTCCC-ATCTTCAAGG",
"AAATTCATGATAGTGTCACTCTTAAATAGATGATTC--------TTCACAT---GATGCCAGCAGGGGGC-AGAGCAGGCTGTGAAAT------------------------TTTCCCTTTCTTCAAAG",
]
class AlignmentMappingTests(unittest.TestCase):
__test__ = False
def test_largescale(self):
f = StringIO(eight_species_mapping)
n, m = bx.seqmapping.alignment_mapping_from_file(f)
t = bx.seqmapping.DNA.translate_list(rows)
m.translate(t)
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