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"""
Tests for `bx.seq.nib`.
"""
import unittest
from bx.seq import nib
test_nib = "test_data/seq_tests/test.nib"
# Same sequence data as stored in test.nib
valid_seq = (
"TGGAGGCATTTGTGATTCAATAGATGCAGAAAGAAACCTTCCTAGAGCTG"
"GCGTTCTCTAACTAAAAGTGGAAAGTTCTGAGGAATGAGGACTGTTATAA"
"ATCCCACCCCACACCGCACCTTCTCCAGGGAAGTTTCATGGCCGTGAAGA"
"GGACAGAAAGTGAGAACCAAGATggaactgaataaacaagcttcacactg"
"ttagtttccccatatgcttaccttcccacagatgccaaccttggaggcct"
"aagaggcctagaatattatcctttgtctgatcatttctctacaaatttat"
"tgttctttgttaagatgctacataagcccaaattctaaccacccctttga"
"gttacccatcatcaagtttctcccatgtg"
)
valid_seq_len = len(valid_seq)
class NIBTestCase(unittest.TestCase):
def test_get(self):
nibfile = nib.NibFile(open(test_nib, "rb"))
# Try all combinations of even / odd boundaries
check_get(nibfile, 0, 10)
check_get(nibfile, 1, 10)
check_get(nibfile, 0, 11)
check_get(nibfile, 1, 11)
# Test near end of file also
check_get(nibfile, valid_seq_len - 10, 10)
check_get(nibfile, valid_seq_len - 11, 11)
# Test really short gets
check_get(nibfile, 0, 0)
check_get(nibfile, 1, 0)
check_get(nibfile, 0, 1)
check_get(nibfile, 1, 1)
# Test negative length
self.assertRaises(AssertionError, nibfile.get, 20, -1)
def check_get(nibfile, start, len):
assert nibfile.get(start, len) == valid_seq[start : start + len]
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