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import pytest
from pyfaidx import Sequence, complement
seq = Sequence(name='gi|557361099|gb|KF435150.1|', seq='TTGAAGATTTTGCATGCAGCAGGTGCGCAAGGTGAAATGTTCACTGTTAAA',
start=100, end=150)
seq_invalid = Sequence(name='gi|557361099|gb|KF435150.1|', seq='TTGAAGATTTPGCATGCAGCAGGTGCGCAAGGTGAAATNTTCACTGTTAAA',
start=100, end=150)
comp_valid = 'TTGAAGATTTnGCATGCAGCAGGtgccaAGGTGAAATGTTNACTGTTAAA'
comp_invalid = 'TTGAAGATTTnGCATGCAGCPQGtgccaAGGTGAAATGTTNACTGTTAAA'
def test_negate():
assert str(-seq) == str(seq.complement[::-1])
def test_negate_metadata():
# Negate should affect __repr__ the same way as reverse and complement
seq_neg = -seq
assert seq_neg.__repr__() == seq.complement[::-1].__repr__()
def test_seq_invalid():
with pytest.raises(ValueError):
seq_invalid.complement()
def test_integer_index():
assert seq[1].seq == 'T'
def test_slice_index():
assert seq[0:10].seq == 'TTGAAGATTT'
def test_comp_invalid():
with pytest.raises(ValueError):
complement(comp_invalid)
def test_check_coordinates():
x = Sequence(name='gi|557361099|gb|KF435150.1|', seq='TTGAAGATTTTGCATGCAGCAGGTGCGCAAGGTGAAATGTTCACTGTTAAA',
start=100, end=110)
with pytest.raises(ValueError):
_ = x[:]
def test_comp_valid():
assert complement(comp_valid).startswith("AACTTCTAAAnCG")
assert complement(complement(comp_valid)) == comp_valid
def test_comp_empty():
assert complement('') == ''
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