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import os
import pytest
from pyfaidx import Faidx, Fasta
path = os.path.dirname(__file__)
os.chdir(path)
@pytest.fixture
def remove_index():
yield
try:
os.remove('data/genes.fasta.fai')
except EnvironmentError:
pass # some tests may delete this file
def test_as_raw_false(remove_index):
fasta = Fasta('data/genes.fasta')
expect = 'TTGAAGATTTTGCATGCAGCAGGTGCGCAAGGTGAAATGTTCACTGTTAAA'.lower()
result = fasta['gi|557361099|gb|KF435150.1|'][100-1:150].seq.lower()
assert result == expect
def test_as_raw_true(remove_index):
fasta = Fasta('data/genes.fasta', as_raw=True)
expect = 'TTGAAGATTTTGCATGCAGCAGGTGCGCAAGGTGAAATGTTCACTGTTAAA'.lower()
result = fasta['gi|557361099|gb|KF435150.1|'][100-1:150].lower()
assert result == expect
def test_as_raw_false_error(remove_index):
fasta = Fasta('data/genes.fasta')
with pytest.raises(AttributeError):
result = fasta['gi|557361099|gb|KF435150.1|'][100-1:150].lower()
def test_as_raw_true_error(remove_index):
fasta = Fasta('data/genes.fasta', as_raw=True)
with pytest.raises(AttributeError):
result = fasta['gi|557361099|gb|KF435150.1|'][100-1:150].seq.lower()
def test_as_raw_type_when_blen_lt_0(remove_index):
fasta = Fasta('data/genes.fasta', as_raw=True)
expect = ''
result = fasta.faidx.fetch('gi|557361099|gb|KF435150.1|', 10, 0)
assert result == expect
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