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import os
import pytest
from pyfaidx import Faidx, Fasta, FetchError
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_buffer_false(remove_index):
fasta = Fasta('data/genes.fasta', strict_bounds=True)
expect = 'TTGAAGATTTTGCATGCAGCAGGTGCGCAAGGTGAAATGTTCACTGTTAAA'.lower()
result = fasta['gi|557361099|gb|KF435150.1|'][100-1:150].seq.lower()
assert result == expect
def test_buffer_true(remove_index):
fasta = Fasta('data/genes.fasta', read_ahead=300, strict_bounds=True)
expect = 'TTGAAGATTTTGCATGCAGCAGGTGCGCAAGGTGAAATGTTCACTGTTAAA'.lower()
result = fasta['gi|557361099|gb|KF435150.1|'][100-1:150].seq.lower()
assert result == expect
def test_buffer_exceed(remove_index):
fasta = Fasta('data/genes.fasta', read_ahead=300, strict_bounds=True)
expect = 'atgacatcattttccacctctgctcagtgttcaacatctgacagtgcttgcaggatctctcctggacaaatcaatcaggtacgaccaaaactgccgcttttgaagattttgcatgcagcaggtgcgcaaggtgaaatgttcactgttaaagaggtcatgcactatttaggtcagtacataatggtgaagcaactttatgatcagcaggagcagcatatggtatattgtggtggagatcttttgggagaactactgggacgtcagagcttctccgtgaaagacccaagccctctctatgatatgctaagaaagaatcttgtcactttagccactgctactacagcaaagtgcagaggaaagttccacttccagaaaaagaactacagaagacgatatcccc'
result = fasta['gi|557361099|gb|KF435150.1|'][0:400].seq.lower()
assert result == expect
def test_bounds_error(remove_index):
fasta = Fasta('data/genes.fasta', read_ahead=300, strict_bounds=True)
with pytest.raises(FetchError):
result = fasta['gi|557361099|gb|KF435150.1|'][100-1:15000].seq.lower()
def test_buffer_value(remove_index):
with pytest.raises(ValueError):
Fasta('data/genes.fasta', read_ahead=0.5)
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