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import os
import pytest
from pyfaidx import Fasta
from itertools import chain
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_fetch_whole_fasta(remove_index):
expect = [line.rstrip('\n') for line in open('data/genes.fasta') if line[0] != '>']
result = list(chain(*([line for line in record] for record in Fasta('data/genes.fasta', as_raw=True))))
assert expect == result
def test_line_len(remove_index):
fasta = Fasta('data/genes.fasta')
for record in fasta:
assert len(next(iter(record))) == fasta.faidx.index[record.name].lenc
def test_reverse_iter(remove_index):
expect = list(chain(*([line[::-1] for line in record][::-1] for record in Fasta('data/genes.fasta', as_raw=True))))
result = list(chain(*([line for line in reversed(record)] for record in Fasta('data/genes.fasta', as_raw=True))))
for a, b in zip(expect, result):
print(a, b)
assert expect == result
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