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import os
import pytest
from pyfaidx import Fasta, FetchError
path = os.path.dirname(__file__)
os.chdir(path)
try:
from Bio import SeqIO
bio = True
except ImportError:
bio = False
@pytest.fixture
def remove_index():
yield
try:
os.remove('data/genes.fasta.fai')
except EnvironmentError:
pass # some tests may delete this file
@pytest.mark.skipif(not bio, reason="Biopython is not installed.")
def test_fetch_whole_entry(remove_index):
fasta = Fasta('data/genes.fasta')
with open('data/genes.fasta', "r") as fh:
seqio = SeqIO.to_dict(SeqIO.parse(fh, "fasta"))
assert str(fasta['gi|557361099|gb|KF435150.1|']) == str(seqio['gi|557361099|gb|KF435150.1|'].seq)
assert fasta['gi|557361099|gb|KF435150.1|'].name == str(seqio['gi|557361099|gb|KF435150.1|'].name)
@pytest.mark.skipif(not bio, reason="Biopython is not installed.")
def test_slice_whole_entry(remove_index):
fasta = Fasta('data/genes.fasta')
with open('data/genes.fasta', "r") as fh:
seqio = SeqIO.to_dict(SeqIO.parse(fh, "fasta"))
assert str(fasta['gi|557361099|gb|KF435150.1|'][::3]) == str(seqio['gi|557361099|gb|KF435150.1|'].seq[::3])
@pytest.mark.skipif(not bio, reason="Biopython is not installed.")
def test_revcomp_whole_entry(remove_index):
fasta = Fasta('data/genes.fasta')
with open('data/genes.fasta', "r") as fh:
seqio = SeqIO.to_dict(SeqIO.parse(fh, "fasta"))
assert str(fasta['gi|557361099|gb|KF435150.1|'][:].reverse.complement) == str(seqio['gi|557361099|gb|KF435150.1|'].reverse_complement().seq)
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