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import os
import sys
import pytest
from pyfaidx import Fasta
from tempfile import NamedTemporaryFile
from difflib import Differ
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_sequence_uppercase(remove_index):
"""Test that the sequence is always returned in
uppercase, even if it is in lowercase in the
reference genome.
"""
filename = "data/genes.fasta.lower"
reference_upper = Fasta(filename, sequence_always_upper=True)
reference_normal = Fasta(filename)
os.remove('data/genes.fasta.lower.fai')
assert reference_upper['gi|557361099|gb|KF435150.1|'][
1:100].seq == reference_normal['gi|557361099|gb|KF435150.1|'][
1:100].seq.upper()
def test_long_names(remove_index):
""" Test that deflines extracted using FastaRecord.long_name are
identical to deflines in the actual file.
"""
deflines = []
with open('data/genes.fasta') as fasta_file:
for line in fasta_file:
if line[0] == '>':
deflines.append(line[1:-1])
fasta = Fasta('data/genes.fasta')
long_names = []
for record in fasta:
long_names.append(record.long_name)
print(tuple(zip(deflines, long_names)))
assert deflines == long_names
def test_issue_62(remove_index):
""" Check for pathogenic FastaRecord.long_name behavior in mdshw5/pyfaidx#62 """
deflines = []
line_len = None
with open('data/genes.fasta', 'rb') as fasta_file:
with open('data/issue_62.fa', 'wb') as fasta_uniform_len:
for line in fasta_file:
if line.startswith(b'>'):
deflines.append(line[1:-1].decode('ascii'))
fasta_uniform_len.write(line)
elif line_len is None:
line_len = len(line)
fasta_uniform_len.write(line)
elif line_len > len(line):
fasta_uniform_len.write(line.rstrip() + b'N' *
(line_len - len(line)) + b'\n')
else:
fasta_uniform_len.write(line)
fasta = Fasta('data/issue_62.fa', as_raw=True)
long_names = []
for record in fasta:
long_names.append(record.long_name)
try:
os.remove('data/issue_62.fa')
os.remove('data/issue_62.fa.fai')
except EnvironmentError:
pass
sys.stdout.writelines(tuple(Differ().compare(deflines, long_names)))
assert deflines == long_names
def test_unpadded_length(remove_index):
filename = "data/padded.fasta"
with open(filename, 'w') as padded:
padded.write(">test_padded\n")
for n in range(10):
padded.write("N" * 80)
padded.write("\n")
padded.write("N" * 30)
padded.write("A" * 20)
padded.write("N" * 30)
padded.write("\n")
for n in range(10):
padded.write("N" * 80)
padded.write("\n")
fasta = Fasta(filename)
expect = 20
result = fasta["test_padded"].unpadded_len
print(expect, result)
assert expect == result
os.remove('data/padded.fasta')
os.remove('data/padded.fasta.fai')
def test_numpy_array(remove_index):
""" Test the __array_interface__ """
import numpy
filename = "data/genes.fasta.lower"
reference = Fasta(filename)
np_array = numpy.asarray(reference[0])
assert isinstance(np_array, numpy.ndarray)
@pytest.fixture
def remove_index_mutable():
with open('data/genes_mutable.fasta', 'wb') as mutable:
mutable.write(open('data/genes.fasta', 'rb').read())
mutable_fasta = Fasta('data/genes_mutable.fasta', mutable=True)
yield
try:
os.remove('data/genes.fasta.fai')
except EnvironmentError:
pass # some tests may delete this file
try:
os.remove('data/genes_mutable.fasta')
except EnvironmentError:
pass # some tests may delete this file
try:
os.remove('data/genes_mutable.fasta.fai')
except EnvironmentError:
pass # some tests may delete this file
def test_mutate_fasta_to_same(remove_index_mutable):
mutable = Fasta('data/genes_mutable.fasta', mutable=True)
fasta = Fasta('data/genes.fasta', mutable=False)
chunk = fasta['gi|557361099|gb|KF435150.1|'][0:100]
mutable['gi|557361099|gb|KF435150.1|'][0:100] = chunk.seq
assert str(fasta['gi|557361099|gb|KF435150.1|']) == str(
mutable['gi|557361099|gb|KF435150.1|'])
def test_mutate_fasta_to_N(remove_index_mutable):
mutable = Fasta('data/genes_mutable.fasta', mutable=True)
chunk = 100 * 'N'
mutable['gi|557361099|gb|KF435150.1|'][0:100] = chunk
assert mutable['gi|557361099|gb|KF435150.1|'][0:100].seq == chunk
def test_mutate_single_position(remove_index_mutable):
mutable = Fasta('data/genes_mutable.fasta', mutable=True)
chunk = 'N'
mutable['gi|557361099|gb|KF435150.1|'][0] = chunk
assert mutable['gi|557361099|gb|KF435150.1|'][0].seq == chunk
@pytest.mark.xfail(raises=TypeError)
def test_mutate_immutable_fasta(remove_index_mutable):
mutable = Fasta('data/genes_mutable.fasta', mutable=False)
chunk = 100 * 'N'
mutable['gi|557361099|gb|KF435150.1|'][0:100] = chunk
@pytest.mark.xfail(raises=IOError)
def test_mutate_too_long(remove_index_mutable):
mutable = Fasta('data/genes_mutable.fasta', mutable=True)
chunk = 101 * 'N'
mutable['gi|557361099|gb|KF435150.1|'][0:100] = chunk
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