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# Copyright (c) 2008-2015, Michigan State University
"""
Test the use of `screed.open` as a ContextManager.
"""
from . import screed_tst_utils as utils
import screed
import screed.openscreed
def test_empty_open():
filename = utils.get_test_data('empty.fa')
with screed.open(filename) as f:
assert len(list(f)) == 0
def test_simple_open():
filename = utils.get_test_data('test.fa')
n = -1
with screed.open(filename, parse_description=True) as f:
for n, record in enumerate(f):
assert record.name == 'ENSMICT00000012722'
break
assert n == 0, n
def test_simple_close():
filename = utils.get_test_data('test.fa')
n = -1
f = screed.open(filename, parse_description=True)
for n, record in enumerate(f):
assert record.name == 'ENSMICT00000012722'
break
assert n == 0, n
f.close()
def test_simple_open_fq():
filename = utils.get_test_data('test.fastq')
n = -1
with screed.open(filename) as f:
for n, record in enumerate(f):
assert record.name == 'HWI-EAS_4_PE-FC20GCB:2:1:492:573/2'
break
assert n == 0
def test_gz_open():
filename1 = utils.get_test_data('test.fa')
filename2 = utils.get_test_data('test.fa.gz')
with screed.open(filename1) as f1, screed.open(filename2) as f2:
for n, (r1, r2) in enumerate(zip(f1, f2)):
assert r1.name == r2.name
assert n > 0
def test_bz2_open():
filename1 = utils.get_test_data('test.fa')
filename2 = utils.get_test_data('test.fa.bz2')
with screed.open(filename1) as f1, screed.open(filename2) as f2:
for n, (r1, r2) in enumerate(zip(f1, f2)):
assert r1.name == r2.name
assert n > 0
def test_gz_open_fastq():
filename1 = utils.get_test_data('test.fastq')
filename2 = utils.get_test_data('test.fastq.gz')
with screed.open(filename1) as f1, screed.open(filename2) as f2:
for n, (r1, r2) in enumerate(zip(f1, f2)):
assert r1.name == r2.name
assert n > 0
def test_unknown_fileformat():
try:
with screed.open(__file__):
pass
except ValueError as err:
assert "unknown file format" in str(err)
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