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"""
Unit tests for alignment module
"""
from cStringIO import StringIO
import os
import os.path
import unittest
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
import refpkg_align
class ParseStockholmConsensus(unittest.TestCase):
def setUp(self):
self.value = """
#=GC RF xxx.xx
#=GC RF xx.xxx
#=GC RF xxx.x.
#=GF TT IGNORED
"""
self.expected = [True, True, True, False, True, True,
True, True, False, True, True, True,
True, True, True, False, True, False]
self.handle = StringIO(self.value)
def _get_result(self):
return refpkg_align._parse_stockholm_consensus(self.handle).mask
def test_length(self):
result = self._get_result()
self.assertEqual(len(self.expected), len(result))
def test_value(self):
self.assertEqual(self.expected, self._get_result())
def test_no_other_chars(self):
handle = StringIO('#=GC RF xxxCx.x.\n')
self.assertRaises(ValueError, refpkg_align._parse_stockholm_consensus,
handle)
class AlignmentMaskTestCase(unittest.TestCase):
def setUp(self):
self.sequences = [
SeqRecord(Seq('ACGTACGT')),
SeqRecord(Seq('AAAAAAAT')),
SeqRecord(Seq('ACGTAAAA')),
]
def test_invalid_seq_length(self):
mask = [True, True, False, True]
instance = refpkg_align.AlignmentMask(mask)
self.assertRaises(ValueError,
instance.mask_records(self.sequences).next)
def test_mask(self):
mask = [True, False, True, True, False, False, False, True]
instance = refpkg_align.AlignmentMask(mask)
actual = list(instance.mask_records(self.sequences))
# equality isn't defined for SeqRecord, so this is basic
actual = [str(r.seq) for r in actual]
expected = ['AGTT', 'AAAT', 'AGTA']
self.assertEqual(expected, actual)
def test_from_csv_file(self):
value = """
1, 2,5,
8, 10,
11
"""
handle = StringIO(value)
expected = [False, True, True, False, False, True,
False, False, True, False, True, True, False]
actual = refpkg_align.AlignmentMask.from_csv_file(handle, 13)
self.assertEqual(expected, actual.mask)
def test_len(self):
mask = [True, True, False, True]
instance = refpkg_align.AlignmentMask(mask)
expected = 4
self.assertEqual(expected, len(instance))
def test_unmasked_count(self):
mask = [True, True, False, True, False]
instance = refpkg_align.AlignmentMask(mask)
expected = 3
self.assertEqual(expected, instance.unmasked_count)
class MockSubprocess(object):
"""
Mock of the subprocess module to support Check Call
"""
def __init__(self):
self.commands = []
pass
def check_call(self, cmd, *args, **kwargs):
self.commands.append(cmd)
class MockRefpkg(object):
def __init__(self):
self.contents = {'files': {}}
def resource_path(self, path):
return 'resource-' + path
class SubprocessMixIn(object):
"""
Converts the subprocess.check_call function to a mock for the test
"""
def setUp(self):
self._old_subproc = refpkg_align.subprocess
refpkg_align.subprocess = MockSubprocess()
def tearDown(self):
refpkg_align.subprocess = self._old_subproc
@property
def latest_command(self):
return refpkg_align.subprocess.commands[-1]
class TempFileTestCase(unittest.TestCase):
def test_close(self):
with refpkg_align._temp_file() as tf:
self.assertFalse(tf.closed)
tf.close()
self.assertTrue(os.path.isfile(tf.name))
self.assertFalse(os.path.exists(tf.name))
def test_remove_ok(self):
"""Test that the file can be removed without error"""
with refpkg_align._temp_file() as tf:
tf.close()
os.unlink(tf.name)
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