def test_compilebwaoptions(self):
''' Make sure options supplied to constructor make it through to running '''
bwa_path = self.mkbwa('$@')
ops = {
'R': None,
'E': '',
't': 3,
'a': 5,
'f': True,
'j': 1,
'bwa_path': bwa_path,
'command': 'cmd'
}
bwa = BWASubTest(**ops)
del ops['bwa_path']
del ops['command']
bwa.run('output')
with open('output') as fh:
result_output = fh.read().strip()
print "Expect: {0}".format(ops)
print "Result: {0}".format(result_output)
for op, val in ops.items():
uval = ''
val = str(val)
if val.lower() not in ('true', 'false'):
uval = ' ' + val
if val.lower() not in ('', 'none'):
opval = '-{0}{1}'.format(op, uval)
assert opval in result_output, '{0} not in {1}'.format(
opval, result_output)
else:
assert op not in result_output, '{0} should not be in {1}'.format(
op, result_output)
def test_run_outputfile(self):
''' Test that output file can be specified and is used '''
output_file = 'output.sai'
output_text = "test output"
path = self.mkbwa(output_text)
bwa = BWASubTest(bwa_path=path, command='')
# Should write output_text to output_file
bwa.run(output_file)
eq_(output_text, open(output_file).read().rstrip('\n'))
def test_validfasta(self):
ref = 'ref.fa'
# Make copy in tempdir
shutil.copy(REF_PATH, 'ref.fa')
bwa = BWAIndex(ref, bwa_path=BWA_PATH)
eq_(0, bwa.run())
indexes = glob.glob(ref + '.*')
print indexes
eq_(len(indexes), 5, "Did not create all index files")
def test_nooutputfile(self):
''' Ensure no output file is created '''
os.mkdir('dir1')
os.chdir('dir1')
ref = 'ref.fa'
# Make copy in tempdir
shutil.copy(REF_PATH, 'ref.fa')
bwa = BWAIndex(ref, bwa_path=BWA_PATH)
eq_(0, bwa.run())
assert not os.path.exists('bwa.sai')
os.chdir('..')
