def test_call_output_to_file_sorted(self):
"""GenericRepSetPicker.__call__ output to file sorts when requested
"""
fd, tmp_result_filepath = mkstemp(
prefix='GenericRepSetPickerTest.test_call_output_to_file_',
suffix='.txt')
close(fd)
app = GenericRepSetPicker(params=self.params)
obs = app(self.tmp_seq_filepath,
self.tmp_otu_filepath,
result_path=tmp_result_filepath,
sort_by='seq_id')
result_file = open(tmp_result_filepath)
result_file_str = result_file.read()
result_file.close()
# remove the result file before running the test, so in
# case it fails the temp file is still cleaned up
remove(tmp_result_filepath)
# compare data in result file to fake expected file
self.assertEqual(result_file_str, rep_seqs_result_file_sorted_exp)
# confirm that nothing is returned when result_path is specified
self.assertEqual(obs, None)
def test_call_log_file(self):
"""GenericRepSetPicker.__call__ writes log when expected
"""
tmp_log_filepath = get_tmp_filename(\
prefix='GenericRepSetPickerTest.test_call_output_to_file_l_',\
suffix='.txt')
tmp_result_filepath = get_tmp_filename(\
prefix='GenericRepSetPickerTest.test_call_output_to_file_r_',\
suffix='.txt')
app = GenericRepSetPicker(params=self.params)
obs = app(self.tmp_seq_filepath, self.tmp_otu_filepath,\
result_path=tmp_result_filepath,log_path=tmp_log_filepath)
log_file = open(tmp_log_filepath)
log_file_str = log_file.read()
log_file.close()
# remove the temp files before running the test, so in
# case it fails the temp file is still cleaned up
remove(tmp_log_filepath)
remove(tmp_result_filepath)
log_file_exp = ["GenericRepSetPicker parameters:",\
'Algorithm:first',\
"Application:None",\
'ChoiceF:first',
'ChoiceFRequiresSeqs:False',
"Result path: %s" % tmp_result_filepath,]
# compare data in log file to fake expected log file
for i, j in zip(log_file_str.splitlines(), log_file_exp):
if not i.startswith('ChoiceF:'): #can't test, different each time
self.assertEqual(i, j)
def test_call_wrapped_function(self):
"""GenericRepSetPicker.__call__ returns expected clusters default params"""
# adapted from test_app.test_cd_hit.test_cdhit_clusters_from_seqs
exp = {'0':'R27DLI_4812',\
'1':'U1PLI_7889',\
'2':'W3Cecum_4858',\
'3':'R27DLI_3243',\
}
app = GenericRepSetPicker(params={'Algorithm':'most_abundant',
'ChoiceF':make_most_abundant, 'ChoiceFRequiresSeqs':True})
obs = app(self.tmp_seq_filepath, self.tmp_otu_filepath)
self.assertEqual(obs, exp)
def test_call_default_params(self):
"""GenericRepSetPicker.__call__ returns expected clusters default params"""
# adapted from test_app.test_cd_hit.test_cdhit_clusters_from_seqs
exp = {'0':'R27DLI_4812',\
'1':'U1PLI_7889',\
'2':'W3Cecum_4858',\
'3':'R27DLI_3243',\
}
app = GenericRepSetPicker(params={'Algorithm':'first',
'ChoiceF':first_id})
obs = app(self.tmp_seq_filepath, self.tmp_otu_filepath)
self.assertEqual(obs, exp)
