def test_call_ref_only(self):
"""ReferenceRepSetPicker.__call__ functions with no non-refseqs"""
fd, tmp_otu_filepath = mkstemp(prefix='ReferenceRepSetPickerTest_',
suffix='.otu')
close(fd)
otu_file = open(tmp_otu_filepath, 'w')
otu_file.write(otus_all_ref)
otu_file.close()
self.files_to_remove.append(tmp_otu_filepath)
exp = {
'ref1': ('ref1', 'GGGGGGGAAAAAAAAAAAAA'),
'ref0': ('ref0', 'CCCAAAAAAATTTTTT')
}
# passing only reference (not input seqs)
app = ReferenceRepSetPicker(params={
'Algorithm': 'first',
'ChoiceF': first_id
})
obs = app(None, tmp_otu_filepath, self.ref_seq_filepath)
self.assertEqual(obs, exp)
# passing reference and input seqs
app = ReferenceRepSetPicker(params={
'Algorithm': 'first',
'ChoiceF': first_id
})
obs = app(self.tmp_seq_filepath, tmp_otu_filepath,
self.ref_seq_filepath)
self.assertEqual(obs, exp)
def test_call_invalid_id(self):
"""ReferenceRepSetPicker.__call__ expected clusters default params"""
app = ReferenceRepSetPicker(params={
'Algorithm': 'first',
'ChoiceF': first_id
})
fd, tmp_otu_filepath = mkstemp(prefix='ReferenceRepSetPickerTest_',
suffix='.otu')
close(fd)
otu_file = open(tmp_otu_filepath, 'w')
# replace a valid sequence identifier with an invalid
# sequence identifier (i.e., one that we don't have a sequence for)
otu_file.write(otus_w_ref.replace('R27DLI_4812', 'bad_seq_identifier'))
otu_file.close()
self.files_to_remove.append(tmp_otu_filepath)
# returning in dict
self.assertRaises(KeyError, app, self.tmp_seq_filepath,
tmp_otu_filepath, self.ref_seq_filepath)
# writing to file
self.assertRaises(KeyError,
app,
self.tmp_seq_filepath,
tmp_otu_filepath,
self.ref_seq_filepath,
result_path=self.result_filepath)
def test_non_ref_otus(self):
"""ReferenceRepSetPicker.__call__ same result as Generic when no ref otus
"""
exp = {
'0': ('R27DLI_4812', 'CTGGGCCGTATCTC'),
'1': ('U1PLI_7889', 'TTGGACCGTG'),
'2': ('W3Cecum_4858', 'TTGGGCCGTGTCTCAGT'),
'3': ('R27DLI_3243', 'CTGGACCGTGTCT')
}
fd, tmp_otu_filepath = mkstemp(prefix='ReferenceRepSetPickerTest_',
suffix='.otu')
close(fd)
otu_file = open(tmp_otu_filepath, 'w')
otu_file.write(otus)
otu_file.close()
self.files_to_remove.append(tmp_otu_filepath)
app = ReferenceRepSetPicker(params={
'Algorithm': 'first',
'ChoiceF': first_id
})
obs = app(self.tmp_seq_filepath, tmp_otu_filepath,
self.ref_seq_filepath)
self.assertEqual(obs, exp)
def test_call_write_to_file(self):
"""ReferenceRepSetPicker.__call__ otu map correctly written to file"""
app = ReferenceRepSetPicker(params={'Algorithm':'first',
'ChoiceF':first_id})
app(self.tmp_seq_filepath,
self.tmp_otu_filepath,
self.ref_seq_filepath,
result_path=self.result_filepath)
exp = rep_seqs_reference_result_file_exp
self.assertEqual(LoadSeqs(self.result_filepath,aligned=False),
LoadSeqs(data=exp,aligned=False))
def test_call_default_params(self):
"""ReferenceRepSetPicker.__call__ expected clusters default params"""
exp = {'0':('R27DLI_4812','CTGGGCCGTATCTC'),\
'ref1':('ref1','GGGGGGGAAAAAAAAAAAAA'),\
'2':('W3Cecum_4858','TTGGGCCGTGTCTCAGT'),\
'ref0':('ref0','CCCAAAAAAATTTTTT'),\
}
app = ReferenceRepSetPicker(params={'Algorithm':'first',
'ChoiceF':first_id})
obs = app(self.tmp_seq_filepath,
self.tmp_otu_filepath,
self.ref_seq_filepath)
self.assertEqual(obs, exp)
def test_call_write_to_file(self):
"""ReferenceRepSetPicker.__call__ otu map correctly written to file"""
app = ReferenceRepSetPicker(params={
'Algorithm': 'first',
'ChoiceF': first_id
})
app(self.tmp_seq_filepath,
self.tmp_otu_filepath,
self.ref_seq_filepath,
result_path=self.result_filepath)
with open(self.result_filepath) as f:
actual = SequenceCollection.from_fasta_records(parse_fasta(f), DNA)
expected = SequenceCollection.from_fasta_records(
parse_fasta(rep_seqs_reference_result_file_exp.split('\n')), DNA)
# we don't care about order in the results
self.assertEqual(set(actual), set(expected))
def test_call_alt_non_ref_picker(self):
"""ReferenceRepSetPicker.__call__ handles alt non-ref picking method"""
exp = {'0':('U1PLI_9526','CTGGGCCGTATCTCAGTCCCAATGTGGCCGGTCG'
'GTCTCTCAACCCGGCTACCCATCGCGGGCTAGGTGGGCCGTT'
'ACCCCGCCTACTACCTAATGGGCCGCGACCCCATCCCTTGCCGTCTGGGC'
'TTTCCCGGGCCCCCCAGGAGGGGGGCGAGGAGTATCCGGTATTAGCCTCGGTT'
'TCCCAAGGTTGTCCCGGAGCAAGGGGCAGGTTGGTCACGTGTTACTCACCCGT'
'TCGCCACTTCATGTCCGCCCGAGGGCGGTTTCATCG'),\
'ref1':('ref1','GGGGGGGAAAAAAAAAAAAA'),\
'2':('W3Cecum_4858','TTGGGCCGTGTCTCAGT'),\
'ref0':('ref0','CCCAAAAAAATTTTTT'),\
}
app = ReferenceRepSetPicker(params={'Algorithm':'longest',
'ChoiceF':longest_id})
obs = app(self.tmp_seq_filepath,
self.tmp_otu_filepath,
self.ref_seq_filepath)
self.assertEqual(obs, exp)