def test_exit_on_unqual_blast_meta(self):
op = os.path.join(test_data_dir, 'two_fasta.fa')
with open(op, 'w') as f:
f.write(">a\nCAGCATGCTAGCTGATGCTA\n>b\nAGCTGATCGTAGCTGCTAGTCGTA\n")
self.args.blast_query = op
self.args.mode = 'meta'
with self.assertRaises(SystemExit):
lunch_with_args(self.args)
remove_files_with_try([op])
def test_exit_on_missing_rfam(self):
op = os.path.join(test_data_dir, 'config_rfam_here.txt')
with open(op, 'w') as f:
f.write("[TOOL_PATHS]\n[DATA]\nrfam_dir = test_func/test_data\n")
self.args.config_file = op
self.args.download_rfam = False
with self.assertRaises(SystemExit):
lunch_with_args(lunch_with_args(self.args))
remove_files_with_try([op])
def test_if_missing_db_entry_is_reported(self):
aa = Pseudoargs(blast_query=os.path.join(fwd, test_dir,
'RF00005_query.fasta'),
blast_in=os.path.join(fwd, test_dir,
'RF00005.blastout'),
blast_db=os.path.join(fwd, test_dir, 'blastdb',
'RF00001-art.blastdb'),
b_type='plain',
prediction_method=['rnafold'],
blast_regexp=r'(?<=\|)[A-Z0-9]*\.?\d*$',
enable_overwrite=True,
mode='locarna')
with self.assertRaises(SystemExit):
lunch_with_args(aa)
def test_simple_extension(self):
self.args.mode = 'simple'
out = lunch_with_args(self.args)
self.assertEqual(1, 1)
# test_output
for i in range(len(out)):
out[0].to_csv(self.csv)
j_obj = json.dumps(blastsearchrecompute2dict(out[0]), indent=2)
with open(self.json, 'w') as ff:
ff.write(j_obj)
with open(self.html, 'wb') as h:
h.write(write_html_output(out[0]))
out[0].to_pandas_dump(self.pandas_dump)
out[0].write_results_fasta(self.fasta)
out[0].write_results_structures(self.fasta_structures)
t = tab_output_equal(
csvfile=self.csv,
jsonfile=self.json,
pdfile=self.pandas_dump,
fastafile=self.fasta,
fastastructures=self.fasta_structures,
ref_seqs_file=os.path.join(fwd, test_data_dir, 'simple.json')
)
self.assertEqual(t, True)
def test_logs_and_correct_seqs_joined(self):
with self.assertLogs('rboAnalyzer', level='WARNING') as l:
args = self.args
args.mode = 'meta'
out = lunch_with_args(args)
for o in l.output:
self.assertIn('Sequence cannot be extended sufficiently', o.split(':')[-1])
recs = out[0].res_2_record_list()
with open(source_fasta, 'r') as fh:
for seq in SeqIO.parse(fh, format='fasta'):
ss = re.sub('[a-z]', '', str(seq.seq))
if 'rc' == seq.description.split()[-1]:
strand = -1
else:
strand = 1
for rec in recs:
if seq.id in rec.id:
if strand == 1:
rec_s = str(rec.seq)
else:
rec_s = str(rec.seq.reverse_complement())
self.assertEqual(ss, rec_s)
def test_wrong_blast_meta(self):
op = os.path.join(test_data_dir, 'wrong_blast.txt')
with open(self.args.blast_in, 'r') as f, open(op, 'w') as o:
blast_raw = f.read()
blast_altered = blast_raw.replace(
'CGGAGGGGGAACA-CCCGGTCCCATTCCGAACCC',
'CGGAGGGGGAACA-CCCGGTKYLATTCCGAACCC')
if blast_raw == blast_altered:
assert False
o.write(blast_altered)
self.args.blast_in = op
self.args.mode = 'meta'
with self.assertRaises(SystemExit):
lunch_with_args(self.args)
remove_files_with_try([op] + glob.glob(op + '.r-*'))
def test_meta_with_one_seq_fail(self):
op = os.path.join(test_data_dir, 'wrong_blast.txt')
with open(self.args.blast_in, 'r') as f, open(op, 'w') as o:
blast_raw = f.read()
blast_altered = re.sub(
'AGCGGAGGGGAAACCGCCCGGTCCCATTCCGAACCCGGAAGC',
'AGCGGAGGGGAAACCGCAGTCGATGTTTCCGAACCCACGTCG', blast_raw, 1)
if blast_raw == blast_altered:
assert False
o.write(blast_altered)
self.args.blast_in = op
self.args.mode = 'meta'
self.args.threads = 4
out = lunch_with_args(self.args)
self.assertEqual(len(out[0].hits_failed), 0)
remove_files_with_try([op] + glob.glob(op + '.r-*'))
def test_continuation2(self):
with open(blast_output, 'r') as f, open(self.test_backup_file,
'w') as ff:
data = blastsearchrecomputefromdict(json.load(f))
data.args.blast_in = blast_in
data.args.json = None
data.args.html = test_output_file
data.args.sha1 = self.sha1
data.args.prediction_method += ['centroid']
new_structures = {'rnafold': []}
for h in data.hits:
n = copy(h.extension)
n.letter_annotations['ss0'] = n.letter_annotations['rnafold']
del n.letter_annotations['rnafold']
new_structures['rnafold'].append(n)
json.dump([blastsearchrecompute2dict(data)], ff, indent=2)
out = lunch_with_args(self.args)
self.assertEqual(1, 1)
# test_output
for i in range(len(out)):
out[0].to_csv(self.csv)
j_obj = json.dumps(blastsearchrecompute2dict(out[0]), indent=2)
with open(self.json, 'w') as ff:
ff.write(j_obj)
out[0].write_results_fasta(self.fasta)
out[0].write_results_structures(self.fasta_structures)
t = tab_output_equal(csvfile=self.csv,
jsonfile=self.json,
fastafile=self.fasta,
fastastructures=self.fasta_structures,
ref_seqs_file=os.path.join(
fwd, test_data_dir, 'simple.json'))
self.assertEqual(t, True)
def test_meta_complete_fail(self, callMock):
self.args.mode = 'locarna'
with self.assertRaises(SystemExit):
out = lunch_with_args(self.args)