def tearDown(self):
files = glob.glob(
os.path.join(fwd, test_data_dir, 'RF00001_short.blastout') +
'.r-*')
remove_files_with_try([
self.csv, self.html, self.json, self.fasta, self.fasta_structures
] + files)
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 setUp(self):
f = open(ref_json_file, 'r')
mydata = json.load(f)
f.close()
bb = convert_classes.blastsearchrecomputefromdict(mydata)
self.data = bb
ff, csv = tempfile.mkstemp(prefix='rba_', suffix='_t1')
os.close(ff)
self.csv = csv
ff, html = tempfile.mkstemp(prefix='rba_', suffix='_t2')
os.close(ff)
self.html = blast_query + 'test_html.html'
ff, pandas_dump = tempfile.mkstemp(prefix='rba_', suffix='_t3')
os.close(ff)
self.pandas_dump = pandas_dump
ff, json_file = tempfile.mkstemp(prefix='rba_', suffix='_t4')
os.close(ff)
self.json = json_file
ff, fasta = tempfile.mkstemp(prefix='rba_', suffix='_t5')
os.close(ff)
self.fasta = fasta
ff, allHits_fasta = tempfile.mkstemp(prefix='rba_', suffix='_t6')
with os.fdopen(ff, 'w') as f:
SeqIO.write([i.extension for i in self.data.hits], f, 'fasta')
self.fasta_structures = allHits_fasta
self.args = Pseudoargs(
blast_query,
blast_in,
blast_db,
b_type='plain',
prediction_method=['rnafold'],
blast_regexp=r'(?<=\|)[A-Z0-9]*\.?\d*$',
enable_overwrite=True,
html=self.html,
)
self.func_args = {
'query': self.data.query,
'seqs2predict_fasta': allHits_fasta,
'pred_method_params': {},
'all_hits_list': [i.extension for i in self.data.hits],
'seqs2predict_list': [i.extension for i in self.data.hits],
'use_cm_file': 'abc',
}
remove_files_with_try([blast_in + '.tmp_rboAnalyzer'])
def test_wrong_blast_meta(self):
op = os.path.join(test_data_dir, 'wrong_blast.txt')
with open(self.args.blast_in, 'r') as f, open(op, 'w') as o:
blast_raw = f.read()
blast_altered = blast_raw.replace(
'CGGAGGGGGAACA-CCCGGTCCCATTCCGAACCC',
'CGGAGGGGGAACA-CCCGGTKYLATTCCGAACCC')
if blast_raw == blast_altered:
assert False
o.write(blast_altered)
self.args.blast_in = op
self.args.mode = 'meta'
with self.assertRaises(SystemExit):
lunch_with_args(self.args)
remove_files_with_try([op] + glob.glob(op + '.r-*'))
def run_with_fasta(fasta_example, func, expect):
fd, fdpath = tempfile.mkstemp()
with os.fdopen(fd, 'w') as f:
f.write(fasta_example)
a = base_script + [
'--blast_in', blast_in, '--blast_query', fdpath, '--blast_db',
blast_db, '--mode', 'simple', '--blast_regexp',
r'"(?<=\|)[A-Z0-9]*\.?\d*$"', '--b_type', 'plain',
'--prediction_method', 'rnafold', '--enable_overwrite', '--html',
test_html_file
]
bb = subprocess.call(' '.join(a), cwd=root, shell=True)
func(bb, expect)
remove_files_with_try([
fdpath,
test_html_file,
], '')
print(test_html_file)
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_locarna_partial_fail(self):
bb = self.data
hit = bb.hits.pop(1)
hit.extension = None
bb.hits_failed.append(hit)
fda, all_hits_fasta = tempfile.mkstemp(prefix='rba_', suffix='_22')
os.close(fda)
bb.write_results_fasta(all_hits_fasta)
ih_model, analyzed_hits = find_and_extract_cm_model(bb.args, bb)
# this part predicts homology - it is not truly part of repredict
homology_prediction, homol_seqs, cm_file_rfam_user = infer_homology(
analyzed_hits=bb,
args=bb.args,
cm_model_file=ih_model,
multi_query=False,
iteration=0)
self.assertIsNone(cm_file_rfam_user)
self.assertEqual(len(analyzed_hits.hits), len(homology_prediction))
remove_files_with_try([ih_model, all_hits_fasta])
def tearDown(self):
remove_files_with_try([
self.csv, self.html, self.json, self.fasta, self.fasta_structures
], '')
def tearDown(self):
files = glob.glob(blast_in + '.r-*')
remove_files_with_try([
self.csv, self.html, self.json, self.fasta, self.fasta_structures
] + files, '')