def setUp(self):
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 = 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, fasta_structures = tempfile.mkstemp(prefix='rba_', suffix='_t6')
os.close(ff)
self.fasta_structures = fasta_structures
self.args = Pseudoargs(
blast_query,
blast_in,
blast_db,
b_type='plain',
prediction_method=['rnafold'],
blast_regexp='(?<=\|)[A-Z0-9]*\.?\d*$',
enable_overwrite=True,
html=self.html,
)
def setUp(self):
f = open(ref_json_file, 'r')
mydata = json.load(f)
f.close()
bb = convert_classes.blastsearchrecomputefromdict(mydata)
self.data = bb
ff, csv = tempfile.mkstemp(prefix='rba_', suffix='_t1')
os.close(ff)
self.csv = csv
ff, html = tempfile.mkstemp(prefix='rba_', suffix='_t2')
os.close(ff)
self.html = blast_query + 'test_html.html'
ff, pandas_dump = tempfile.mkstemp(prefix='rba_', suffix='_t3')
os.close(ff)
self.pandas_dump = pandas_dump
ff, json_file = tempfile.mkstemp(prefix='rba_', suffix='_t4')
os.close(ff)
self.json = json_file
ff, fasta = tempfile.mkstemp(prefix='rba_', suffix='_t5')
os.close(ff)
self.fasta = fasta
ff, allHits_fasta = tempfile.mkstemp(prefix='rba_', suffix='_t6')
with os.fdopen(ff, 'w') as f:
SeqIO.write([i.extension for i in self.data.hits], f, 'fasta')
self.fasta_structures = allHits_fasta
self.args = Pseudoargs(
blast_query,
blast_in,
blast_db,
b_type='plain',
prediction_method=['rnafold'],
blast_regexp=r'(?<=\|)[A-Z0-9]*\.?\d*$',
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 setUp(self):
self.args = Pseudoargs(
blast_query,
blast_in,
blast_db,
b_type='plain',
prediction_method=['rnafold'],
blast_regexp=r'(?<=\|)[A-Z0-9]*\.?\d*$',
enable_overwrite=True,
html=test_output_file,
)
with open(source_fasta, 'r') as fh:
self.seqs = [s for s in SeqIO.parse(fh, format='fasta')]
def test_if_missing_db_entry_is_reported(self):
aa = Pseudoargs(blast_query=os.path.join(fwd, test_dir,
'RF00005_query.fasta'),
blast_in=os.path.join(fwd, test_dir,
'RF00005.blastout'),
blast_db=os.path.join(fwd, test_dir, 'blastdb',
'RF00001-art.blastdb'),
b_type='plain',
prediction_method=['rnafold'],
blast_regexp=r'(?<=\|)[A-Z0-9]*\.?\d*$',
enable_overwrite=True,
mode='locarna')
with self.assertRaises(SystemExit):
lunch_with_args(aa)
def setUp(self):
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,
mode='simple',
html=test_output_file,
)
ff, csv = tempfile.mkstemp(prefix='rba_', suffix='_t1')
os.close(ff)
self.csv = csv
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, fasta_structures = tempfile.mkstemp(prefix='rba_', suffix='_t6')
os.close(ff)
self.fasta_structures = fasta_structures
tp = tools_paths(
os.path.join(os.path.dirname(os.path.dirname(__file__)),
'rna_blast_analyze', 'BR_core', 'config.txt'))
CONFIG.override(tp)
rfam = RfamInfo()
self.sha1 = compute_args_hash(
self.args, os.path.join(CONFIG.rfam_dir, rfam.gzname))
self.test_backup_file = blast_in + '.r-' + self.sha1[:10]