def test__exit(self):
"Test TemporaryFile __exit__() method"
tfile = TemporaryFile()
trace = """ Called tempfile.mkstemp('', 'tmp', None, False)
Called os.unlink('/fake/tmp/file')"""
tfile.__exit__(None, None, None)
assert_same_trace(self.tt, trace)
def test__enter(self):
"Test TemporaryFile __enter__() method"
expected = "/fake/tmp/file"
trace = """ Called tempfile.mkstemp('', 'tmp', None, False)"""
tfile = TemporaryFile()
f = tfile.__enter__()
self.assertEqual(f.name, expected)
self.assertEqual(f.handle, 42)
assert_same_trace(self.tt, trace)
def test__exit(self):
"Test TemporaryFile __exit__() method"
tfile = TemporaryFile()
trace = """ Called tempfile.mkstemp('', 'tmp', None, False)
Called os.close(42)
Called os.unlink('/fake/tmp/file')"""
tfile.__exit__(None, None, None)
assert_same_trace(self.tt, trace)
def test__enter(self):
"Test TemporaryFile __enter__() method"
expected = "/fake/tmp/file"
trace = """ Called tempfile.mkstemp('', 'tmp', None, False)"""
tfile = TemporaryFile()
f = tfile.__enter__()
self.assertEqual(f.name, expected)
self.assertEqual(f.handle, 42)
assert_same_trace(self.tt, trace)
def identify_lasso_motifs(
leader: str, core: str) -> Tuple[List[int], int, Dict[int, float]]:
"""Run FIMO to identify lasso peptide-specific motifs"""
motif_file = path.get_full_path(__file__, 'data', "lasso_motifs_meme.txt")
with TemporaryFile() as tempfile:
out_file = open(tempfile.name, "w")
out_file.write(">query\n%s%s" % (leader, core))
out_file.close()
fimo_output = subprocessing.run_fimo_simple(motif_file, tempfile.name)
fimo_motifs = [
int(line.partition("\t")[0]) for line in fimo_output.split("\n")
if "\t" in line and line.partition("\t")[0].isdigit()
]
fimo_scores = {
int(line.split("\t")[0]): float(line.split("\t")[5])
for line in fimo_output.split("\n")
if "\t" in line and line.partition("\t")[0].isdigit()
}
# Calculate score
motif_score = 0
if 2 in fimo_motifs:
motif_score += 4
elif fimo_motifs:
motif_score += 2
else:
motif_score += -1
return fimo_motifs, motif_score, fimo_scores
def _run_external_tool(self, analysisResource, SeqFeatureList):
"Generate tempfile containing the extracted Feature sequences and run tool defined in XML file"
# write fasta file for the features to tempfile
# FastA header is aSDomain_id
tempfile = ""
fastafile = []
for SeqFeature in SeqFeatureList:
fastaHeader = SeqFeature.qualifiers['asDomain_id'][0]
fastaSeq = SeqFeature.qualifiers['translation'][0]
# Never write empty fasta entries
if len(fastaSeq) == 0:
logging.warn("No translation for %s, skipping", fastaHeader)
continue
fastafile.append(">%s\n" % fastaHeader)
fastafile.append("%s\n" % fastaSeq)
querydata = "".join(fastafile)
# DEBUG
# print "\nTempfile for %s:\n" % analysisResource.attrib['name']
# print "".join(fastafile)
UseSTDIN = "False"
executeObj = analysisResource.find('./Execute')
if 'UseSTDIN' in executeObj.attrib:
UseSTDIN = executeObj.attrib['UseSTDIN']
if UseSTDIN == "False":
with TemporaryFile(prefix='antiSMASH_ASP') as tempfile:
out_file = open(tempfile.name, "w")
out_file.write(querydata)
out_file.close()
if len(fastafile) == 0:
logging.warn(
"ASP: No features found containing feature/tag/value %s / %s / %s",
analysisResource.find('./Prerequisite/primary_tag_type').text,
analysisResource.find('./Prerequisite/tag').text,
analysisResource.find('./Prerequisite/tag_value').text)
return []
results = []
if UseSTDIN == "True":
results = self._execute_tool(analysisResource,
stdin_data=querydata)
else:
results = self._execute_tool(analysisResource,
fileName=tempfile.name)
return results
def test__init(self):
"Test TemporaryFile object creation"
tfile = TemporaryFile()
self.assertEqual(tfile.handle, 42)
self.assertEqual(tfile.name, '/fake/tmp/file')