def getSeqFromFile(seq_fp):
_, ext = _ospath.splitext(seq_fp)
if ext in ('.gb', '.gbk', '.genbank'):
rec = gb_reader.parse(seq_fp)
return str(rec['seq'])
elif ext in ('.fa', '.fasta'):
# Just returns the first sequence in the file for now --
# this may be undesirable as a general behavior
return fasta.parseFasta(seq_fp)[0][1]
def getSeqFromFile(seq_fp):
_, ext = _ospath.splitext(seq_fp)
if ext in ('.gb', '.gbk', '.genbank'):
rec = gb_reader.parse(seq_fp)
return str(rec['seq'])
elif ext in ('.fa', '.fasta'):
# Just returns the first sequence in the file for now --
# this may be undesirable as a general behavior
return fasta.parseFasta(seq_fp)[0][1]
def checkFile(self, fn, should_fail=False):
fn_gb = join(LOCAL_DIR, 'test_data', fn)
d_gb = gb_reader.parse(fn_gb)
fn_json = fn_gb + '.json'
with io.open(fn_json, 'r', encoding='utf-8') as fd_json:
d_json = json.load(fd_json)
if should_fail:
self.assertNotEqual(d_gb['info'], d_json['info'])
else:
self.assertEqual(d_gb['info'], d_json['info'])
def checkFile(self, fn, should_fail=False):
fn_gb = join(LOCAL_DIR, 'test_data', fn)
d_gb = gb_reader.parse(fn_gb)
fn_json = fn_gb + '.json'
with io.open(fn_json, 'r', encoding='utf-8') as fd_json:
d_json = json.load(fd_json)
if should_fail:
self.assertNotEqual(d_gb['info'], d_json['info'])
else:
self.assertEqual(d_gb['info'], d_json['info'])
def checkFile(self, fn, should_be_true):
fn_gb = join(LOCAL_DIR, 'test_data', fn)
d_gb = gb_reader.parse(fn_gb, is_ordered=True)
f_temp = NamedTemporaryFile(mode='w', delete=False, encoding='utf-8')
gb_writer.write(f_temp, d_gb)
f_temp.close()
if should_be_true:
self.assertTrue(filecmp.cmp(fn_gb, f_temp.name))
else:
self.assertFalse(filecmp.cmp(fn_gb, f_temp.name))
os.unlink(f_temp.name)
self.assertFalse(os.path.exists(f_temp.name))
def checkFile(self, fn, should_be_true):
fn_gb = join(LOCAL_DIR, 'test_data', fn)
d_gb = gb_reader.parse(fn_gb, is_ordered=True)
f_temp = NamedTemporaryFile(mode='w', delete=False, encoding='utf-8')
gb_writer.write(f_temp, d_gb)
f_temp.close()
if should_be_true:
self.assertTrue(filecmp.cmp(fn_gb, f_temp.name))
else:
self.assertFalse(filecmp.cmp(fn_gb, f_temp.name))
os.unlink(f_temp.name)
self.assertFalse(os.path.exists(f_temp.name))