def _clean_accession(self, accession_string):
if accession_string.startswith(">"):
accession_string = accession_string[1:]
accession_string = accession_string.strip()
result = None
if "|" in accession_string:
try:
fields = fasta.default_parser(accession_string)
result = fields.accession
except fasta.UnparsableDeflineError:
result = accession_string
else:
result = accession_string
return result
def name_getter(x):
header = fasta.default_parser(x)
try:
return header.accession
except Exception:
return header[0]
def test_accession_alone(self):
header = "P16066"
result = fasta.default_parser(header)
self.assertRaises(AttributeError, lambda: result.accession)
self.assertEqual(result[0], "P16066")
def test_partial_uniprot(self):
header = "P16066|ANPRA_HUMAN"
result = fasta.default_parser(header)
self.assertEqual(result.accession, "P16066")
def test_without_prefix(self):
header = "sp|P16066|ANPRA_HUMAN Atrial natriuretic peptide receptor 1"
result = fasta.default_parser(header)
self.assertEqual(result.accession, "P16066")