def test_get_sprot_raw(self): """Bio.ExPASy.get_sprot_raw("O23729")""" identifier = "O23729" # This is to catch an error page from our proxy: handle = UndoHandle(ExPASy.get_sprot_raw(identifier)) if _as_string(handle.peekline()).startswith("<!DOCTYPE HTML"): raise IOError record = SeqIO.read(handle, "swiss") handle.close() self.assertEqual(record.id, identifier) self.assertEqual(len(record), 394) self.assertEqual(seguid(record.seq), "5Y08l+HJRDIlhLKzFEfkcKd1dkM")
def extract_organisms(file, num_records): scanner = Fasta._Scanner() consumer = SpeciesExtractor() file_to_parse = UndoHandle(open(file, "r")) for fasta_record in range(num_records): scanner.feed(file_to_parse, consumer) file_to_parse.close() return consumer.species_list
def test_get_sprot_raw(self): """Bio.ExPASy.get_sprot_raw("O23729")""" identifier = "O23729" try: #This is to catch an error page from our proxy: handle = UndoHandle(ExPASy.get_sprot_raw(identifier)) if _as_string(handle.peekline()).startswith("<!DOCTYPE HTML"): raise IOError record = SeqIO.read(handle, "swiss") handle.close() except IOError: raise MissingExternalDependencyError( "internet (or maybe just ExPASy) not available") self.assertEqual(record.id, identifier) self.assertEqual(len(record), 394) self.assertEqual(seguid(record.seq), "5Y08l+HJRDIlhLKzFEfkcKd1dkM")