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 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")
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")
