def do_comparison(good_record, test_record):
"""Compare two records to see if they are the same.
Ths compares the two GenBank record, and will raise an AssertionError
if two lines do not match, showing the non-matching lines.
"""
good_handle = StringIO(good_record)
test_handle = StringIO(test_record)
while True:
good_line = good_handle.readline()
test_line = test_handle.readline()
if not (good_line) and not (test_line):
break
if not (good_line):
raise AssertionError("Extra info in Test: %r" % test_line)
if not (test_line):
raise AssertionError("Extra info in Expected: %r" % good_line)
test_normalized = " ".join(x for x in test_line.split() if x)
good_normalized = " ".join(x for x in good_line.split() if x)
assert test_normalized == good_normalized, "Expected does not match Test.\nExpect: %r\nTest: %r\n" % (
good_line,
test_line,
)
def do_comparison(good_record, test_record):
"""Compare two records to see if they are the same.
Ths compares the two GenBank record, and will raise an AssertionError
if two lines do not match, showing the non-matching lines.
"""
good_handle = StringIO(good_record)
test_handle = StringIO(test_record)
while True:
good_line = good_handle.readline()
test_line = test_handle.readline()
if not good_line and not test_line:
break
if not good_line:
raise AssertionError("Extra info in Test: %r" % test_line)
if not test_line:
raise AssertionError("Extra info in Expected: %r" % good_line)
test_normalized = " ".join(x for x in test_line.split() if x)
good_normalized = " ".join(x for x in good_line.split() if x)
assert test_normalized == good_normalized, \
"Expected does not match Test.\nExpect: %r\nTest: %r\n" % (good_line, test_line)
def test_long_names(self):
"""Various GenBank names which push the column based LOCUS line."""
original = SeqIO.read("GenBank/iro.gb", "gb")
self.assertEqual(len(original), 1326)
# Acceptability of LOCUS line with length > 80 invalidates some of these tests
for name, seq_len, ok in [
("short", 1, True),
("max_length_of_16", 1000, True),
("overly_long_at_17", 1000, True),
("excessively_long_at_22", 99999, True),
("excessively_long_at_22", 100000, True),
("pushing_the_limits_at_24", 999, True),
("pushing_the_limits_at_24", 1000, True),
("old_max_name_length_was_26", 10, True), # 2 digits
("old_max_name_length_was_26", 9, True)]: # 1 digit
# Make the length match the desired target
record = original[:]
# TODO - Implement Seq * int
record.seq = Seq("N" * seq_len, original.seq.alphabet)
# Set the identifer to the desired name
record.id = record.name = name
# Attempt to output the record...
if not ok:
# e.g. ValueError: Locus identifier 'excessively_long_at_22' is too long
self.assertRaises(ValueError, record.format, "gb")
continue
with warnings.catch_warnings():
# e.g. BiopythonWarning: Stealing space from length field to
# allow long name in LOCUS line
warnings.simplefilter("ignore", BiopythonWarning)
# output = record.format("gb")
handle = StringIO()
self.assertEqual(1, SeqIO.write(record, handle, "gb"))
handle.seek(0)
line = handle.readline()
self.assertIn(" %s " % name, line)
self.assertIn(" %i bp " % seq_len, line)
# Splitting based on whitespace rather than position due to
# updated GenBank specification
name_and_length = line.split()[1:3]
self.assertEqual(name_and_length, [name, str(seq_len)], line)
handle.seek(0)
with warnings.catch_warnings():
# e.g. BiopythonParserWarning: GenBank LOCUS line
# identifier over 16 characters
warnings.simplefilter("ignore", BiopythonWarning)
new = SeqIO.read(handle, "gb")
self.assertEqual(name, new.name)
self.assertEqual(seq_len, len(new))
