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refactorization of GenBank check output script #5

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refactorization of GenBank check output script #5

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29 changes: 13 additions & 16 deletions Scripts/GenBank/check_output.py
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Original file line number Diff line number Diff line change
Expand Up @@ -33,13 +33,9 @@ def do_comparison(good_record, test_record):
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

good_line = good_handle.readline()
test_line = test_handle.readline()
while good_line or test_line:
if not(good_line):
if good_line.strip():
raise AssertionError("Extra info in Test: `%s`" % test_line)
Expand All @@ -51,12 +47,16 @@ def do_comparison(good_record, test_record):
assert test_line == good_line, \
"Expected does not match Test.\nExpect:`%s`\nTest :`%s`\n" % \
(good_line, test_line)

good_line = good_handle.readline()
test_line = test_handle.readline()


def write_format(file):
record_parser = GenBank.RecordParser(debug_level=2)

print("Testing GenBank writing for %s..." % os.path.basename(file))

# be able to handle gzipped files
if '.gz' in file:
cur_handle = gzip.open(file, "r")
Expand All @@ -68,22 +68,19 @@ def write_format(file):
iterator = GenBank.Iterator(cur_handle, record_parser)
compare_iterator = GenBank.Iterator(compare_handle)

while True:
cur_record = next(iterator)
compare_record = next(compare_iterator)

if cur_record is None or compare_record is None:
break

# print("\tTesting for %s" % cur_record.version)

cur_record = next(iterator)
compare_record = next(compare_iterator)
while cur_record != None and compare_record != None:
output_record = str(cur_record) + "\n"
try:
do_comparison(compare_record, output_record)
except AssertionError as msg:
print("\tTesting for %s" % cur_record.version)
print(msg)

cur_record = next(iterator)
compare_record = next(compare_iterator)

cur_handle.close()
compare_handle.close()

Expand Down