def compare_txt_xml(self, old, new):
"""Compare text and XML based parser output."""
self.assertEqual(old.id, new.id)
self.assertEqual(old.name, new.name)
self.assertEqual(len(old), len(new))
self.assertEqual(str(old.seq), str(new.seq))
for key in set(old.annotations).intersection(new.annotations):
if key == "references":
self.assertEqual(len(old.annotations[key]),
len(new.annotations[key]))
for r1, r2 in zip(old.annotations[key], new.annotations[key]):
# Tweak for line breaks in plain text SwissProt
r1.title = r1.title.replace("- ", "-")
r2.title = r2.title.replace("- ", "-")
r1.journal = r1.journal.rstrip(".") # Should parser do this?
r1.medline_id = "" # Missing in UniPort XML? TODO - check
# Lots of extra comments in UniProt XML
r1.comment = ""
r2.comment = ""
if not r2.journal:
r1.journal = ""
compare_reference(r1, r2)
elif old.annotations[key] == new.annotations[key]:
pass
elif key in ["date"]:
# TODO - Why is this a list vs str?
pass
elif not isinstance(old.annotations[key], type(new.annotations[key])):
raise TypeError("%s gives %s vs %s" %
(key, old.annotations[key], new.annotations[key]))
elif key in ["organism"]:
if old.annotations[key] == new.annotations[key]:
pass
elif old.annotations[key].startswith(new.annotations[key] + " "):
pass
else:
raise ValueError(key)
elif (isinstance(old.annotations[key], list) and
sorted(old.annotations[key]) == sorted(new.annotations[key])):
pass
else:
raise ValueError("%s gives %s vs %s" %
(key, old.annotations[key], new.annotations[key]))
self.assertEqual(len(old.features), len(new.features),
"Features in %s, %i vs %i" %
(old.id, len(old.features), len(new.features)))
for f1, f2 in zip(old.features, new.features):
"""
self.assertEqual(f1.location.nofuzzy_start, f2.location.nofuzzy_start,
"%s %s vs %s %s" %
(f1.location, f1.type, f2.location, f2.type))
self.assertEqual(f1.location.nofuzzy_end, f2.location.nofuzzy_end,
"%s %s vs %s %s" %
(f1.location, f1.type, f2.location, f2.type))
"""
self.assertEqual(repr(f1.location), repr(f2.location),
"%s %s vs %s %s" %
(f1.location, f1.type, f2.location, f2.type))
def compare_txt_xml(self, old, new):
"""Compare text and XML based parser output."""
self.assertEqual(old.id, new.id)
self.assertEqual(old.name, new.name)
self.assertEqual(len(old), len(new))
self.assertEqual(str(old.seq), str(new.seq))
for key in set(old.annotations).intersection(new.annotations):
if key == "references":
self.assertEqual(len(old.annotations[key]),
len(new.annotations[key]))
for r1, r2 in zip(old.annotations[key], new.annotations[key]):
# Tweak for line breaks in plain text SwissProt
r1.title = r1.title.replace("- ", "-")
r2.title = r2.title.replace("- ", "-")
r1.journal = r1.journal.rstrip(".") # Should parser do this?
r1.medline_id = "" # Missing in UniPort XML? TODO - check
# Lots of extra comments in UniProt XML
r1.comment = ""
r2.comment = ""
if not r2.journal:
r1.journal = ""
compare_reference(r1, r2)
elif old.annotations[key] == new.annotations[key]:
pass
elif key in ["date"]:
# TODO - Why is this a list vs str?
pass
elif not isinstance(old.annotations[key], type(new.annotations[key])):
raise TypeError("%s gives %s vs %s" %
(key, old.annotations[key], new.annotations[key]))
elif key in ["organism"]:
if old.annotations[key] == new.annotations[key]:
pass
elif old.annotations[key].startswith(new.annotations[key] + " "):
pass
else:
raise ValueError(key)
elif isinstance(old.annotations[key], list) \
and sorted(old.annotations[key]) == sorted(new.annotations[key]):
pass
else:
raise ValueError("%s gives %s vs %s" %
(key, old.annotations[key], new.annotations[key]))
self.assertEqual(len(old.features), len(new.features),
"Features in %s, %i vs %i" %
(old.id, len(old.features), len(new.features)))
for f1, f2 in zip(old.features, new.features):
"""
self.assertEqual(f1.location.nofuzzy_start, f2.location.nofuzzy_start,
"%s %s vs %s %s" %
(f1.location, f1.type, f2.location, f2.type))
self.assertEqual(f1.location.nofuzzy_end, f2.location.nofuzzy_end,
"%s %s vs %s %s" %
(f1.location, f1.type, f2.location, f2.type))
"""
self.assertEqual(repr(f1.location), repr(f2.location),
"%s %s vs %s %s" %
(f1.location, f1.type, f2.location, f2.type))