def _read_sts(line):
"""Reads STS lines: format is in the full docstring.
Format:
Name|Chromosome|StsId|Segment|SequenceKnown|Evidence
"""
return MappedRecord(sts_wrapper(line))
def __init__(self, *args, **kwargs):
"""Returns new Info object. Creates DbRefs if necessary."""
temp = dict(*args, **kwargs)
if "Refs" in temp:
refs = temp["Refs"]
if not isinstance(refs, DbRefs):
refs = DbRefs(refs)
else:
refs = DbRefs()
# move keys into refs if they belong there: allows init from flat dict
for key, val in list(temp.items()):
if key in KnownDatabases:
refs[key] = val
del temp[key]
Delegator.__init__(self, refs)
self["Refs"] = refs
MappedRecord.__init__(self, temp)
def _read_cdd(line):
"""Reads CDD lines: format is Name|Key|Score|EValue|BitScore."""
return MappedRecord(cdd_wrapper(line))
def _read_map(line):
"""Reads MAP lines: format is Location|Source|Type."""
return MappedRecord(map_wrapper(line))
def test_init_data(self):
"""MappedRecord should work like normal dict init"""
exp = {"a": 3, "b": 4}
self.assertEqual(MappedRecord({"a": 3, "b": 4}), exp)
self.assertEqual(MappedRecord(a=3, b=4), exp)
self.assertEqual(MappedRecord([["a", 3], ["b", 4]]), exp)
def test_init_empty(self):
"""MappedRecord empty init should work OK"""
g = MappedRecord()
self.assertEqual(g, {})
def setUp(self):
"""Define a few standard MappedRecords"""
self.empty = MappedRecord()
self.single = MappedRecord({"a": 3})
self.several = MappedRecord(a=4, b=5, c="a", d=[1, 2, 3])
