def test_init_data(self):
"""Info init with data should put items in correct places"""
#need to check init, setting, and resetting of attributes that belong
#in the Info object and attributes that belong in Info.Refs. Also need
#to check __getitem__, __setitem__, and __contains__.
d = Info({'x':3, 'GO':12345})
self.assertEqual(d.x, 3)
self.assertEqual(d.GO, [12345])
self.assertEqual(d.Refs.GO, [12345])
try:
del d.Refs
except AttributeError:
pass
else:
raise Exception, "Failed to prevent deletion of required key Refs"""
d.GenBank = ('qaz', 'wsx')
self.assertEqual(d.GenBank, ['qaz', 'wsx'])
assert 'GenBank' in d.Refs
assert 'GenBank' in d
d.GenBank = 'xyz'
self.assertEqual(d.GenBank, ['xyz'])
assert d.GenBank is d.Refs.GenBank
d.GO = 'x'
self.assertEqual(d.GO, ['x'])
d.GO.append('y')
self.assertEqual(d.GO, ['x', 'y'])
d.ZZZ = 'zzz'
self.assertEqual(d.ZZZ, 'zzz')
assert 'ZZZ' not in d.Refs
assert 'XXX' not in d
self.assertEqual(d.XXX, None)
def test_full(self):
"""InfoMaker should return Info object with name, value pairs"""
test_header = ['acc: X3402','abc:1','mty: ssu','seq: Mit. X3402',\
'','nonsense',':no_name']
obs = InfoMaker(test_header)
exp = Info()
exp.rRNA = 'X3402'
exp.abc = '1'
exp.Species = 'Mit. X3402'
exp.Gene = 'ssu'
self.assertEqual(obs,exp)
def NcbiFastaLabelParser(line):
"""Creates an Info object and populates it with the line contents.
As of 11/12/03, all records in genpept.fsa and the human RefSeq fasta
files were consistent with this format.
"""
info = Info()
try:
ignore, gi, db, db_ref, description = map(strip, line.split('|', 4))
except ValueError: #probably got wrong value
raise RecordError, "Unable to parse label line %s" % line
info.GI = gi
info[NcbiLabels[db]] = db_ref
info.Description = description
return info