def _seq_from_string(string, serializer):
'Given a json string it returns a SeqRecord'
if serializer == 'json':
struct = json.loads(string)
struct = fix_seq_struct_for_json(struct, alleles_to_string=False)
return create_seq_from_struct(struct)
else:
return pickle.loads(string)
def test_seq_from_stuct():
'It tests that we can get create a SeqWithQuality'
struct = {'seq': {'seq': 'ACTG'},
'name': 'hola',
'features': [{'start':1, 'end':2, 'type':'orf',
'qualifiers':{'dna':{'seq': 'ACT'},
'pep':{'seq': 'M'}}}],
'letter_annotations':{'phred_quality': [1, 2, 3, 4]}
}
seq = create_seq_from_struct(struct)
assert seq.seq == 'ACTG'
assert seq.name == 'hola'
feat = seq.features[0]
assert int(str(feat.location.start)) == 1
assert int(str(feat.location.end)) == 2
assert feat.type == 'orf'
dna = feat.qualifiers['dna']
assert str(dna) == 'ACT'
assert str(dna.alphabet) == str(Alphabet())
#now let's get the struct back
struct2 = seq.struct
assert struct2['features'] == struct['features']
assert struct2['letter_annotations'] == struct['letter_annotations']
assert struct2['seq'] == struct['seq']
assert struct2['name'] == struct['name']
assert struct2 == struct
#with a non-default alphabet
struct = {'seq': {'seq': 'ACTG', 'alphabet': 'dnaalphabet'}}
seq = create_seq_from_struct(struct)
struct2 = seq.struct
assert str(seq.seq.alphabet) == str(DNAAlphabet())
seq = SeqWithQuality(Seq('ACTG', DNAAlphabet()))
assert seq.struct['seq']['alphabet'] == 'dnaalphabet'
