def test_sequence_conversion(self):
pseq = PX.Sequence(
type="protein",
# id_ref=None,
# id_source=None,
symbol="ADHX",
accession=PX.Accession("P81431", source="UniProtKB"),
name="Alcohol dehydrogenase class-3",
# location=None,
mol_seq=PX.MolSeq(
"TDATGKPIKCMAAIAWEAKKPLSIEEVEVAPPKSGEVRIKILHSGVCHTD"),
uri=None,
annotations=[
PX.Annotation(ref="EC:1.1.1.1"),
PX.Annotation(ref="GO:0004022")
],
domain_architecture=PX.DomainArchitecture(
length=50,
domains=[
PX.ProteinDomain(*args) for args in (
# value, start, end, confidence
("FOO", 0, 5, 7.0e-26),
("BAR", 8, 13, 7.2e-117),
("A-OK", 21, 34, 2.4e-06),
("WD40", 40, 50, 0.3))
],
))
srec = pseq.to_seqrecord()
# TODO: check seqrec-specific traits (see args)
# Seq(letters, alphabet), id, name, description, features
pseq2 = PX.Sequence.from_seqrecord(srec)
def test_sequence_conversion(self):
pseq = PX.Sequence(
type='protein',
# id_ref=None,
# id_source=None,
symbol='ADHX',
accession=PX.Accession('P81431', source='UniProtKB'),
name='Alcohol dehydrogenase class-3',
# location=None,
mol_seq=PX.MolSeq(
'TDATGKPIKCMAAIAWEAKKPLSIEEVEVAPPKSGEVRIKILHSGVCHTD'),
uri=None,
annotations=[
PX.Annotation(ref='EC:1.1.1.1'),
PX.Annotation(ref='GO:0004022')
],
domain_architecture=PX.DomainArchitecture(
length=50,
domains=[
PX.ProteinDomain(*args) for args in (
# value, start, end, confidence
('FOO', 0, 5, 7.0e-26),
('BAR', 8, 13, 7.2e-117),
('A-OK', 21, 34, 2.4e-06),
('WD40', 40, 50, 0.3))
],
))
srec = pseq.to_seqrecord()
# TODO: check seqrec-specific traits (see args)
# Seq(letters, alphabet), id, name, description, features
pseq2 = PX.Sequence.from_seqrecord(srec)
def _parse_sequence(self, parent):
"""Parse a molecular sequence (PRIVATE)."""
sequence = PX.Sequence(**parent.attrib)
for event, elem in self.context:
namespace, tag = _split_namespace(elem.tag)
if event == "end":
if tag == "sequence":
parent.clear()
break
if tag in ("accession", "mol_seq", "uri", "domain_architecture"):
setattr(sequence, tag, getattr(self, tag)(elem))
elif tag == "annotation":
sequence.annotations.append(self.annotation(elem))
elif tag == "name":
sequence.name = _collapse_wspace(elem.text)
elif tag in ("symbol", "location"):
setattr(sequence, tag, elem.text)
elif namespace != NAMESPACES["phy"]:
sequence.other.append(self.other(elem, namespace, tag))
parent.clear()
return sequence
def _parse_sequence(self, parent):
sequence = PX.Sequence(**parent.attrib)
for event, elem in self.context:
namespace, tag = _split_namespace(elem.tag)
if event == 'end':
if tag == 'sequence':
parent.clear()
break
if tag in ('accession', 'mol_seq', 'uri',
'domain_architecture'):
setattr(sequence, tag, getattr(self, tag)(elem))
elif tag == 'annotation':
sequence.annotations.append(self.annotation(elem))
elif tag == 'name':
sequence.name = _collapse_wspace(elem.text)
elif tag in ('symbol', 'location'):
setattr(sequence, tag, elem.text)
elif namespace != NAMESPACES['phy']:
sequence.other.append(self.other(elem, namespace, tag))
parent.clear()
return sequence
calculator = DistanceCalculator('identity')
dm = calculator.get_distance(aln)
print(dm)
constructor = DistanceTreeConstructor(calculator, 'nj')
tree = constructor.build_tree(aln)
print(tree)
scorer = ParsimonyScorer()
searcher = NNITreeSearcher(scorer)
constructor = ParsimonyTreeConstructor(searcher, tree)
pars_tree = constructor.build_tree(aln)
egfr_phy = pars_tree.as_phyloxml()
print(pars_tree)
print(egfr_phy)
print(list(pars_tree.find_elements('Inner3')))
for clade in egfr_phy.get_terminals():
key = clade.name
accession = PhyloXML.Accession(key, 'NCBI')
mol_seq = PhyloXML.MolSeq(lookup[key], is_aligned=True)
sequence = PhyloXML.Sequence(type='aa',
accession=accession,
mol_seq=mol_seq)
clade.sequences.append(sequence)
Phylo.write(egfr_phy, 'egfr-family-annotated.xml', 'phyloxml')
