def mol_seq(self, elem):
"""Create molecular sequence object."""
is_aligned = elem.get("is_aligned")
if is_aligned is not None:
is_aligned = _str2bool(is_aligned)
return PX.MolSeq(elem.text.strip(), is_aligned=is_aligned)
def mol_seq(self, elem):
is_aligned = elem.get('is_aligned')
if is_aligned is not None:
is_aligned = _str2bool(is_aligned)
return PX.MolSeq(elem.text.strip(), is_aligned=is_aligned)
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')
