コード例 #1
0
ファイル: PhyloXMLIO.py プロジェクト: ruda830/biovoice
 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)
コード例 #2
0
ファイル: PhyloXMLIO.py プロジェクト: sogada/biopython
 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)
コード例 #3
0
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')