def export(self, path = '', extra_attr = ['aa_muts']):
from Bio import Seq
from itertools import izip
timetree_fname = path+'tree.json'
sequence_fname = path+'sequences.json'
tree_json = tree_to_json(self.tree.root, extra_attr=extra_attr)
write_json(tree_json, timetree_fname, indent=None)
elems = {}
elems['root'] = {}
elems['root']['nuc'] = "".join(self.tree.root.sequence)
for prot in self.proteins:
tmp = str(self.proteins[prot].extract(Seq.Seq(elems['root']['nuc'])))
#elems['root'][prot] = str(Seq.translate(tmp.replace('---', 'NNN'))).replace('X','-')
elems['root'][prot] = str(Seq.translate(tmp.replace('-', 'N'))).replace('X','-')
for node in self.tree.find_clades():
if hasattr(node, "clade") and hasattr(node, "sequence"):
elems[node.clade] = {}
elems[node.clade]['nuc'] = {pos:state for pos, (state, ancstate) in
enumerate(izip(node.sequence, self.tree.root.sequence)) if state!=ancstate}
for node in self.tree.find_clades():
if hasattr(node, "clade") and hasattr(node, "translations"):
for prot in self.proteins:
elems[node.clade][prot] = {pos:state for pos, (state, ancstate) in
enumerate(izip(node.translations[prot], elems['root'][prot])) if state!=ancstate}
write_json(elems, sequence_fname, indent=None)
def export(self,
path='',
extra_attr=['aa_muts', 'clade'],
plain_export=10,
indent=None,
write_seqs_json=True):
'''
export the tree data structure along with the sequence information as
json files for display in web browsers.
parameters:
path -- path (incl prefix) to which the output files are written.
filenames themselves are standardized to *tree.json and *sequences.json
extra_attr -- attributes of tree nodes that are exported to json
plain_export -- store sequences are plain strings instead of
differences to root if number of differences exceeds
len(seq)/plain_export
'''
from Bio import Seq
from itertools import izip
timetree_fname = path + '_tree.json'
sequence_fname = path + '_sequences.json'
tree_json = tree_to_json(self.tree.root, extra_attr=extra_attr)
write_json(tree_json, timetree_fname, indent=indent)
# prepare a json with sequence information to export.
# first step: add the sequence & translations of the root as string
elems = {}
elems['root'] = {}
elems['root']['nuc'] = "".join(self.tree.root.sequence)
for prot, seq in self.tree.root.translations.iteritems():
elems['root'][prot] = seq
# add sequence for every node in tree. code as difference to root
# or as full strings.
for node in self.tree.find_clades():
if hasattr(node, "clade"):
elems[node.clade] = {}
# loop over proteins and nucleotide sequences
for prot, seq in [('nuc', "".join(node.sequence))
] + node.translations.items():
differences = {
pos: state
for pos, (state, ancstate) in enumerate(
izip(seq, elems['root'][prot]))
if state != ancstate
}
if plain_export * len(differences) <= len(seq):
elems[node.clade][prot] = differences
else:
elems[node.clade][prot] = seq
if write_seqs_json:
write_json(elems, sequence_fname, indent=indent)