def annotate_tree_all(tree, seqs, VERBOSE=0):
'''Annotate tree with metadata'''
from hivwholeseq.utils.tree import add_mutations_tree
from operator import attrgetter
add_mutations_tree(tree, translate=False, mutation_attrname='muts')
seqnames = [seq.name for seq in seqs]
for leaf in tree.get_terminals():
if 'Isolate' not in leaf.name:
leaf.patient = leaf.name.split('_')[0]
else:
leaf.patient = leaf.name[len('Isolate_'):]
sample = seqs[seqnames.index(leaf.name)]
leaf.subtype = sample.subtype
if (leaf.patient[0] == 'p') and (len(leaf.patient) <= 3):
leaf.DSI = float(leaf.name.split('_')[1])
leaf.CD4 = sample.cell_count
leaf.VL = sample.viral_load
leaf.name = None
# Reroot
tree.root_at_midpoint()
# Propagate the properties up the tree
for prop in ['patient', 'subtype']:
groups = defaultdict(list)
for node in tree.get_nonterminals(order='postorder'):
key = set([getattr(child, prop, None) for child in node.clades])
if (None not in key) and (len(key) == 1):
setattr(node, prop, key.pop())
def annotate_tree(patient, tree, ali, VERBOSE=0):
'''Annotate tree with metadata'''
from hivwholeseq.utils.tree import add_mutations_tree
from operator import attrgetter
add_mutations_tree(tree, translate=False, mutation_attrname='muts')
for leaf in tree.get_terminals():
leaf.patient = patient.code
leaf.DSI = float(leaf.name.split('_')[1])
leaf.name = None
sample = patient.samples.loc[patient.times == leaf.DSI].iloc[0]
leaf.CD4 = sample['CD4+ count']
leaf.VL = sample['viral load']
leaf.subtype = patient.Subtype
# Reroot
tmin = min(leaf.DSI for leaf in tree.get_terminals())
newroot = min((leaf for leaf in tree.get_terminals()),
key=attrgetter('DSI'))
tree.root_with_outgroup(newroot)
# Propagate the properties up the tree
for prop in ['patient', 'subtype']:
groups = defaultdict(list)
for node in tree.get_nonterminals(order='postorder'):
key = set([getattr(child, prop, None) for child in node.clades])
if (None not in key) and (len(key) == 1):
setattr(node, prop, key.pop())
def annotate_tree(patient, tree, ali, VERBOSE=0):
'''Annotate tree with metadata'''
from hivwholeseq.utils.tree import add_mutations_tree
from operator import attrgetter
add_mutations_tree(tree, translate=False, mutation_attrname='muts')
for leaf in tree.get_terminals():
leaf.DSI = float(leaf.name.split('_')[0])
leaf.frequency = float(leaf.name.split('_')[2].split('%')[0]) / 100.0
leaf.count = int(leaf.name.split('_')[3])
leaf.name = None
sample = patient.samples.loc[patient.times == leaf.DSI].iloc[0]
leaf.CD4 = sample['CD4+ count']
leaf.VL = sample['viral load']
for node in tree.get_terminals() + tree.get_nonterminals():
node.subtype = patient.Subtype
# Reroot
tmin = min(leaf.DSI for leaf in tree.get_terminals())
newroot = max((leaf for leaf in tree.get_terminals() if leaf.DSI == tmin),
key=attrgetter('frequency'))
tree.root_with_outgroup(newroot)
def annotate_tree_all(tree, seqs, VERBOSE=0):
'''Annotate tree with metadata'''
from hivwholeseq.utils.tree import add_mutations_tree
from operator import attrgetter
add_mutations_tree(tree, translate=False, mutation_attrname='muts')
seqnames = [seq.name for seq in seqs]
for leaf in tree.get_terminals():
if 'Isolate' not in leaf.name:
leaf.patient = leaf.name.split('_')[0]
else:
leaf.patient = leaf.name[len('Isolate_'):]
sample = seqs[seqnames.index(leaf.name)]
leaf.subtype = sample.subtype
if (leaf.patient[0] == 'p') and (len(leaf.patient) <= 3):
leaf.DSI = float(leaf.name.split('_')[1])
leaf.CD4 = sample.cell_count
leaf.VL = sample.viral_load
leaf.name = None
# Reroot
tree.root_at_midpoint()
# Propagate the properties up the tree
for prop in ['patient', 'subtype']:
groups = defaultdict(list)
for node in tree.get_nonterminals(order='postorder'):
key = set([getattr(child, prop, None) for child in node.clades])
if (None not in key) and (len(key) == 1):
setattr(node, prop, key.pop())
def annotate_tree(patient, tree, ali, VERBOSE=0):
'''Annotate tree with metadata'''
from hivwholeseq.utils.tree import add_mutations_tree
from operator import attrgetter
add_mutations_tree(tree, translate=False, mutation_attrname='muts')
for leaf in tree.get_terminals():
leaf.patient = patient.code
leaf.DSI = float(leaf.name.split('_')[1])
leaf.name = None
sample = patient.samples.loc[patient.times == leaf.DSI].iloc[0]
leaf.CD4 = sample['CD4+ count']
leaf.VL = sample['viral load']
leaf.subtype = patient.Subtype
# Reroot
tmin = min(leaf.DSI for leaf in tree.get_terminals())
newroot = min((leaf for leaf in tree.get_terminals()),
key=attrgetter('DSI'))
tree.root_with_outgroup(newroot)
# Propagate the properties up the tree
for prop in ['patient', 'subtype']:
groups = defaultdict(list)
for node in tree.get_nonterminals(order='postorder'):
key = set([getattr(child, prop, None) for child in node.clades])
if (None not in key) and (len(key) == 1):
setattr(node, prop, key.pop())
def annotate_tree(patient,
tree,
VERBOSE=0,
fields=('DSI', 'muts', 'VL', 'ntemplates', 'CD4',
'patient')):
'''Annotate a tree with info on the nodes'''
from hivwholeseq.utils.tree import add_mutations_tree
for node in tree.get_terminals():
label = node.name
entries = label.split('_')
node.name = entries[0]
if node.name == 'reference':
continue
# Days Since Infection
if 'DSI' in fields:
time = float(entries[0])
node.DSI = time
sample = patient.samples.loc[patient.times == time].iloc[0]
if 'CD4' in fields:
node.CD4 = sample['CD4+ count']
if 'VL' in fields:
node.VL = sample['viral load']
# FIXME: shall we check the patient method for this?
# Well, we are going to quantify fragment-by-fragment, so...
if 'ntemplates' in fields:
node.ntemplates = sample['n templates']
if 'subtype' in fields:
for node in tree.get_terminals() + tree.get_nonterminals():
node.subtype = patient.Subtype
if 'patient' in fields:
for node in tree.get_terminals() + tree.get_nonterminals():
node.patient = patient.code
if 'muts' in fields:
add_mutations_tree(tree, translate=False, mutation_attrname='muts')
if 'mutsprot' in fields:
add_mutations_tree(tree, translate=True, mutation_attrname='mutsprot')
def annotate_tree(patient, tree, VERBOSE=0,
fields=('DSI', 'muts', 'VL', 'ntemplates', 'CD4',
'patient')):
'''Annotate a tree with info on the nodes'''
from hivwholeseq.utils.tree import add_mutations_tree
for node in tree.get_terminals():
label = node.name
entries = label.split('_')
node.name = entries[0]
if node.name == 'reference':
continue
# Days Since Infection
if 'DSI' in fields:
time = float(entries[0])
node.DSI = time
sample = patient.samples.loc[patient.times == time].iloc[0]
if 'CD4' in fields:
node.CD4 = sample['CD4+ count']
if 'VL' in fields:
node.VL = sample['viral load']
# FIXME: shall we check the patient method for this?
# Well, we are going to quantify fragment-by-fragment, so...
if 'ntemplates' in fields:
node.ntemplates = sample['n templates']
if 'subtype' in fields:
for node in tree.get_terminals() + tree.get_nonterminals():
node.subtype = patient.Subtype
if 'patient' in fields:
for node in tree.get_terminals() + tree.get_nonterminals():
node.patient = patient.code
if 'muts' in fields:
add_mutations_tree(tree, translate=False, mutation_attrname='muts')
if 'mutsprot' in fields:
add_mutations_tree(tree, translate=True, mutation_attrname='mutsprot')
