def run(args):
# check alignment type, set flags, read in if VCF
is_vcf = False
ref = None
anc_seqs = {}
try:
T = read_tree(args.tree)
except (FileNotFoundError, InvalidTreeError) as error:
print("ERROR: %s" % error, file=sys.stderr)
return 1
import numpy as np
missing_internal_node_names = [
n.name is None for n in T.get_nonterminals()
]
if np.all(missing_internal_node_names):
print("\n*** WARNING: Tree has no internal node names!")
print(
"*** Without internal node names, ancestral sequences can't be linked up to the correct node later."
)
print(
"*** If you want to use 'augur export' or `augur translate` later, re-run this command with the output of 'augur refine'."
)
print(
"*** If you haven't run 'augur refine', you can add node names to your tree by running:"
)
print("*** augur refine --tree %s --output-tree <filename>.nwk" %
(args.tree))
print(
"*** And use <filename>.nwk as the tree when running 'ancestral', 'translate', and 'traits'"
)
if any([args.alignment.lower().endswith(x) for x in ['.vcf', '.vcf.gz']]):
if not args.vcf_reference:
print(
"ERROR: a reference Fasta is required with VCF-format alignments"
)
return 1
compress_seq = read_vcf(args.alignment, args.vcf_reference)
aln = compress_seq['sequences']
ref = compress_seq['reference']
is_vcf = True
else:
aln = args.alignment
# Enfore treetime 0.7 or later
from distutils.version import StrictVersion
import treetime
if StrictVersion(treetime.version) < StrictVersion('0.7.0'):
print("ERROR: this version of augur requires TreeTime 0.7 or later.")
return 1
# Infer ambiguous bases if the user has requested that we infer them (either
# explicitly or by default) and the user has not explicitly requested that
# we keep them.
infer_ambiguous = args.infer_ambiguous and not args.keep_ambiguous
tt = ancestral_sequence_inference(tree=T,
aln=aln,
ref=ref,
marginal=args.inference,
fill_overhangs=not (args.keep_overhangs),
infer_tips=infer_ambiguous)
character_map = {}
for x in tt.gtr.profile_map:
if tt.gtr.profile_map[x].sum() == tt.gtr.n_states:
# TreeTime treats all characters that are not valid IUPAC nucleotide chars as fully ambiguous
# To clean up auspice output, we map all those to 'N'
character_map[x] = 'N'
else:
character_map[x] = x
anc_seqs['nodes'] = collect_mutations_and_sequences(
tt,
full_sequences=not is_vcf,
infer_tips=infer_ambiguous,
character_map=character_map)
# add reference sequence to json structure. This is the sequence with
# respect to which mutations on the tree are defined.
if is_vcf:
anc_seqs['reference'] = {"nuc": compress_seq['reference']}
else:
anc_seqs['reference'] = {
"nuc":
"".join(T.root.sequence) if hasattr(T.root, 'sequence') else ''
}
out_name = get_json_name(
args, '.'.join(args.alignment.split('.')[:-1]) + '_mutations.json')
write_json(anc_seqs, out_name)
print("ancestral mutations written to", out_name, file=sys.stdout)
if args.output_sequences:
if args.output_vcf:
print(
"WARNING: augur only supports sequence output for FASTA alignments and not for VCFs.",
file=sys.stderr)
else:
records = [
SeqRecord(Seq(node_data["sequence"]),
id=node_name,
description="")
for node_name, node_data in anc_seqs["nodes"].items()
]
SeqIO.write(records, args.output_sequences, "fasta")
print("ancestral sequences FASTA written to",
args.output_sequences,
file=sys.stdout)
# If VCF, output VCF including new ancestral seqs
if is_vcf:
if args.output_vcf:
vcf_fname = args.output_vcf
else:
vcf_fname = '.'.join(args.alignment.split('.')[:-1]) + '.vcf'
write_vcf(tt.get_tree_dict(keep_var_ambigs=True), vcf_fname)
print("ancestral sequences as vcf-file written to",
vcf_fname,
file=sys.stdout)
return 0
def run(args):
# check alignment type, set flags, read in if VCF
is_vcf = False
ref = None
anc_seqs = {}
try:
T = read_tree(args.tree)
except (FileNotFoundError, InvalidTreeError) as error:
print("ERROR: %s" % error, file=sys.stderr)
return 1
import numpy as np
missing_internal_node_names = [
n.name is None for n in T.get_nonterminals()
]
if np.all(missing_internal_node_names):
print("\n*** WARNING: Tree has no internal node names!")
print(
"*** Without internal node names, ancestral sequences can't be linked up to the correct node later."
)
print(
"*** If you want to use 'augur export' or `augur translate` later, re-run this command with the output of 'augur refine'."
)
print(
"*** If you haven't run 'augur refine', you can add node names to your tree by running:"
)
print("*** augur refine --tree %s --output-tree <filename>.nwk" %
(args.tree))
print(
"*** And use <filename>.nwk as the tree when running 'ancestral', 'translate', and 'traits'"
)
if any([args.alignment.lower().endswith(x) for x in ['.vcf', '.vcf.gz']]):
if not args.vcf_reference:
print(
"ERROR: a reference Fasta is required with VCF-format alignments"
)
return 1
compress_seq = read_vcf(args.alignment, args.vcf_reference)
aln = compress_seq['sequences']
ref = compress_seq['reference']
is_vcf = True
else:
aln = args.alignment
# Only allow recovery of ambig sites for Fasta-input if TreeTime is version 0.5.6 or newer
# Otherwise it returns nonsense.
from distutils.version import StrictVersion
import treetime
if args.keep_ambiguous and not is_vcf and StrictVersion(
treetime.version) < StrictVersion('0.5.6'):
print(
"ERROR: Keeping ambiguous sites for Fasta-input requires TreeTime version 0.5.6 or newer."
+ "\nYour version is " + treetime.version +
"\nUpdate TreeTime or run without the --keep-ambiguous flag.")
return 1
tt = ancestral_sequence_inference(tree=T,
aln=aln,
ref=ref,
marginal=args.inference,
fill_overhangs=not (args.keep_overhangs))
if is_vcf or args.keep_ambiguous:
# TreeTime overwrites ambig sites on tips during ancestral reconst.
# Put these back in tip sequences now, to avoid misleading
tt.recover_var_ambigs()
anc_seqs['nodes'] = collect_sequences_and_mutations(T, is_vcf)
# add reference sequence to json structure. This is the sequence with
# respect to which mutations on the tree are defined.
if is_vcf:
anc_seqs['reference'] = {"nuc": compress_seq['reference']}
else:
anc_seqs['reference'] = {
"nuc":
"".join(T.root.sequence) if hasattr(T.root, 'sequence') else ''
}
out_name = get_json_name(
args, '.'.join(args.alignment.split('.')[:-1]) + '_mutations.json')
write_json(anc_seqs, out_name)
print("ancestral mutations written to", out_name, file=sys.stdout)
if args.output_sequences:
if args.output_vcf:
print(
"WARNING: augur only supports sequence output for FASTA alignments and not for VCFs.",
file=sys.stderr)
else:
records = [
SeqRecord(Seq(node_data["sequence"]),
id=node_name,
description="")
for node_name, node_data in anc_seqs["nodes"].items()
]
SeqIO.write(records, args.output_sequences, "fasta")
print("ancestral sequences FASTA written to",
args.output_sequences,
file=sys.stdout)
# If VCF, output VCF including new ancestral seqs
if is_vcf:
if args.output_vcf:
vcf_fname = args.output_vcf
else:
vcf_fname = '.'.join(args.alignment.split('.')[:-1]) + '.vcf'
write_vcf(tt.get_tree_dict(keep_var_ambigs=True), vcf_fname)
print("ancestral sequences as vcf-file written to",
vcf_fname,
file=sys.stdout)
return 0
def export_sequences_and_tree(tt, basename, is_vcf=False, zero_based=False,
report_ambiguous=False, timetree=False, confidence=False):
seq_info = is_vcf or tt.aln
if is_vcf:
tt.recover_var_ambigs()
outaln_name = basename + 'ancestral_sequences.vcf'
write_vcf(tt.get_tree_dict(keep_var_ambigs=True), outaln_name)
elif tt.aln:
outaln_name = basename + 'ancestral_sequences.fasta'
AlignIO.write(tt.get_reconstructed_alignment(), outaln_name, 'fasta')
if seq_info:
print("\n--- alignment including ancestral nodes saved as \n\t %s\n"%outaln_name)
# decorate tree with inferred mutations
terminal_count = 0
offset = 0 if zero_based else 1
if timetree:
dates_fname = basename + 'dates.tsv'
fh_dates = open(dates_fname, 'w')
if confidence:
fh_dates.write('#Lower and upper bound delineate the 90% max posterior region\n')
fh_dates.write('#node\tdate\tnumeric date\tlower bound\tupper bound\n')
else:
fh_dates.write('#node\tdate\tnumeric date\n')
for n in tt.tree.find_clades():
if timetree:
if confidence:
conf = tt.get_max_posterior_region(n, fraction=0.9)
fh_dates.write('%s\t%s\t%f\t%f\t%f\n'%(n.name, n.date, n.numdate,conf[0], conf[1]))
else:
fh_dates.write('%s\t%s\t%f\n'%(n.name, n.date, n.numdate))
n.confidence=None
# due to a bug in older versions of biopython that truncated filenames in nexus export
# we truncate them by hand and make them unique.
if n.is_terminal() and len(n.name)>40 and bioversion<"1.69":
n.name = n.name[:35]+'_%03d'%terminal_count
terminal_count+=1
n.comment=''
if seq_info and len(n.mutations):
if report_ambiguous:
n.comment= '&mutations="' + ','.join([a+str(pos + offset)+d for (a,pos, d) in n.mutations])+'"'
else:
n.comment= '&mutations="' + ','.join([a+str(pos + offset)+d for (a,pos, d) in n.mutations
if tt.gtr.ambiguous not in [a,d]])+'"'
if timetree:
n.comment+=(',' if n.comment else '&') + 'date=%1.2f'%n.numdate
# write tree to file
fmt_bl = "%1.6f" if tt.seq_len<1e6 else "%1.8e"
if timetree:
outtree_name = basename + 'timetree.nexus'
print("--- saved divergence times in \n\t %s\n"%dates_fname)
Phylo.write(tt.tree, outtree_name, 'nexus')
else:
outtree_name = basename + 'annotated_tree.nexus'
Phylo.write(tt.tree, outtree_name, 'nexus', format_branch_length=fmt_bl)
print("--- tree saved in nexus format as \n\t %s\n"%outtree_name)
if timetree:
for n in tt.tree.find_clades():
n.branch_length = n.mutation_length
outtree_name = basename + 'divergence_tree.nexus'
Phylo.write(tt.tree, outtree_name, 'nexus', format_branch_length=fmt_bl)
print("--- divergence tree saved in nexus format as \n\t %s\n"%outtree_name)
def run(args):
# check alignment type, set flags, read in if VCF
is_vcf = False
ref = None
tree_meta = {'alignment': args.alignment}
attributes = ['branch_length']
# check if tree is provided an can be read
for fmt in ["newick", "nexus"]:
try:
T = Phylo.read(args.tree, fmt)
tree_meta['input_tree'] = args.tree
break
except:
pass
if T is None:
print("ERROR: reading tree from %s failed." % args.tree)
return -1
if not args.alignment:
# fake alignment to appease treetime when only using it for naming nodes...
if args.ancestral or args.timetree:
print(
"ERROR: alignment is required for ancestral reconstruction or timetree inference"
)
return -1
from Bio import SeqRecord, Seq, Align
seqs = []
for n in T.get_terminals():
seqs.append(
SeqRecord.SeqRecord(seq=Seq.Seq('ACGT'),
id=n.name,
name=n.name,
description=''))
aln = Align.MultipleSeqAlignment(seqs)
elif any([args.alignment.lower().endswith(x)
for x in ['.vcf', '.vcf.gz']]):
if not args.vcf_reference:
print(
"ERROR: a reference Fasta is required with VCF-format alignments"
)
return -1
compress_seq = read_vcf(args.alignment, args.vcf_reference)
sequences = compress_seq['sequences']
ref = compress_seq['reference']
is_vcf = True
aln = sequences
else:
aln = args.alignment
if args.output:
tree_fname = args.output
else:
tree_fname = '.'.join(args.alignment.split('.')[:-1]) + '_tt.nwk'
if args.timetree and T:
if args.metadata is None:
print(
"ERROR: meta data with dates is required for time tree reconstruction"
)
return -1
metadata, columns = read_metadata(args.metadata)
if args.year_limit:
args.year_limit.sort()
dates = get_numerical_dates(metadata,
fmt=args.date_fmt,
min_max_year=args.year_limit)
for n in T.get_terminals():
if n.name in metadata and 'date' in metadata[n.name]:
n.raw_date = metadata[n.name]['date']
if args.root and len(
args.root
) == 1: #if anything but a list of seqs, don't send as a list
args.root = args.root[0]
tt = timetree(
tree=T,
aln=aln,
ref=ref,
dates=dates,
confidence=args.date_confidence,
reroot=args.root or 'best',
Tc=args.coalescent if args.coalescent is not None else
0.01, #Otherwise can't set to 0
use_marginal=args.time_marginal or False,
branch_length_mode=args.branch_length_mode or 'auto',
clock_rate=args.clock_rate,
n_iqd=args.n_iqd)
tree_meta['clock'] = {
'rate': tt.date2dist.clock_rate,
'intercept': tt.date2dist.intercept,
'rtt_Tmrca': -tt.date2dist.intercept / tt.date2dist.clock_rate
}
attributes.extend([
'numdate', 'clock_length', 'mutation_length', 'mutations',
'raw_date', 'date'
])
if not is_vcf:
attributes.extend(['sequence'
]) #don't add sequences if VCF - huge!
if args.date_confidence:
attributes.append('num_date_confidence')
elif args.ancestral in ['joint', 'marginal']:
tt = ancestral_sequence_inference(
tree=T,
aln=aln,
ref=ref,
marginal=args.ancestral,
optimize_branch_length=args.branchlengths,
branch_length_mode=args.branch_length_mode)
attributes.extend(['mutation_length', 'mutations'])
if not is_vcf:
attributes.extend(['sequence'
]) #don't add sequences if VCF - huge!
else:
from treetime import TreeAnc
# instantiate treetime for the sole reason to name internal nodes
tt = TreeAnc(tree=T, aln=aln, ref=ref, gtr='JC69', verbose=1)
if is_vcf:
#TreeTime overwrites ambig sites on tips during ancestral reconst.
#Put these back in tip sequences now, to avoid misleading
tt.recover_var_ambigs()
tree_meta['nodes'] = prep_tree(T, attributes, is_vcf)
if T:
import json
tree_success = Phylo.write(T,
tree_fname,
'newick',
format_branch_length='%1.8f')
if args.node_data:
node_data_fname = args.node_data
else:
node_data_fname = '.'.join(
args.alignment.split('.')[:-1]) + '.node_data'
with open(node_data_fname, 'w') as ofile:
meta_success = json.dump(tree_meta, ofile)
#If VCF and ancestral reconst. was done, output VCF including new ancestral seqs
if is_vcf and (args.ancestral or args.timetree):
if args.output_vcf:
vcf_fname = args.output_vcf
else:
vcf_fname = '.'.join(args.alignment.split('.')[:-1]) + '.vcf'
write_vcf(tt.get_tree_dict(keep_var_ambigs=True), vcf_fname)
return 0 if (tree_success and meta_success) else -1
else:
return -1
def export_sequences_and_tree(tt, basename, is_vcf=False, zero_based=False,
report_ambiguous=False, timetree=False, confidence=False):
seq_info = is_vcf or tt.aln
if is_vcf:
tt.recover_var_ambigs()
outaln_name = basename + 'ancestral_sequences.vcf'
write_vcf(tt.get_tree_dict(keep_var_ambigs=True), outaln_name)
elif tt.aln:
outaln_name = basename + 'ancestral_sequences.fasta'
AlignIO.write(tt.get_reconstructed_alignment(), outaln_name, 'fasta')
if seq_info:
print("\n--- alignment including ancestral nodes saved as \n\t %s\n"%outaln_name)
# decorate tree with inferred mutations
terminal_count = 0
offset = 0 if zero_based else 1
if timetree:
dates_fname = basename + 'dates.tsv'
fh_dates = open(dates_fname, 'w')
if confidence:
fh_dates.write('#Lower and upper bound delineate the 90% max posterior region\n')
fh_dates.write('#node\tdate\tnumeric date\tlower bound\tupper bound\n')
else:
fh_dates.write('#node\tdate\tnumeric date\n')
for n in tt.tree.find_clades():
if timetree:
if confidence:
conf = tt.get_max_posterior_region(n, fraction=0.9)
fh_dates.write('%s\t%s\t%f\t%f\t%f\n'%(n.name, n.date, n.numdate,conf[0], conf[1]))
else:
fh_dates.write('%s\t%s\t%f\n'%(n.name, n.date, n.numdate))
n.confidence=None
# due to a bug in older versions of biopython that truncated filenames in nexus export
# we truncate them by hand and make them unique.
if n.is_terminal() and len(n.name)>40 and bioversion<"1.69":
n.name = n.name[:35]+'_%03d'%terminal_count
terminal_count+=1
n.comment=''
if seq_info and len(n.mutations):
if report_ambiguous:
n.comment= '&mutations="' + ','.join([a+str(pos + offset)+d for (a,pos, d) in n.mutations])+'"'
else:
n.comment= '&mutations="' + ','.join([a+str(pos + offset)+d for (a,pos, d) in n.mutations
if tt.gtr.ambiguous not in [a,d]])+'"'
if timetree:
n.comment+=(',' if n.comment else '&') + 'date=%1.2f'%n.numdate
# write tree to file
fmt_bl = "%1.6f" if tt.seq_len<1e6 else "%1.8e"
if timetree:
outtree_name = basename + 'timetree.nexus'
print("--- saved divergence times in \n\t %s\n"%dates_fname)
Phylo.write(tt.tree, outtree_name, 'nexus')
else:
outtree_name = basename + 'annotated_tree.nexus'
Phylo.write(tt.tree, outtree_name, 'nexus', format_branch_length=fmt_bl)
print("--- tree saved in nexus format as \n\t %s\n"%outtree_name)
if timetree:
for n in tt.tree.find_clades():
n.branch_length = n.mutation_length
outtree_name = basename + 'divergence_tree.nexus'
Phylo.write(tt.tree, outtree_name, 'nexus', format_branch_length=fmt_bl)
print("--- divergence tree saved in nexus format as \n\t %s\n"%outtree_name)
def run(args):
# check alignment type, set flags, read in if VCF
is_vcf = False
ref = None
anc_seqs = {}
# check if tree is provided and can be read
for fmt in ["newick", "nexus"]:
try:
T = Phylo.read(args.tree, fmt)
break
except:
pass
if T is None:
print("ERROR: reading tree from %s failed."%args.tree)
return 1
if any([args.alignment.lower().endswith(x) for x in ['.vcf', '.vcf.gz']]):
if not args.vcf_reference:
print("ERROR: a reference Fasta is required with VCF-format alignments")
return 1
compress_seq = read_vcf(args.alignment, args.vcf_reference)
aln = compress_seq['sequences']
ref = compress_seq['reference']
is_vcf = True
else:
aln = args.alignment
# Only allow recovery of ambig sites for Fasta-input if TreeTime is version 0.5.6 or newer
# Otherwise it returns nonsense.
from distutils.version import StrictVersion
import treetime
if args.keep_ambiguous and not is_vcf and StrictVersion(treetime.version) < StrictVersion('0.5.6'):
print("ERROR: Keeping ambiguous sites for Fasta-input requires TreeTime version 0.5.6 or newer."+
"\nYour version is "+treetime.version+
"\nUpdate TreeTime or run without the --keep-ambiguous flag.")
return 1
tt = ancestral_sequence_inference(tree=T, aln=aln, ref=ref, marginal=args.inference,
fill_overhangs = not(args.keep_overhangs))
if is_vcf or args.keep_ambiguous:
# TreeTime overwrites ambig sites on tips during ancestral reconst.
# Put these back in tip sequences now, to avoid misleading
tt.recover_var_ambigs()
anc_seqs['nodes'] = collect_sequences_and_mutations(T, is_vcf)
if args.output:
anc_seqs_fname = args.output
else:
anc_seqs_fname = '.'.join(args.alignment.split('.')[:-1]) + '.anc_seqs.json'
write_json(anc_seqs, anc_seqs_fname)
print("ancestral sequences written to",anc_seqs_fname, file=sys.stdout)
# If VCF, output VCF including new ancestral seqs
if is_vcf:
if args.output_vcf:
vcf_fname = args.output_vcf
else:
vcf_fname = '.'.join(args.alignment.split('.')[:-1]) + '.vcf'
write_vcf(tt.get_tree_dict(keep_var_ambigs=True), vcf_fname)
print("ancestral sequences as vcf-file written to",vcf_fname, file=sys.stdout)
return 0
def run(args):
# check alignment type, set flags, read in if VCF
is_vcf = False
ref = None
anc_seqs = {}
# check if tree is provided and can be read
for fmt in ["newick", "nexus"]:
try:
T = Phylo.read(args.tree, fmt)
break
except:
pass
if T is None:
print("ERROR: reading tree from %s failed." % args.tree)
return -1
if any([args.alignment.lower().endswith(x) for x in ['.vcf', '.vcf.gz']]):
if not args.vcf_reference:
print(
"ERROR: a reference Fasta is required with VCF-format alignments"
)
return -1
compress_seq = read_vcf(args.alignment, args.vcf_reference)
aln = compress_seq['sequences']
ref = compress_seq['reference']
is_vcf = True
else:
aln = args.alignment
tt = ancestral_sequence_inference(tree=T,
aln=aln,
ref=ref,
marginal=args.inference)
if is_vcf:
# TreeTime overwrites ambig sites on tips during ancestral reconst.
# Put these back in tip sequences now, to avoid misleading
tt.recover_var_ambigs()
anc_seqs['nodes'] = collect_sequences_and_mutations(T, is_vcf)
if args.output:
anc_seqs_fname = args.output
else:
anc_seqs_fname = '.'.join(
args.alignment.split('.')[:-1]) + '.anc_seqs.json'
anc_seqs_success = write_json(anc_seqs, anc_seqs_fname)
print("ancestral sequences written to", anc_seqs_fname, file=sys.stdout)
# If VCF, output VCF including new ancestral seqs
if is_vcf:
if args.output_vcf:
vcf_fname = args.output_vcf
else:
vcf_fname = '.'.join(args.alignment.split('.')[:-1]) + '.vcf'
write_vcf(tt.get_tree_dict(keep_var_ambigs=True), vcf_fname)
print("ancestral sequences as vcf-file written to",
vcf_fname,
file=sys.stdout)
if anc_seqs_success:
return 0
else:
return 1
