parser.add_argument('--ancestral', action='store_true', default=False,
help='calculate ancestral sequences')
parser.add_argument('--timetree', action='store_true', default=False,
help='infer time stamped phylogeny')
parser.add_argument('--confidence', action='store_true', default=False,
help='estimate confidence intervals for node timing')
parser.add_argument('--Tc', type=float, default=0.0,
help='coalescence time scale measured in substitution rate units')
parser.add_argument('--keeproot', action='store_true', default=False,
help="don't reroot the tree")
args = parser.parse_args()
path = args.path
date_fmt = '%Y-%m-%d'
T = build_fasttree(ref_alignment(path), tree_newick(path))
#T = tree_newick(path)
meta = read_sequence_meta_data(path)
fields = ['branchlength', 'clade']
if args.timetree:
tt = timetree(tree=T, aln=ref_alignment(path), confidence=args.confidence,
seq_meta=meta, reroot=None if args.keeproot else 'best',Tc=args.Tc)
T = tt.tree
fields.extend(['mutations', 'mutation_length', 'num_date', 'clock_length'])
if args.confidence:
fields.append('num_date_confidence')
elif args.ancestral:
tt = ancestral_sequence_inference(tree=T, aln=ref_alignment(path))
T = tt.tree
fields.extend(['mutations', 'mutation_length'])
start = time.time()
write_out_variable_fasta(compress_seq, path, args.drm)
end = time.time()
print "Writing out variable sites took {}".format(str(end - start))
if args.iqmodel and not args.iqtree:
print "Cannot specify model unless using IQTree. Model specification ignored."
if args.vcf:
treebuild_align = var_site_alignment(path)
else:
treebuild_align = ref_alignment(path)
start = time.time()
if args.raxml:
T = build_raxml(treebuild_align, tree_newick(path), path,
args.nthreads)
elif args.iqtree:
T = build_iqtree(treebuild_align, tree_newick(path), args.iqmodel,
args.nthreads)
else: #use fasttree - if add more options, put another check here
T = build_fasttree(treebuild_align, tree_newick(path))
end = time.time()
print "Building original tree took {}".format(str(end - start))
meta = read_sequence_meta_data(path)
fields = ['branchlength', 'clade']
#Anything but a list of sequences to root by, shouldn't go as a "list".
if len(args.roottype) == 1:
args.roottype = args.roottype[0]
if __name__ == '__main__':
parser = generic_argparse("Export precomputed data as auspice jsons")
parser.add_argument(
'--prefix',
required=True,
help=
"prefix for json files that are passed on to auspice (e.g., zika.fasta)"
)
parser.add_argument(
'--reference',
required=True,
help="reference sequence needed for entropy feature export")
args = parser.parse_args()
path = args.path
T = Phylo.read(tree_newick(path), 'newick')
seq_meta = read_sequence_meta_data(path)
tree_meta = read_tree_meta_data(path)
attach_tree_meta_data(T, tree_meta)
tree_layout(T)
fields_to_export = tree_meta.values()[0].keys() + [
"tvalue", "yvalue", "xvalue", "attr", "muts", "aa_muts"
]
tjson = tree_to_json(T.root, extra_attr=fields_to_export)
write_json(tjson, tree_json(path, args.prefix))
export_sequence_json(T, path, args.prefix)
export_diversity(path, args.prefix, args.reference)
return tt, alphabet
if __name__ == '__main__':
parser = generic_argparse("Infer ancestral states for a discrete character")
parser.add_argument('--field', default='region',
help='meta data field to perform discrete reconstruction on')
parser.add_argument('--confidence',action="store_true",
help='record the distribution of subleading mugration states')
parser.add_argument('--vcf', action='store_true', default=False,
help="sequence is in VCF format")
args = parser.parse_args()
path = args.path
T = tree_newick(path)
import time
start = time.time()
seq_meta = read_sequence_meta_data(path)
tree_meta = read_tree_meta_data(path)
end = time.time()
print "Reading in meta files took {}".format(str(end-start))
start = time.time()
tt, alphabet = mugration_inference(tree=T, seq_meta=seq_meta,
field=args.field, confidence=args.confidence)
end = time.time()
print "Mugration took {}".format(str(end-start))