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print treetime version #552

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merged 1 commit into from
May 20, 2020
Merged

print treetime version #552

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4 changes: 3 additions & 1 deletion augur/ancestral.py
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Original file line number Diff line number Diff line change
Expand Up @@ -41,7 +41,9 @@ def ancestral_sequence_inference(tree=None, aln=None, ref=None, infer_gtr=True,
treetime.TreeAnc instance
"""

from treetime import TreeAnc
from treetime import TreeAnc, version as treetime_version
print(f"augur ancestral is using TreeTime version {treetime_version}")

tt = TreeAnc(tree=tree, aln=aln, ref=ref, gtr='JC69',
fill_overhangs=fill_overhangs, verbose=1)

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2 changes: 2 additions & 0 deletions augur/refine.py
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Expand Up @@ -166,6 +166,8 @@ def run(args):
else:
aln = args.alignment

from treetime import version as treetime_version
print(f"augur refine is using TreeTime version {treetime_version}")

# if not specified, construct default output file name with suffix _tt.nwk
if args.output_tree:
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4 changes: 4 additions & 0 deletions augur/traits.py
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Expand Up @@ -161,6 +161,10 @@ def run(args):
mugration_states = defaultdict(dict)
models = defaultdict(dict)
out_prefix = '.'.join(args.tree.split('.')[:-1])

from treetime import version as treetime_version
print(f"augur traits is using TreeTime version {treetime_version}")

for column in args.columns:
T, gtr, alphabet = mugration_inference(tree=tree_fname, seq_meta=traits,
field=column, confidence=args.confidence,
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