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add better error handling if treetime fails #1023

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merged 3 commits into from
Aug 12, 2022
Merged

add better error handling if treetime fails #1023

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7a32847
add better error handling if treetime fails
anna-parker Aug 11, 2022
e131a4d
use AugurError for treetime error handling
anna-parker Aug 12, 2022
f3634b8
with import statement
anna-parker Aug 12, 2022
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22 changes: 13 additions & 9 deletions augur/refine.py
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Original file line number Diff line number Diff line change
Expand Up @@ -7,6 +7,7 @@
from .dates import get_numerical_dates
from .io import read_metadata
from .utils import read_tree, write_json, InvalidTreeError
from .errors import AugurError
from treetime.vcf_utils import read_vcf, write_vcf
from treetime.seq_utils import profile_maps

Expand Down Expand Up @@ -211,15 +212,18 @@ def run(args):
if n.name in metadata.index and 'date' in metadata.columns:
n.raw_date = metadata.loc[n.name, 'date']

tt = refine(tree=T, aln=aln, ref=ref, dates=dates, confidence=args.date_confidence,
reroot=args.root, # or 'best', # We now have a default in param spec - this just adds confusion.
Tc=0.01 if args.coalescent is None else args.coalescent, #use 0.01 as default coalescent time scale
use_marginal = args.date_inference == 'marginal',
branch_length_inference = args.branch_length_inference or 'auto',
precision = 'auto' if args.precision is None else args.precision,
clock_rate=args.clock_rate, clock_std=args.clock_std_dev,
clock_filter_iqd=args.clock_filter_iqd,
covariance=args.covariance, resolve_polytomies=(not args.keep_polytomies))
try:
tt = refine(tree=T, aln=aln, ref=ref, dates=dates, confidence=args.date_confidence,
reroot=args.root, # or 'best', # We now have a default in param spec - this just adds confusion.
Tc=0.01 if args.coalescent is None else args.coalescent, #use 0.01 as default coalescent time scale
use_marginal = args.date_inference == 'marginal',
branch_length_inference = args.branch_length_inference or 'auto',
precision = 'auto' if args.precision is None else args.precision,
clock_rate=args.clock_rate, clock_std=args.clock_std_dev,
clock_filter_iqd=args.clock_filter_iqd,
covariance=args.covariance, resolve_polytomies=(not args.keep_polytomies))
except BaseException as err:
raise AugurError(f"Was unable to refine time trees:\n\n{err}")

node_data['clock'] = {'rate': tt.date2dist.clock_rate,
'intercept': tt.date2dist.intercept,
Expand Down