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frequencies: Fix --regions flag #1424

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merged 5 commits into from
Feb 23, 2024
Merged

frequencies: Fix --regions flag #1424

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878dc1f
Add test showing current behavior
joverlee521 Feb 23, 2024
696a9ca
frequencies: use "region" column for `--regions`
joverlee521 Feb 23, 2024
d47999b
frequencies: only use "region" column for non-global regions
joverlee521 Feb 23, 2024
56bf16a
frequencies: update `--region` help text
joverlee521 Feb 23, 2024
455bcfa
Update changelog
joverlee521 Feb 23, 2024
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2 changes: 2 additions & 0 deletions CHANGES.md
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Original file line number Diff line number Diff line change
Expand Up @@ -5,8 +5,10 @@
### Bug Fixes

* filter: Updated the help and report text of `--min-length` to explicitly state that the minimum length filter only counts standard nucleotide characters A, C, G, or T (case-insensitive). This has been the behavior since version 3.0.3.dev1, but has never been explicitly documented. [#1422][] (@joverlee521)
* frequencies: Fixed a bug introduced in 24.2.0 and 24.1.0 that prevented `--regions` from working when providing regions other than the default "global" region. [#1424]

[#1422]: https://github.com/nextstrain/augur/pull/1422
[#1424]: https://github.com/nextstrain/augur/pull/1424

## 24.2.2 (16 February 2024)

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20 changes: 16 additions & 4 deletions augur/frequencies.py
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Expand Up @@ -14,6 +14,8 @@
from .io.metadata import DEFAULT_DELIMITERS, DEFAULT_ID_COLUMNS, METADATA_DATE_COLUMN, InvalidDelimiter, Metadata, read_metadata
from .utils import write_json

REGION_COLUMN = 'region'
DEFAULT_REGION = 'global'

def register_parser(parent_subparsers):
parser = parent_subparsers.add_parser("frequencies", help=__doc__)
Expand All @@ -26,8 +28,10 @@ def register_parser(parent_subparsers):
help="delimiters to accept when reading a metadata file. Only one delimiter will be inferred.")
parser.add_argument('--metadata-id-columns', default=DEFAULT_ID_COLUMNS, nargs="+",
help="names of possible metadata columns containing identifier information, ordered by priority. Only one ID column will be inferred.")
parser.add_argument('--regions', type=str, nargs='+', default=['global'],
help="region to subsample to")
parser.add_argument('--regions', type=str, nargs='+', default=[DEFAULT_REGION],
help="region to filter to. " \
f"Regions should match values in the {REGION_COLUMN!r} column of the metadata file " \
f"if specifying values other than the default {DEFAULT_REGION!r} region.")
parser.add_argument("--pivot-interval", type=int, default=3,
help="number of units between pivots")
parser.add_argument("--pivot-interval-units", type=str, default="months", choices=['months', 'weeks'],
Expand Down Expand Up @@ -97,6 +101,11 @@ def run(args):
columns_to_load = [metadata_object.id_column, METADATA_DATE_COLUMN]
if args.weights_attribute:
columns_to_load.append(args.weights_attribute)

filter_to_region = any(region != DEFAULT_REGION for region in args.regions)
if filter_to_region:
columns_to_load.append(REGION_COLUMN)

metadata = read_metadata(
args.metadata,
delimiters=[metadata_object.delimiter],
Expand Down Expand Up @@ -130,6 +139,9 @@ def run(args):
# Annotate tip with weight attribute.
tip.attr[weights_attribute] = metadata.loc[tip.name, weights_attribute]

if filter_to_region:
tip.attr[REGION_COLUMN] = metadata.loc[tip.name, REGION_COLUMN]

if args.method == "diffusion":
# estimate tree frequencies
pivots = get_pivots(tps, args.pivot_interval, args.min_date, args.max_date, args.pivot_interval_units)
Expand All @@ -139,10 +151,10 @@ def run(args):
for region in args.regions:
# Omit strains sampled prior to the first pivot from frequency calculations.
# (these tend to be reference strains included for phylogenetic context)
if region=='global':
if region==DEFAULT_REGION:
node_filter_func = lambda node: node.attr["num_date"] >= pivots[0]
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else:
node_filter_func = lambda node: (node.attr["region"] == region
node_filter_func = lambda node: (node.attr[REGION_COLUMN] == region
and node.attr["num_date"] >= pivots[0])

tree_freqs = tree_frequencies(tree, pivots, method='SLSQP',
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247 changes: 247 additions & 0 deletions tests/functional/frequencies/cram/diffusion-region.t
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@@ -0,0 +1,247 @@
Setup

$ source "$TESTDIR"/_setup.sh

Calculate diffusion-based tip frequencies from a refined tree with `--regions`.

$ ${AUGUR} frequencies \
> --method diffusion \
> --tree "$TESTDIR/../data/tree.nwk" \
> --metadata "$TESTDIR/../data/metadata.tsv" \
> --regions "global" "North America" "South America" \
> --pivot-interval 3 \
> --output tip-frequencies.json > /dev/null

$ cat tip-frequencies.json
{
"BRA/2016/FC_6706": {
"North America": [
0.0,
0.0,
0.0,
0.0
],
"South America": [
0.2,
0.2,
0.2,
0.2
],
"global": [
0.1,
0.1,
0.1,
0.1
]
},
"COL/FLR_00008/2015": {
"North America": [
0.0,
0.0,
0.0,
0.0
],
"South America": [
0.2,
0.2,
0.2,
0.2
],
"global": [
0.1,
0.1,
0.1,
0.1
]
},
"Colombia/2016/ZC204Se": {
"North America": [
0.0,
0.0,
0.0,
0.0
],
"South America": [
0.2,
0.2,
0.2,
0.2
],
"global": [
0.1,
0.1,
0.1,
0.1
]
},
"DOM/2016/BB_0183": {
"North America": [
0.25,
0.25,
0.25,
0.25
],
"South America": [
0.0,
0.0,
0.0,
0.0
],
"global": [
0.1,
0.1,
0.1,
0.1
]
},
"EcEs062_16": {
"North America": [
0.0,
0.0,
0.0,
0.0
],
"South America": [
0.2,
0.2,
0.2,
0.2
],
"global": [
0.1,
0.1,
0.1,
0.1
]
},
"HND/2016/HU_ME59": {
"North America": [
0.25,
0.25,
0.25,
0.25
],
"South America": [
0.0,
0.0,
0.0,
0.0
],
"global": [
0.1,
0.1,
0.1,
0.1
]
},
"PAN/CDC_259359_V1_V3/2015": {
"North America": [
0.25,
0.25,
0.25,
0.25
],
"South America": [
0.0,
0.0,
0.0,
0.0
],
"global": [
0.1,
0.1,
0.1,
0.1
]
},
"PRVABC59": {
"North America": [
0.25,
0.25,
0.25,
0.25
],
"South America": [
0.0,
0.0,
0.0,
0.0
],
"global": [
0.1,
0.1,
0.1,
0.1
]
},
"VEN/UF_1/2016": {
"North America": [
0.0,
0.0,
0.0,
0.0
],
"South America": [
0.2,
0.2,
0.2,
0.2
],
"global": [
0.1,
0.1,
0.1,
0.1
]
},
"ZKC2/2016": {
"North America": [
0.0,
0.0,
0.0,
0.0
],
"South America": [
0.0,
0.0,
0.0,
0.0
],
"global": [
0.1,
0.1,
0.1,
0.1
]
},
"counts": {
"North America": [
0,
2,
2,
0
],
"South America": [
0,
2,
3,
0
],
"global": [
0,
5,
5,
0
]
},
"generated_by": {
"program": "augur",
"version": ".*" (re)
},
"pivots": [
2015.7521,
2016.0041,
2016.2527,
2016.5014
]
} (no-eol)
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