Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Filter date bounds inclusive #708

Merged
merged 2 commits into from
Apr 2, 2021
Merged

Filter date bounds inclusive #708

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
25927e4
Change date bounds for filter --min-date and --max-date to be inclusi…
benjaminotter Mar 31, 2021
8d7e2df
Adds tests to assure filter --min-date and --max-date are inclusive
benjaminotter Mar 31, 2021
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
8 changes: 4 additions & 4 deletions augur/filter.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -105,8 +105,8 @@ def register_arguments(parser):
Uses Pandas Dataframe querying, see https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#indexing-query for syntax.
(e.g., --query "country == 'Colombia'" or --query "(country == 'USA' & (division == 'Washington'))")"""
)
metadata_filter_group.add_argument('--min-date', type=numeric_date, help="minimal cutoff for date; may be specified as an Augur-style numeric date (with the year as the integer part) or YYYY-MM-DD")
metadata_filter_group.add_argument('--max-date', type=numeric_date, help="maximal cutoff for date; may be specified as an Augur-style numeric date (with the year as the integer part) or YYYY-MM-DD")
metadata_filter_group.add_argument('--min-date', type=numeric_date, help="minimal cutoff for date, the cutoff date is inclusive; may be specified as an Augur-style numeric date (with the year as the integer part) or YYYY-MM-DD")
metadata_filter_group.add_argument('--max-date', type=numeric_date, help="maximal cutoff for date, the cutoff date is inclusive; may be specified as an Augur-style numeric date (with the year as the integer part) or YYYY-MM-DD")
metadata_filter_group.add_argument('--exclude-ambiguous-dates-by', choices=['any', 'day', 'month', 'year'],
help='Exclude ambiguous dates by day (e.g., 2020-09-XX), month (e.g., 2020-XX-XX), year (e.g., 200X-10-01), or any date fields. An ambiguous year makes the corresponding month and day ambiguous, too, even if those fields have unambiguous values (e.g., "201X-10-01"). Similarly, an ambiguous month makes the corresponding day ambiguous (e.g., "2010-XX-01").')
metadata_filter_group.add_argument('--exclude', type=str, nargs="+", help="file(s) with list of strains to exclude")
Expand Down Expand Up @@ -348,9 +348,9 @@ def run(args):
dates = get_numerical_dates(meta_dict, fmt="%Y-%m-%d")
tmp = {s for s in seq_keep if dates[s] is not None}
if args.min_date:
tmp = {s for s in tmp if (np.isscalar(dates[s]) or all(dates[s])) and np.max(dates[s])>args.min_date}
tmp = {s for s in tmp if (np.isscalar(dates[s]) or all(dates[s])) and np.max(dates[s])>=args.min_date}
if args.max_date:
tmp = {s for s in tmp if (np.isscalar(dates[s]) or all(dates[s])) and np.min(dates[s])<args.max_date}
tmp = {s for s in tmp if (np.isscalar(dates[s]) or all(dates[s])) and np.min(dates[s])<=args.max_date}
num_excluded_by_date = len(seq_keep) - len(tmp)
seq_keep = tmp

Expand Down
28 changes: 28 additions & 0 deletions tests/test_filter.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -215,3 +215,31 @@ def test_filter_run_with_query_and_include_where(self, tmpdir, fasta_fn, argpars
augur.filter.run(args)
output = SeqIO.to_dict(SeqIO.parse(out_fn, "fasta"))
assert list(output.keys()) == ["SEQ_1", "SEQ_3"]

def test_filter_run_min_date(self, tmpdir, fasta_fn, argparser):
"""Test that filter --min-date is inclusive"""
out_fn = str(tmpdir / "out.fasta")
min_date = "2020-02-26"
meta_fn = write_metadata(tmpdir, (("strain","date"),
("SEQ_1","2020-02-XX"),
("SEQ_2","2020-02-26"),
("SEQ_3","2020-02-25")))
args = argparser('-s %s --metadata %s -o %s --min-date %s'
% (fasta_fn, meta_fn, out_fn, min_date))
augur.filter.run(args)
output = SeqIO.to_dict(SeqIO.parse(out_fn, "fasta"))
assert list(output.keys()) == ["SEQ_1", "SEQ_2"]

def test_filter_run_max_date(self, tmpdir, fasta_fn, argparser):
"""Test that filter --max-date is inclusive"""
out_fn = str(tmpdir / "out.fasta")
max_date = "2020-03-01"
meta_fn = write_metadata(tmpdir, (("strain","date"),
("SEQ_1","2020-03-XX"),
("SEQ_2","2020-03-01"),
("SEQ_3","2020-03-02")))
args = argparser('-s %s --metadata %s -o %s --max-date %s'
% (fasta_fn, meta_fn, out_fn, max_date))
augur.filter.run(args)
output = SeqIO.to_dict(SeqIO.parse(out_fn, "fasta"))
assert list(output.keys()) == ["SEQ_1", "SEQ_2"]