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

Move filter expression code to filter.py #65

Merged
merged 1 commit into from
Aug 27, 2024
Merged

Move filter expression code to filter.py #65

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
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
136 changes: 136 additions & 0 deletions tests/test_filter.py
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,136 @@
import pathlib

import numpy as np
import pyparsing as pp
import pytest
import zarr
from numpy.testing import assert_array_equal

from tests.utils import vcz_path_cache
from vcztools.filter import FilterExpressionEvaluator, FilterExpressionParser


class TestFilterExpressionParser:
@pytest.fixture()
def identifier_parser(self, parser):
return parser._identifier_parser

@pytest.fixture()
def parser(self):
return FilterExpressionParser()

@pytest.mark.parametrize(
("expression", "expected_result"),
[
("1", [1]),
("1.0", [1.0]),
("1e-4", [0.0001]),
('"String"', ["String"]),
("POS", ["POS"]),
("INFO/DP", ["INFO/DP"]),
("FORMAT/GT", ["FORMAT/GT"]),
("FMT/GT", ["FMT/GT"]),
("GT", ["GT"]),
],
)
def test_valid_identifiers(self, identifier_parser, expression, expected_result):
assert identifier_parser(expression).as_list() == expected_result

@pytest.mark.parametrize(
"expression",
[
"",
"FORMAT/ GT",
"format / GT",
"fmt / GT",
"info / DP",
"'String'",
],
)
def test_invalid_identifiers(self, identifier_parser, expression):
with pytest.raises(pp.ParseException):
identifier_parser(expression)

@pytest.mark.parametrize(
("expression", "expected_result"),
[
("POS>=100", [["POS", ">=", 100]]),
(
"FMT/DP>10 && FMT/GQ>10",
[[["FMT/DP", ">", 10], "&&", ["FMT/GQ", ">", 10]]],
),
("QUAL>10 || FMT/GQ>10", [[["QUAL", ">", 10], "||", ["FMT/GQ", ">", 10]]]),
(
"FMT/DP>10 && FMT/GQ>10 || QUAL > 10",
[
[
[["FMT/DP", ">", 10], "&&", ["FMT/GQ", ">", 10]],
"||",
["QUAL", ">", 10],
]
],
),
(
"QUAL>10 || FMT/DP>10 && FMT/GQ>10",
[
[
["QUAL", ">", 10],
"||",
[["FMT/DP", ">", 10], "&&", ["FMT/GQ", ">", 10]],
]
],
),
(
"QUAL>10 | FMT/DP>10 & FMT/GQ>10",
[
[
["QUAL", ">", 10],
"|",
[["FMT/DP", ">", 10], "&", ["FMT/GQ", ">", 10]],
],
],
),
(
"(QUAL>10 || FMT/DP>10) && FMT/GQ>10",
[
[
[["QUAL", ">", 10], "||", ["FMT/DP", ">", 10]],
"&&",
["FMT/GQ", ">", 10],
]
],
),
],
)
def test_valid_expressions(self, parser, expression, expected_result):
assert parser(expression=expression).as_list() == expected_result


class TestFilterExpressionEvaluator:
@pytest.mark.parametrize(
("expression", "expected_result"),
[
("POS < 1000", [1, 1, 0, 0, 0, 0, 0, 0, 1]),
("FMT/GQ > 20", [0, 0, 1, 1, 1, 1, 1, 0, 0]),
("FMT/DP >= 5 && FMT/GQ > 10", [0, 0, 1, 1, 1, 0, 0, 0, 0]),
("FMT/DP >= 5 & FMT/GQ>10", [0, 0, 1, 0, 1, 0, 0, 0, 0]),
("QUAL > 10 || FMT/GQ>10", [0, 0, 1, 1, 1, 1, 1, 0, 0]),
("(QUAL > 10 || FMT/GQ>10) && POS > 100000", [0, 0, 0, 0, 1, 1, 1, 0, 0]),
("(FMT/DP >= 8 | FMT/GQ>40) && POS > 100000", [0, 0, 0, 0, 0, 1, 0, 0, 0]),
("INFO/DP > 10", [0, 0, 1, 1, 0, 1, 0, 0, 0]),
("GT > 0", [1, 1, 1, 1, 1, 0, 1, 0, 1]),
("GT > 0 & FMT/HQ >= 10", [0, 0, 1, 1, 1, 0, 0, 0, 0]),
],
)
def test(self, expression, expected_result):
original = pathlib.Path("tests/data/vcf") / "sample.vcf.gz"
vcz = vcz_path_cache(original)
root = zarr.open(vcz, mode="r")

parser = FilterExpressionParser()
parse_results = parser(expression)[0]
evaluator = FilterExpressionEvaluator(parse_results)
assert_array_equal(evaluator(root, 0), expected_result)

invert_evaluator = FilterExpressionEvaluator(parse_results, invert=True)
assert_array_equal(invert_evaluator(root, 0), np.logical_not(expected_result))
134 changes: 0 additions & 134 deletions tests/test_utils.py
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,15 +1,7 @@
import pathlib

import numpy as np
import pyparsing as pp
import pytest
import zarr
from numpy.testing import assert_array_equal

from tests.utils import vcz_path_cache
from vcztools.utils import (
FilterExpressionEvaluator,
FilterExpressionParser,
search,
vcf_name_to_vcz_name,
)
Expand Down Expand Up @@ -50,129 +42,3 @@ def test_search(a, v, expected_ind):
)
def test_vcf_to_vcz(vczs, vcf, expected_vcz):
assert vcf_name_to_vcz_name(vczs, vcf) == expected_vcz


class TestFilterExpressionParser:
@pytest.fixture()
def identifier_parser(self):
return FilterExpressionParser()._identifier_parser

@pytest.fixture()
def parser(self):
return FilterExpressionParser()

@pytest.mark.parametrize(
("expression", "expected_result"),
[
("1", [1]),
("1.0", [1.0]),
("1e-4", [0.0001]),
('"String"', ["String"]),
("POS", ["POS"]),
("INFO/DP", ["INFO/DP"]),
("FORMAT/GT", ["FORMAT/GT"]),
("FMT/GT", ["FMT/GT"]),
("GT", ["GT"]),
],
)
def test_valid_identifiers(self, identifier_parser, expression, expected_result):
assert identifier_parser(expression).as_list() == expected_result

@pytest.mark.parametrize(
"expression",
[
"",
"FORMAT/ GT",
"format / GT",
"fmt / GT",
"info / DP",
"'String'",
],
)
def test_invalid_identifiers(self, identifier_parser, expression):
with pytest.raises(pp.ParseException):
identifier_parser(expression)

@pytest.mark.parametrize(
("expression", "expected_result"),
[
("POS>=100", [["POS", ">=", 100]]),
(
"FMT/DP>10 && FMT/GQ>10",
[[["FMT/DP", ">", 10], "&&", ["FMT/GQ", ">", 10]]],
),
("QUAL>10 || FMT/GQ>10", [[["QUAL", ">", 10], "||", ["FMT/GQ", ">", 10]]]),
(
"FMT/DP>10 && FMT/GQ>10 || QUAL > 10",
[
[
[["FMT/DP", ">", 10], "&&", ["FMT/GQ", ">", 10]],
"||",
["QUAL", ">", 10],
]
],
),
(
"QUAL>10 || FMT/DP>10 && FMT/GQ>10",
[
[
["QUAL", ">", 10],
"||",
[["FMT/DP", ">", 10], "&&", ["FMT/GQ", ">", 10]],
]
],
),
(
"QUAL>10 | FMT/DP>10 & FMT/GQ>10",
[
[
["QUAL", ">", 10],
"|",
[["FMT/DP", ">", 10], "&", ["FMT/GQ", ">", 10]],
],
],
),
(
"(QUAL>10 || FMT/DP>10) && FMT/GQ>10",
[
[
[["QUAL", ">", 10], "||", ["FMT/DP", ">", 10]],
"&&",
["FMT/GQ", ">", 10],
]
],
),
],
)
def test_valid_expressions(self, parser, expression, expected_result):
assert parser(expression=expression).as_list() == expected_result


class TestFilterExpressionEvaluator:
@pytest.mark.parametrize(
("expression", "expected_result"),
[
("POS < 1000", [1, 1, 0, 0, 0, 0, 0, 0, 1]),
("FMT/GQ > 20", [0, 0, 1, 1, 1, 1, 1, 0, 0]),
("FMT/DP >= 5 && FMT/GQ > 10", [0, 0, 1, 1, 1, 0, 0, 0, 0]),
("FMT/DP >= 5 & FMT/GQ>10", [0, 0, 1, 0, 1, 0, 0, 0, 0]),
("QUAL > 10 || FMT/GQ>10", [0, 0, 1, 1, 1, 1, 1, 0, 0]),
("(QUAL > 10 || FMT/GQ>10) && POS > 100000", [0, 0, 0, 0, 1, 1, 1, 0, 0]),
("(FMT/DP >= 8 | FMT/GQ>40) && POS > 100000", [0, 0, 0, 0, 0, 1, 0, 0, 0]),
("INFO/DP > 10", [0, 0, 1, 1, 0, 1, 0, 0, 0]),
("GT > 0", [1, 1, 1, 1, 1, 0, 1, 0, 1]),
("GT > 0 & FMT/HQ >= 10", [0, 0, 1, 1, 1, 0, 0, 0, 0]),
],
)
def test(self, expression, expected_result):
original = pathlib.Path("tests/data/vcf") / "sample.vcf.gz"
vcz = vcz_path_cache(original)
root = zarr.open(vcz, mode="r")

parser = FilterExpressionParser()
parse_results = parser(expression)[0]
evaluator = FilterExpressionEvaluator(parse_results)
assert_array_equal(evaluator(root, 0), expected_result)

invert_evaluator = FilterExpressionEvaluator(parse_results, invert=True)
assert_array_equal(invert_evaluator(root, 0), np.logical_not(expected_result))
Loading