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authorFrederick Muriuki Muriithi2023-12-27 08:08:31 +0300
committerFrederick Muriuki Muriithi2023-12-27 08:08:31 +0300
commit46410163ca402660434b09a8fc8ec7b12b89d8a1 (patch)
tree7fc55ed054a4770ca4fd72c44e6dd501deb668b6
parent8ababbb1cfbdbf3c26d9599253c6d45670c49046 (diff)
downloadgn-uploader-46410163ca402660434b09a8fc8ec7b12b89d8a1.tar.gz
Tests: Add tests for parsing gmap files.
-rw-r--r--pytest.ini3
-rw-r--r--r_qtl/r_qtl2.py31
-rw-r--r--tests/r_qtl/test_files/test_gmap.zipbin0 -> 542 bytes
-rw-r--r--tests/r_qtl/test_files/test_gmap_transposed.zipbin0 -> 594 bytes
-rw-r--r--tests/r_qtl/test_r_qtl2.py47
5 files changed, 67 insertions, 14 deletions
diff --git a/pytest.ini b/pytest.ini
index 9fd309c..99e2c59 100644
--- a/pytest.ini
+++ b/pytest.ini
@@ -1,4 +1,5 @@
[pytest]
addopts = --strict-markers
markers =
- slow \ No newline at end of file
+ slow
+ unit_test \ No newline at end of file
diff --git a/r_qtl/r_qtl2.py b/r_qtl/r_qtl2.py
index 26d6dd4..a221f26 100644
--- a/r_qtl/r_qtl2.py
+++ b/r_qtl/r_qtl2.py
@@ -65,20 +65,27 @@ def genotype_data(zfile: ZipFile, cdata: dict) -> Iterator[dict]:
def map_data(zfile: ZipFile, map_type: str, cdata: dict) -> dict:
"""Read gmap files to get the genome mapping data"""
assert map_type in ("genetic-map", "physical-map"), "Invalid map type"
- map_key = {"genetic-map": "gmap", "physical-map": "pmap"}[map_type]
- if not cdata.get("geno_transposed", False):
- with zfile.open(cdata[map_key]) as gmapfile:
+ map_file = cdata[{
+ "genetic-map": "gmap",
+ "physical-map": "pmap"
+ }[map_type]]
+ # TODO: Might need to check `gmap_transposed` and `pmap_transposed` instead
+ # of `geno_transposed` -- see
+ # https://github.com/rqtl/qtl2data/blob/main/ArabMAGIC/arabmagic_tair8.json
+ # for the *_transposed values
+ transposed_dict = {
+ "genetic-map": "gmap_transposed",
+ "physical-map": "pmap_transposed"
+ }
+ if not cdata.get(transposed_dict[map_type], False):
+ with zfile.open(map_file) as gmapfile:
reader = csv.DictReader(
filter(lambda line: not line.startswith("#"),
io.TextIOWrapper(gmapfile)),
delimiter=cdata.get("sep", ","))
- return {
- line["marker"]: {
- key: value for key,value in line.items() if key != "marker"
- } for line in reader
- }
+ return tuple(row for row in reader)
- with zfile.open(cdata["gmap"]) as gmapfile:
+ with zfile.open(map_file) as gmapfile:
lines = [[field.strip() for field in
line.strip().split(cdata.get("sep", ","))]
for line in
@@ -87,11 +94,9 @@ def map_data(zfile: ZipFile, map_type: str, cdata: dict) -> dict:
headers = tuple(line[0] for line in lines)
return reduce(
- lambda gmap, row: {
- **gmap,
- row[0]: dict(zip(headers[1:], row[1:]))},
+ lambda gmap, row: gmap + (dict(zip(headers, row)),),
zip(*(line[1:] for line in lines)),
- {})
+ tuple())
def read_r_qtl2_files(filepath: Path):
"""Read R/qtl2 format zip files."""
diff --git a/tests/r_qtl/test_files/test_gmap.zip b/tests/r_qtl/test_files/test_gmap.zip
new file mode 100644
index 0000000..c8d452a
--- /dev/null
+++ b/tests/r_qtl/test_files/test_gmap.zip
Binary files differ
diff --git a/tests/r_qtl/test_files/test_gmap_transposed.zip b/tests/r_qtl/test_files/test_gmap_transposed.zip
new file mode 100644
index 0000000..74a956e
--- /dev/null
+++ b/tests/r_qtl/test_files/test_gmap_transposed.zip
Binary files differ
diff --git a/tests/r_qtl/test_r_qtl2.py b/tests/r_qtl/test_r_qtl2.py
new file mode 100644
index 0000000..a72b300
--- /dev/null
+++ b/tests/r_qtl/test_r_qtl2.py
@@ -0,0 +1,47 @@
+"""Test the parsing of the R/qtl2 data files."""
+from pathlib import Path
+
+import pytest
+from zipfile import ZipFile
+
+from r_qtl import r_qtl2 as rqtl2
+
+@pytest.mark.unit_test
+@pytest.mark.parametrize(
+ "relpath,expected",
+ (("tests/r_qtl/test_files/test_gmap.zip",
+ ({"marker": "PVV4", "chr": "1", "pos": "0.000000"},
+ {"marker": "AXR-1", "chr": "1", "pos": "6.250674"},
+ {"marker": "HH.335C-Col/PhyA", "chr": "1", "pos": "9.303868"},
+ {"marker": "EC.480C", "chr": "1", "pos": "12.577629"},
+ {"marker": "EC.66C", "chr": "1", "pos": "18.392830"})),
+ ("tests/r_qtl/test_files/test_gmap_transposed.zip",
+ ({"marker": "PVV4", "chr": "1", "pos": "0.000000"},
+ {"marker": "AXR-1", "chr": "1", "pos": "6.250674"},
+ {"marker": "HH.335C-Col/PhyA", "chr": "1", "pos": "9.303868"},
+ {"marker": "EC.480C", "chr": "1", "pos": "12.577629"},
+ {"marker": "EC.66C", "chr": "1", "pos": "18.392830"}))))
+def test_parse_gmap_files(relpath, expected):
+ """
+ GIVEN: A path to a zip file, `relpath`
+ WHEN: we parse a gmap file
+ THEN: ensure the parsed data is as expected.
+ """
+ with ZipFile(Path(relpath).absolute(), "r") as zfile:
+ assert rqtl2.map_data(
+ zfile, "genetic-map", rqtl2.control_data(zfile)) == expected
+
+@pytest.mark.skip(reason="Test not implemented yet.")
+@pytest.mark.unit_test
+@pytest.mark.parametrize(
+ "relpath,expected",
+ (("tests/r_qtl/test_files/test_pmap.zip",
+ ()),
+ ("tests/r_qtl/test_files/test_pmap_transposed.zip",
+ ())))
+def test_parse_pmap_files(relpath, expected):
+ """
+ GIVEN: A path to a zip file, `relpath`
+ WHEN: we parse a pmap file
+ THEN: ensure the parsed data is as expected.
+ """