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authorFrederick Muriuki Muriithi2024-01-03 16:53:40 +0300
committerFrederick Muriuki Muriithi2024-01-03 16:53:40 +0300
commit3e51fb24fd34bab2164a5f4056bc78d21827ca29 (patch)
tree690a4f7453dd276ccb90c7101140117fdeb6f9e7 /tests/r_qtl
parent95d2b868adebbc7ebbc2435f9184c30c014ec513 (diff)
downloadgn-uploader-3e51fb24fd34bab2164a5f4056bc78d21827ca29.tar.gz
Use generic parser. Remove obsoleted functions.
Diffstat (limited to 'tests/r_qtl')
-rw-r--r--tests/r_qtl/test_r_qtl2_geno.py8
-rw-r--r--tests/r_qtl/test_r_qtl2_gmap.py12
-rw-r--r--tests/r_qtl/test_r_qtl2_pheno.py4
3 files changed, 14 insertions, 10 deletions
diff --git a/tests/r_qtl/test_r_qtl2_geno.py b/tests/r_qtl/test_r_qtl2_geno.py
index 787d13a..c33984e 100644
--- a/tests/r_qtl/test_r_qtl2_geno.py
+++ b/tests/r_qtl/test_r_qtl2_geno.py
@@ -171,8 +171,12 @@ def test_parse_geno_files(relpath, expected):
THEN: ensure that the data we get is as expected
"""
with ZipFile(Path(relpath).absolute(), "r") as zfile:
- assert tuple(
- rqtl2.genotype_data(zfile, rqtl2.control_data(zfile))) == expected
+ cdata = rqtl2.control_data(zfile)
+ assert tuple(rqtl2.file_data(
+ zfile,
+ "geno",
+ cdata,
+ *rqtl2.make_process_data_geno(cdata))) == expected
@pytest.mark.unit_test
@pytest.mark.parametrize(
diff --git a/tests/r_qtl/test_r_qtl2_gmap.py b/tests/r_qtl/test_r_qtl2_gmap.py
index ba46c42..5c8ca6a 100644
--- a/tests/r_qtl/test_r_qtl2_gmap.py
+++ b/tests/r_qtl/test_r_qtl2_gmap.py
@@ -10,28 +10,28 @@ from r_qtl import r_qtl2 as rqtl2
@pytest.mark.parametrize(
"relpath,mapfiletype,expected",
(("tests/r_qtl/test_files/test_gmap.zip",
- "genetic-map",
+ "gmap",
({"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",
- "genetic-map",
+ "gmap",
({"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_pmap.zip",
- "physical-map",
+ "pmap",
({"marker": "D1Mit18", "chr": "1", "pos": "52.418656"},
{"marker": "D1Mit80", "chr": "1", "pos": "86.377953"},
{"marker": "D1Mit17", "chr": "1", "pos": "189.571337"},
{"marker": "D2Mit379", "chr": "2", "pos": "37.451062"},
{"marker": "D2Mit75", "chr": "2", "pos": "80.584782"})),
("tests/r_qtl/test_files/test_pmap_transposed.zip",
- "physical-map",
+ "pmap",
({"marker": "D1Mit18", "chr": "1", "pos": "52.418656"},
{"marker": "D1Mit80", "chr": "1", "pos": "86.377953"},
{"marker": "D1Mit17", "chr": "1", "pos": "189.571337"},
@@ -44,5 +44,5 @@ def test_parse_map_files(relpath, mapfiletype, expected):
THEN: ensure the parsed data is as expected.
"""
with ZipFile(Path(relpath).absolute(), "r") as zfile:
- assert tuple(rqtl2.map_data(
- zfile, mapfiletype, rqtl2.control_data(zfile))) == expected
+ cdata = rqtl2.control_data(zfile)
+ assert tuple(rqtl2.file_data(zfile, mapfiletype, cdata)) == expected
diff --git a/tests/r_qtl/test_r_qtl2_pheno.py b/tests/r_qtl/test_r_qtl2_pheno.py
index 554d9c8..46be469 100644
--- a/tests/r_qtl/test_r_qtl2_pheno.py
+++ b/tests/r_qtl/test_r_qtl2_pheno.py
@@ -29,5 +29,5 @@ def test_parse_pheno_files(filepath, expected):
THEN: verify the parsed data is as expected
"""
with ZipFile(Path(filepath).absolute(), "r") as zfile:
- assert tuple(
- rqtl2.phenotype_data(zfile, rqtl2.control_data(zfile))) == expected
+ cdata = rqtl2.control_data(zfile)
+ assert tuple(rqtl2.file_data(zfile, "pheno", cdata)) == expected