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-rw-r--r--r_qtl/r_qtl2.py13
-rw-r--r--tests/r_qtl/test_files/test_pheno.zipbin0 -> 485 bytes
-rw-r--r--tests/r_qtl/test_files/test_pheno_transposed.zipbin0 -> 536 bytes
-rw-r--r--tests/r_qtl/test_r_qtl2_pheno.py33
4 files changed, 46 insertions, 0 deletions
diff --git a/r_qtl/r_qtl2.py b/r_qtl/r_qtl2.py
index bc3a86f..2256609 100644
--- a/r_qtl/r_qtl2.py
+++ b/r_qtl/r_qtl2.py
@@ -163,3 +163,16 @@ def map_data(zfile: ZipFile, map_type: str, cdata: dict) -> Iterator[dict]:
for row in with_transposed(zfile, map_file_key, cdata, __merge__):
yield row
+
+def phenotype_data(zfile: ZipFile, cdata: dict) -> Iterator[dict]:
+ """Load phenotype file data."""
+ if not cdata.get("pheno_transposed", False):
+ for row in with_non_transposed(zfile, "pheno", cdata, lambda val: val):
+ yield row
+ return
+
+ def __merge__(id_key, ids, vals):
+ return tuple(dict(zip([id_key, vals[0]], items))
+ for items in zip(ids, vals[1:]))
+ for row in with_transposed(zfile, "pheno", cdata, __merge__):
+ yield row
diff --git a/tests/r_qtl/test_files/test_pheno.zip b/tests/r_qtl/test_files/test_pheno.zip
new file mode 100644
index 0000000..5c709e7
--- /dev/null
+++ b/tests/r_qtl/test_files/test_pheno.zip
Binary files differ
diff --git a/tests/r_qtl/test_files/test_pheno_transposed.zip b/tests/r_qtl/test_files/test_pheno_transposed.zip
new file mode 100644
index 0000000..9bff030
--- /dev/null
+++ b/tests/r_qtl/test_files/test_pheno_transposed.zip
Binary files differ
diff --git a/tests/r_qtl/test_r_qtl2_pheno.py b/tests/r_qtl/test_r_qtl2_pheno.py
new file mode 100644
index 0000000..554d9c8
--- /dev/null
+++ b/tests/r_qtl/test_r_qtl2_pheno.py
@@ -0,0 +1,33 @@
+"""Test parsing of pheno files in a R/qtl2 bundle."""
+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(
+ "filepath,expected",
+ (("tests/r_qtl/test_files/test_pheno.zip",
+ ({"id": "1", "liver": "61.92", "spleen": "153.16"},
+ {"id": "2", "liver": "88.33", "spleen": "178.58"},
+ {"id": "3", "liver": "58", "spleen": "131.91"},
+ {"id": "4", "liver": "78.06", "spleen": "126.13"},
+ {"id": "5", "liver": "65.31", "spleen": "181.05"})),
+ ("tests/r_qtl/test_files/test_pheno_transposed.zip",
+ ({"id": "1", "liver": "61.92", "spleen": "153.16"},
+ {"id": "2", "liver": "88.33", "spleen": "178.58"},
+ {"id": "3", "liver": "58", "spleen": "131.91"},
+ {"id": "4", "liver": "78.06", "spleen": "126.13"},
+ {"id": "5", "liver": "65.31", "spleen": "181.05"}))))
+def test_parse_pheno_files(filepath, expected):
+ """Test parsing of 'pheno' files from the R/qtl2 bundle.
+
+ GIVEN: path to a R/qtl2 bundle
+ WHEN: the 'pheno' file is parsed
+ 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