From a4324cd24b5a14fbcf19a6e04d2b76fb2838038e Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Tue, 20 Feb 2024 06:32:56 +0300
Subject: Generalise fetching of samples/cases/individuals.

---
 r_qtl/r_qtl2.py                  | 26 +++++++++++++++++---------
 tests/r_qtl/test_r_qtl2_pheno.py | 11 +++++++++++
 2 files changed, 28 insertions(+), 9 deletions(-)

diff --git a/r_qtl/r_qtl2.py b/r_qtl/r_qtl2.py
index f03aff5..1e28bc0 100644
--- a/r_qtl/r_qtl2.py
+++ b/r_qtl/r_qtl2.py
@@ -368,19 +368,27 @@ def read_geno_file_data(
             replace_genotype_codes, genocodes=cdata.get("genotypes", {})))
 
 
-def load_geno_samples(zipfilepath: Union[str, Path]) -> tuple[str, ...]:
-    """Load the samples/cases/individuals from the 'geno' file(s)."""
+def load_samples(
+        zipfilepath: Union[str, Path], filetype: str) -> tuple[str, ...]:
+    """Load the samples/cases/individuals from file(s) of type 'filetype'."""
     cdata = read_control_file(zipfilepath)
-    samples = set()
-    for genofile in cdata.get("geno", []):
-        gdata = read_geno_file_data(zipfilepath, genofile)
-        if cdata.get("geno_transposed", False):
-            samples.update(next(gdata)[1:])
+    samples: set[str] = set()
+    for afile in cdata.get(filetype, []):
+        filedata = read_geno_file_data(zipfilepath, afile)
+        if cdata.get(f"{filetype}_transposed", False):
+            samples.update(
+                item for item in next(filedata)[1:] if item is not None)
         else:
             try:
-                next(gdata)# Ignore first row.
-                samples.update(line[0] for line in gdata)
+                next(filedata)# Ignore first row.
+                samples.update(
+                    line[0] for line in filedata if line[0] is not None)
             except StopIteration:# Empty file.
                 pass
 
     return tuple(samples)
+
+
+load_geno_samples = partial(load_samples, filetype="geno")
+load_founder_geno_samples = partial(load_samples, filetype="founder_geno")
+load_pheno_samples = partial(load_samples, filetype="pheno")
diff --git a/tests/r_qtl/test_r_qtl2_pheno.py b/tests/r_qtl/test_r_qtl2_pheno.py
index c7c0c86..d31ad54 100644
--- a/tests/r_qtl/test_r_qtl2_pheno.py
+++ b/tests/r_qtl/test_r_qtl2_pheno.py
@@ -57,3 +57,14 @@ def test_parse_phenocovar_files(filepath, expected):
     with ZipFile(Path(filepath).absolute(), "r") as zfile:
         cdata = rqtl2.control_data(zfile)
         assert tuple(rqtl2.file_data(zfile, "phenocovar", cdata)) == expected
+
+
+@pytest.mark.unit_test
+@pytest.mark.parametrize(
+    "filepath,expected",
+    (("tests/r_qtl/test_files/test_pheno.zip",
+      ("1", "2", "3", "4", "5")),
+     ("tests/r_qtl/test_files/test_pheno_transposed.zip",
+      ("1", "2", "3", "4", "5"))))
+def test_load_geno_samples(filepath, expected):
+    assert sorted(rqtl2.load_pheno_samples(filepath)) == sorted(expected)
-- 
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