From 075b554cdde11f32e73981222a2cede3bb249151 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Wed, 21 Feb 2024 09:20:37 +0300
Subject: Check that samples/cases are consistent

Ensure that **ALL** samples/cases/individuals mentioned in any of the
pheno files actually exist in at least one of the geno files.
---
 r_qtl/r_qtl2.py | 34 ++++++++++++++--------------------
 1 file changed, 14 insertions(+), 20 deletions(-)

(limited to 'r_qtl/r_qtl2.py')

diff --git a/r_qtl/r_qtl2.py b/r_qtl/r_qtl2.py
index 1e28bc0..87491d0 100644
--- a/r_qtl/r_qtl2.py
+++ b/r_qtl/r_qtl2.py
@@ -368,27 +368,21 @@ def read_geno_file_data(
             replace_genotype_codes, genocodes=cdata.get("genotypes", {})))
 
 
-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)
+def load_samples(zipfilepath: Union[str, Path],
+                 member: str,
+                 transposed: bool) -> tuple[str, ...]:
+    """Load the samples/cases/individuals from file 'member'."""
+    filedata = read_geno_file_data(zipfilepath, member)
     samples: set[str] = set()
-    for afile in cdata.get(filetype, []):
-        filedata = read_geno_file_data(zipfilepath, afile)
-        if cdata.get(f"{filetype}_transposed", False):
+    if transposed:
+        samples.update(
+            item for item in next(filedata)[1:] if item is not None)
+    else:
+        try:
+            next(filedata)# Ignore first row.
             samples.update(
-                item for item in next(filedata)[1:] if item is not None)
-        else:
-            try:
-                next(filedata)# Ignore first row.
-                samples.update(
-                    line[0] for line in filedata if line[0] is not None)
-            except StopIteration:# Empty file.
-                pass
+                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")
-- 
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