Fix file paths: append the path to the extraction directory.

1 files changed, 15 insertions, 11 deletions

diff --git a/scripts/load_phenotypes_to_db.py b/scripts/load_phenotypes_to_db.py
index 5027a9b..0797db5 100644
--- a/scripts/load_phenotypes_to_db.py
+++ b/scripts/load_phenotypes_to_db.py
@@ -94,7 +94,7 @@ def save_pheno_data(
 ):
     """Read the `datafiles` and save the data in the database."""
     phenofiles = tuple(
-        filesdir.joinpath(_file) for file in control_data["pheno"])
+        filesdir.joinpath(_file) for _file in control_data["pheno"])
     if len(phenofiles) <= 0:
         return tuple()
 
@@ -128,10 +128,12 @@ def save_phenotype_se(
         conn: mysqldb.Connection,
         dataidmap: dict,
         samples: tuple[dict, ...],
-        control_data: dict
+        control_data: dict,
+        filesdir: Path
 ):
     """Read the `sefiles` and save the data in the database."""
-    sefiles = control_data["phenose"]
+    sefiles = tuple(
+        filesdir.joinpath(_file) for _file in control_data["phenose"])
     if len(sefiles) <= 0:
         return tuple()
 
@@ -142,9 +144,9 @@ def save_phenotype_se(
                 _file,
                 build_line_splitter(control_data),
                 build_line_joiner(control_data))
-            for _file in control_data["phenose"])
+            for _file in sefiles)
 
-    _headers = rqtl2.read_csv_file_headers(control_data["phenose"][0],
+    _headers = rqtl2.read_csv_file_headers(sefiles[0],
                                            control_data["phenose_transposed"],
                                            control_data["sep"],
                                            control_data["comment.char"])
@@ -165,23 +167,25 @@ def save_phenotype_n(
         conn: mysqldb.Connection,
         dataidmap: dict,
         samples: tuple[dict, ...],
-        control_data: dict
+        control_data: dict,
+        filesdir: Path
 ):
     """Read the `nfiles` and save the data in the database."""
-    sefiles = control_data["phenonum"]
-    if len(sefiles) <= 0:
+    nfiles = tuple(
+        filesdir.joinpath(_file) for _file in control_data["phenonum"])
+    if len(nfiles) <= 0:
         return tuple()
 
     if control_data["phenonum_transposed"]:
         logger.info("Undoing transposition of the files rows and columns.")
-        sefiles = (
+        nfiles = (
             rqtl2.transpose_csv_with_rename(
                 _file,
                 build_line_splitter(control_data),
                 build_line_joiner(control_data))
-            for _file in control_data["phenonum"])
+            for _file in nfiles)
 
-    _headers = rqtl2.read_csv_file_headers(control_data["phenonum"][0],
+    _headers = rqtl2.read_csv_file_headers(nfiles[0],
                                            control_data["phenonum_transposed"],
                                            control_data["sep"],
                                            control_data["comment.char"])