From b0991ec5cea1411237b82e92467603bf9da803f5 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Tue, 17 Jun 2025 14:18:24 -0500
Subject: Allow users to provide transposed files.
---
uploader/phenotypes/views.py | 4 ++++
.../phenotypes/add-phenotypes-raw-files.html | 22 ++++++++++++++++++++++
2 files changed, 26 insertions(+)
(limited to 'uploader')
diff --git a/uploader/phenotypes/views.py b/uploader/phenotypes/views.py
index 6bc7471..f4a302a 100644
--- a/uploader/phenotypes/views.py
+++ b/uploader/phenotypes/views.py
@@ -366,6 +366,7 @@ def process_phenotypes_rqtl2_bundle(error_uri):
def process_phenotypes_individual_files(error_uri):
"""Process the uploaded individual files."""
form = request.form
+ _transposed = (form.get("file-transposed") or "off") == "on"
cdata = {
"sep": form["file-separator"],
"comment.char": form["file-comment-character"],
@@ -400,6 +401,9 @@ def process_phenotypes_individual_files(error_uri):
arcname=filepath.name)
cdata[rqtlkey] = cdata.get(rqtlkey, []) + [filepath.name]
+ if rqtlkey not in ("phenocovar",):
+ cdata[f"{rqtlkey}_transposed"] = _transposed
+
zfile.writestr("control_data.json", data=json.dumps(cdata, indent=2))
return bundlepath
diff --git a/uploader/templates/phenotypes/add-phenotypes-raw-files.html b/uploader/templates/phenotypes/add-phenotypes-raw-files.html
index 697c7ad..5c6aaab 100644
--- a/uploader/templates/phenotypes/add-phenotypes-raw-files.html
+++ b/uploader/templates/phenotypes/add-phenotypes-raw-files.html
@@ -103,6 +103,28 @@
documentation for more information.
+
+
+
+
+
+
+
+ We expect the data in the file as a matrix of
+ samples × phenotypes, but it could be your file is
+ transposed, (i.e. it is a matrix of
+ “phenotypes × samples”, rather than the expected
+ form).
+
+ If that is the case for your files, mark your files as trasposed by
+ ensuring that this checkbox is checked.
+
+