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-rw-r--r--gn3/db/datasets.py23
1 files changed, 20 insertions, 3 deletions
diff --git a/gn3/db/datasets.py b/gn3/db/datasets.py
index 171a70e..9a05890 100644
--- a/gn3/db/datasets.py
+++ b/gn3/db/datasets.py
@@ -1,12 +1,14 @@
"""
This module contains functions relating to specific trait dataset manipulation
"""
+import json
+
from typing import Any
from pathlib import Path
from flask import current_app as app
-def retrieve_sample_list(group: str):
+def retrieve_sample_list(group: str, inc_par: bool = True, inc_f1: bool = True):
"""
Get the sample list for a group (a category that datasets belong to)
@@ -15,6 +17,21 @@ def retrieve_sample_list(group: str):
"""
samplelist = []
+ if inc_par or inc_f1:
+ par_f1_path = Path(
+ app.config.get(
+ "GENENETWORK_FILES",
+ "/home/gn2/production/genotype_files/"
+ ), f'parents_and_f1s.json'
+ )
+ if par_f1_path.is_file():
+ with open(par_f1_path, encoding="utf-8") as par_f1_file:
+ par_f1s = json.load(par_f1_file)[group]
+ if inc_par:
+ samplelist += [par_f1s['paternal']['strain'], par_f1s['maternal']['strain']]
+ if inc_f1:
+ samplelist += [f1['strain'] for f1 in par_f1s['f1s']]
+
genofile_path = Path(
app.config.get(
"GENENETWORK_FILES",
@@ -35,9 +52,9 @@ def retrieve_sample_list(group: str):
headers = line.split("\t")
if headers[3] == "Mb":
- samplelist = headers[4:]
+ samplelist += headers[4:]
else:
- samplelist = headers[3:]
+ samplelist += headers[3:]
return samplelist
def retrieve_mrna_group_name(connection: Any, probeset_id: int, dataset_name: str):