diff options
| -rw-r--r-- | gn3/db/datasets.py | 23 |
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): |