From ced5dccf5d06e7cd5009f556f183a092f1713117 Mon Sep 17 00:00:00 2001 From: danlu1 Date: Tue, 26 Nov 2024 00:35:55 +0000 Subject: [PATCH] reformat consortium_to_public --- genie/consortium_to_public.py | 13 ++++++++++--- 1 file changed, 10 insertions(+), 3 deletions(-) diff --git a/genie/consortium_to_public.py b/genie/consortium_to_public.py index 299bd4fe..f1a3a09b 100644 --- a/genie/consortium_to_public.py +++ b/genie/consortium_to_public.py @@ -5,8 +5,13 @@ import pandas as pd import synapseutils -from genie import (create_case_lists, database_to_staging, extract, load, - process_functions) +from genie import ( + create_case_lists, + database_to_staging, + extract, + load, + process_functions, +) logger = logging.getLogger(__name__) @@ -148,7 +153,9 @@ def consortiumToPublic( allClin = clinicalDf[clinicalDf["SAMPLE_ID"].isin(publicReleaseSamples)] # check if cfDNA samples are present if not process_functions.check_values_in_column(allClin, "SAMPLE_CLASS", "cfDNA"): - logger.error("cfDNA samples should not be filtered out in the clinical dataframe.") + logger.error( + "cfDNA samples should not be filtered out in the clinical dataframe." + ) allClin.to_csv(clinical_path, sep="\t", index=False)