From 1f82483c0d0e138fd7228d74ecfaa6d2b8e7fb37 Mon Sep 17 00:00:00 2001 From: Thomas Yu Date: Mon, 1 Jul 2019 09:35:20 -0700 Subject: [PATCH] Remove maf header --- genie/consortium_to_public.py | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/genie/consortium_to_public.py b/genie/consortium_to_public.py index 402972b3..194beb6e 100644 --- a/genie/consortium_to_public.py +++ b/genie/consortium_to_public.py @@ -142,16 +142,13 @@ def consortiumToPublic(syn, processingDate, genie_version, releaseId, databaseSy elif "mutation" in entName: mutation = syn.get(entId, followLink=True) - with open(mutation.path, 'r') as f: - sequenced_samples = f.readline() mutationDf = pd.read_csv(mutation.path, sep="\t", comment="#") mutationDf = commonVariantFilter(mutationDf) mutationDf['FILTER'] = "PASS" mutationDf = mutationDf[mutationDf['Tumor_Sample_Barcode'].isin(publicReleaseSamples)] text = process.removeFloat(mutationDf) with open(MUTATIONS_PATH, 'w') as f: - f.write(sequenced_samples) - f.write(text) + f.write(text) storeFile(syn, MUTATIONS_PATH, PUBLIC_RELEASE_PREVIEW, ANONYMIZE_CENTER_DF, genie_version, name="data_mutations_extended.txt") elif "fusion" in entName: