Merge pull request #163 from Sage-Bionetworks/remove-maf-header

URGENT: Remove maf header
Sage-Bionetworks · Jul 3, 2019 · 24769c3 · 24769c3
2 parents ae9585f + 7d914f5
commit 24769c3
Showing 1 changed file with 1 addition and 4 deletions.
diff --git 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: