Merge pull request #136 from Sage-Bionetworks/hotfix

Urgent: mutincis maf flag, clinical file duplication bugs
Sage-Bionetworks · Jun 4, 2019 · 9ad8aa4 · 9ad8aa4
2 parents 30de946 + 4c861c5
commit 9ad8aa4
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diff --git a/genie/database_to_staging.py b/genie/database_to_staging.py
@@ -743,6 +743,8 @@ def stagingToCbio(
             header = mafFile.readline()
             headers = header.replace("\n", "").split("\t")
             headers.append("mutationInCis_Flag")
+            # New header
+            header = "\t".join(headers) + "\n"
             if index == 0:
                 with open(MUTATIONS_PATH, 'a') as f:
                     f.write(header)

diff --git a/genie/input_to_database.py b/genie/input_to_database.py
@@ -245,6 +245,11 @@ def validation(syn, center, process, center_mapping_df, databaseToSynIdMappingDf
         cbsSegFiles = inputValidStatus[cbsSegBool]
         if len(cbsSegFiles) >1:
             duplicatedFiles = duplicatedFiles.append(cbsSegFiles)
+        clinical_bool = ["clinical" in i for i in inputValidStatus['name']]
+        clinical_files = inputValidStatus[clinical_bool]
+        if len(clinical_files) > 2:
+            duplicatedFiles = duplicatedFiles.append(clinical_files)
+
         # nodups = ["data_mutations_extended"]
         # allDuplicatedFiles = []
         # for nodup in nodups: