From 63c6db620f247ed868368a16bbe4c4bb5ce0aa34 Mon Sep 17 00:00:00 2001 From: Thomas Yu Date: Tue, 4 Jun 2019 09:54:28 -0700 Subject: [PATCH 1/3] Add in mutation in cis flag header --- genie/database_to_staging.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/genie/database_to_staging.py b/genie/database_to_staging.py index 003f08a3..bf759ba4 100644 --- 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) From fa49dff0c893d983fe7eec59c0ef9f08af709957 Mon Sep 17 00:00:00 2001 From: Thomas Yu Date: Tue, 4 Jun 2019 10:31:40 -0700 Subject: [PATCH 2/3] look for clinical duplicates --- genie/input_to_database.py | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/genie/input_to_database.py b/genie/input_to_database.py index 12f888a1..b2925e0e 100644 --- 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_bool) > 2: + duplicatedFiles = duplicatedFiles.append(clinical_files) + # nodups = ["data_mutations_extended"] # allDuplicatedFiles = [] # for nodup in nodups: From 4c861c5eccebb0d0a402d85b658924df1e6a8819 Mon Sep 17 00:00:00 2001 From: Thomas Yu Date: Tue, 4 Jun 2019 10:43:00 -0700 Subject: [PATCH 3/3] Fix --- genie/input_to_database.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/genie/input_to_database.py b/genie/input_to_database.py index b2925e0e..2285408e 100644 --- a/genie/input_to_database.py +++ b/genie/input_to_database.py @@ -247,7 +247,7 @@ def validation(syn, center, process, center_mapping_df, databaseToSynIdMappingDf duplicatedFiles = duplicatedFiles.append(cbsSegFiles) clinical_bool = ["clinical" in i for i in inputValidStatus['name']] clinical_files = inputValidStatus[clinical_bool] - if len(clinical_bool) > 2: + if len(clinical_files) > 2: duplicatedFiles = duplicatedFiles.append(clinical_files) # nodups = ["data_mutations_extended"]