add flags to scripts

EBIvariation · Dec 7, 2023 · 2d14a3e · 2d14a3e
1 parent a9776db
commit 2d14a3e
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Showing 2 changed files with 10 additions and 2 deletions.
diff --git a/bin/consequence_prediction/run_repeat_expansion_variants.py b/bin/consequence_prediction/run_repeat_expansion_variants.py
@@ -9,6 +9,10 @@
     '--clinvar-xml', required=True,
     help='ClinVar XML dump file (ClinVarFullRelease_00-latest.xml.gz)'
 )
+parser.add_argument(
+    '--include-transcripts', required=False, action='store_true',
+    help='Whether to include transcript IDs along with consequence terms'
+)
 parser.add_argument(
     '--output-consequences', required=True,
     help='File to output functional consequences to. Format is compatible with the main VEP mapping pipeline.'
@@ -18,4 +22,4 @@
     help='File to output full dataframe for subsequent analysis and debugging.'
 )
 args = parser.parse_args()
-pipeline.main(args.clinvar_xml, args.output_consequences, args.output_dataframe)
+pipeline.main(args.clinvar_xml, args.include_transcripts, args.output_consequences, args.output_dataframe)
diff --git a/bin/consequence_prediction/run_structural_variants.py b/bin/consequence_prediction/run_structural_variants.py
@@ -9,10 +9,14 @@
     '--clinvar-xml', required=True,
     help='ClinVar XML dump file (ClinVarFullRelease_00-latest.xml.gz)'
 )
+parser.add_argument(
+    '--include-transcripts', required=False, action='store_true',
+    help='Whether to include transcript IDs along with consequence terms'
+)
 parser.add_argument(
     '--output-consequences', required=True,
     help='File to output functional consequences to. Format is compatible with the main VEP mapping pipeline.'
 )
 
 args = parser.parse_args()
-pipeline.main(args.clinvar_xml, args.output_consequences)
+pipeline.main(args.clinvar_xml, args.include_transcripts, args.output_consequences)