From 04676cf9621f2ce42d4cf6189a125af8c3c97d3c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Pablo=20S=C3=A1nchez-Izquierdo=20Besora?= Date: Wed, 6 May 2026 14:33:53 +0200 Subject: [PATCH] Adding isoform flag to pancancer.py --- mavisp_templates/GENE_NAME/cancermuts_metatable/pancancer.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/mavisp_templates/GENE_NAME/cancermuts_metatable/pancancer.py b/mavisp_templates/GENE_NAME/cancermuts_metatable/pancancer.py index 72f0a43..cf9a1e5 100755 --- a/mavisp_templates/GENE_NAME/cancermuts_metatable/pancancer.py +++ b/mavisp_templates/GENE_NAME/cancermuts_metatable/pancancer.py @@ -14,6 +14,7 @@ parser.add_argument("-p", "--prt", dest="prt", help="hugo name of your protein") parser.add_argument("-i", "--uniprotID", dest="uniprotID", help="uniprot_id of your protein (the one ending with _HUMAN)") parser.add_argument("-a", "--uniprotAC", dest="uniprotAC", default= None, help="uniprot_ac of your protein") +parser.add_argument("-f", "--isoform", dest="isoform", default=None, help="UniProt isoform ID, e.g. P61812-1") parser.add_argument("-r", "--refseq", dest="refseq", required=False, help="RefSeq isoform ID required for ClinVar mapping") parser.add_argument("-e", "--external_mutations", dest="external_mutations", nargs='+', default= None, help="csv file containing the external mutations to study") @@ -22,7 +23,7 @@ up = UniProt() # get the sequence for the protein -seq = up.get_sequence(args.prt, upid=args.uniprotID, upac=args.uniprotAC) +seq = up.get_sequence(args.prt, upid=args.uniprotID, upac=args.uniprotAC, isoform=args.isoform) print(seq.sequence) # add mutations from cBioPortal