From 88ffc9b55af1dcc16c5100bd4b8e214588dc2b0b Mon Sep 17 00:00:00 2001 From: "samira.vandenbogaard" Date: Tue, 28 Jan 2025 14:25:48 +0100 Subject: [PATCH] bugfixes --- src/PAModelpy/utils/pam_generation.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/src/PAModelpy/utils/pam_generation.py b/src/PAModelpy/utils/pam_generation.py index 7c394f6..39a01fa 100644 --- a/src/PAModelpy/utils/pam_generation.py +++ b/src/PAModelpy/utils/pam_generation.py @@ -108,7 +108,8 @@ def parse_gpr_information(gpr_info:str, # enzyme_relations = _filter_sublists(enzyme_relations, enzyme_id.split('_'), how='all') return sorted(gpr_list), sorted(enzyme_relations) -def get_protein_gene_mapping(enzyme_db: pd.DataFrame, model) -> tuple[dict, dict]: +def get_protein_gene_mapping(enzyme_db: pd.DataFrame, + model) -> tuple[dict, dict]: protein2gene = defaultdict(list) gene2protein = {} for index, row in enzyme_db.iterrows(): @@ -118,7 +119,7 @@ def get_protein_gene_mapping(enzyme_db: pd.DataFrame, model) -> tuple[dict, dict rxn = model.reactions.get_by_id(rxn_id) # get the identifiers and replace nan values by dummy placeholders enzyme_id = row['enzyme_id'] - gene_id = row['genes'] + gene_id = row['gene'] # check if there are genes associates with the reaction if len(rxn.genes) > 0 or isinstance(gene_id, str):